| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000001065-ENSMUSG00000032815 |
CGP |
10090 |
8:123254195-123318576  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_000063_0002 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_000063_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000075399' => 'VPS9 domain containing 1',
'ENSG00000158805' => 'zinc finger protein 276',
'ENSG00000187741' => 'Fanconi anemia, complementation group A',
'ENSMUSG00000001062' => 'VPS9 domain containing 1',
'ENSMUSG00000001065' => 'zinc finger protein (C2H2 type) 276',
'ENSMUSG00000032815' => 'Fanconi anemia, complementation group A'
),
'gene_name_arr' => array(
'ENSG00000075399' => 'VPS9D1',
'ENSG00000158805' => 'ZNF276',
'ENSG00000187741' => 'FANCA',
'ENSMUSG00000001062' => 'Vps9d1',
'ENSMUSG00000001065' => 'Zfp276',
'ENSMUSG00000032815' => 'Fanca'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 11 => 'Brain',
(int) 15 => 'Breast',
(int) 19 => 'Colon',
(int) 22 => 'Heart',
(int) 25 => 'Kidney',
(int) 28 => 'Liver',
(int) 32 => 'Lung',
(int) 38 => 'Muscle',
(int) 43 => 'Ovary',
(int) 49 => 'Placenta',
(int) 52 => 'Testis'
),
'column_titles' => array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
),
'geneviewer' => array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
),
'transcript_count' => (int) 83,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000389386' => array(
'start' => '89707134',
'end' => '89720986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-002'
),
'ENST00000561976' => array(
'start' => '89707134',
'end' => '89719369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-001'
),
'ENST00000563798' => array(
'start' => '89711393',
'end' => '89720885',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'VPS9D1-003'
),
'ENST00000565023' => array(
'start' => '89707784',
'end' => '89710642',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-007'
),
'ENST00000565452' => array(
'start' => '89710965',
'end' => '89711644',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'VPS9D1-006'
),
'ENST00000567379' => array(
'start' => '89711359',
'end' => '89713040',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS9D1-005'
),
'ENST00000568691' => array(
'start' => '89710933',
'end' => '89713080',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS9D1-004'
),
'ENST00000614968' => array(
'start' => '89707134',
'end' => '89719369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-201'
),
'ENST00000289816' => array(
'start' => '89720985',
'end' => '89740903',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-001'
),
'ENST00000443381' => array(
'start' => '89721544',
'end' => '89738571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-004'
),
'ENST00000561536' => array(
'start' => '89722869',
'end' => '89738589',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-006'
),
'ENST00000562530' => array(
'start' => '89720400',
'end' => '89738281',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-007'
),
'ENST00000563541' => array(
'start' => '89723489',
'end' => '89733537',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-009'
),
'ENST00000563983' => array(
'start' => '89721160',
'end' => '89739816',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-005'
),
'ENST00000564004' => array(
'start' => '89731526',
'end' => '89738570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-008'
),
'ENST00000568064' => array(
'start' => '89721007',
'end' => '89738520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-002'
),
'ENST00000568295' => array(
'start' => '89721573',
'end' => '89738571',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-003'
),
'ENST00000569426' => array(
'start' => '89723606',
'end' => '89733470',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-010'
),
'ENST00000569582' => array(
'start' => '89733249',
'end' => '89737883',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-011'
),
'ENST00000569901' => array(
'start' => '89737712',
'end' => '89738329',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-012'
),
'ENST00000305699' => array(
'start' => '89739741',
'end' => '89765039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-009'
),
'ENST00000389301' => array(
'start' => '89737549',
'end' => '89816646',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-001'
),
'ENST00000389302' => array(
'start' => '89798374',
'end' => '89816657',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-003'
),
'ENST00000534992' => array(
'start' => '89798919',
'end' => '89816655',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-201'
),
'ENST00000543736' => array(
'start' => '89798919',
'end' => '89816657',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-004'
),
'ENST00000561660' => array(
'start' => '89745027',
'end' => '89765044',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-022'
),
'ENST00000561667' => array(
'start' => '89769915',
'end' => '89770583',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-018'
),
'ENST00000561722' => array(
'start' => '89738493',
'end' => '89740078',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-027'
),
'ENST00000562424' => array(
'start' => '89738495',
'end' => '89739758',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-029'
),
'ENST00000563318' => array(
'start' => '89752161',
'end' => '89767147',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-020'
),
'ENST00000563510' => array(
'start' => '89748764',
'end' => '89764947',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-019'
),
'ENST00000563513' => array(
'start' => '89808311',
'end' => '89816621',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-011'
),
'ENST00000563673' => array(
'start' => '89798385',
'end' => '89816635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-006'
),
'ENST00000563767' => array(
'start' => '89791044',
'end' => '89792011',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-017'
),
'ENST00000564475' => array(
'start' => '89738744',
'end' => '89742894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-028'
),
'ENST00000564870' => array(
'start' => '89738883',
'end' => '89742828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-030'
),
'ENST00000564969' => array(
'start' => '89739363',
'end' => '89745008',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-024'
),
'ENST00000565582' => array(
'start' => '89798991',
'end' => '89815978',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-012'
),
'ENST00000566133' => array(
'start' => '89791563',
'end' => '89792725',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-014'
),
'ENST00000566409' => array(
'start' => '89795906',
'end' => '89799232',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-007'
),
'ENST00000566889' => array(
'start' => '89798354',
'end' => '89816647',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-005'
),
'ENST00000567205' => array(
'start' => '89767142',
'end' => '89770024',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-008'
),
'ENST00000567284' => array(
'start' => '89770430',
'end' => '89778850',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FANCA-031'
),
'ENST00000567510' => array(
'start' => '89773320',
'end' => '89779957',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-016'
),
'ENST00000567621' => array(
'start' => '89791508',
'end' => '89808366',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-013'
),
'ENST00000567879' => array(
'start' => '89738630',
'end' => '89745062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-026'
),
'ENST00000567883' => array(
'start' => '89810572',
'end' => '89816608',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-032'
),
'ENST00000567943' => array(
'start' => '89810985',
'end' => '89816648',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-010'
),
'ENST00000567988' => array(
'start' => '89742902',
'end' => '89765004',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-021'
),
'ENST00000568369' => array(
'start' => '89738403',
'end' => '89816646',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-002'
),
'ENST00000568626' => array(
'start' => '89739282',
'end' => '89749816',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-023'
),
'ENST00000568983' => array(
'start' => '89744687',
'end' => '89749796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-025'
),
'ENSMUST00000117643' => array(
'start' => '123242356',
'end' => '123254176',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-003'
),
'ENSMUST00000118279' => array(
'start' => '123242359',
'end' => '123254092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-007'
),
'ENSMUST00000122363' => array(
'start' => '123242356',
'end' => '123254348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-001'
),
'ENSMUST00000124508' => array(
'start' => '123246857',
'end' => '123248013',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-011'
),
'ENSMUST00000127978' => array(
'start' => '123246516',
'end' => '123247996',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Vps9d1-012'
),
'ENSMUST00000129591' => array(
'start' => '123249712',
'end' => '123254050',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-008'
),
'ENSMUST00000130275' => array(
'start' => '123244947',
'end' => '123254105',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-006'
),
'ENSMUST00000130965' => array(
'start' => '123248553',
'end' => '123248983',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-010'
),
'ENSMUST00000137569' => array(
'start' => '123248828',
'end' => '123251071',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-009'
),
'ENSMUST00000146136' => array(
'start' => '123242358',
'end' => '123254163',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-004'
),
'ENSMUST00000149490' => array(
'start' => '123242356',
'end' => '123254222',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-002'
),
'ENSMUST00000155853' => array(
'start' => '123245143',
'end' => '123246930',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Vps9d1-013'
),
'ENSMUST00000155869' => array(
'start' => '123242358',
'end' => '123254109',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Vps9d1-005'
),
'ENSMUST00000001092' => array(
'start' => '123254195',
'end' => '123269745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zfp276-001'
),
'ENSMUST00000130333' => array(
'start' => '123264821',
'end' => '123265643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-005'
),
'ENSMUST00000146158' => array(
'start' => '123258328',
'end' => '123268122',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-003'
),
'ENSMUST00000147312' => array(
'start' => '123259460',
'end' => '123267917',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-004'
),
'ENSMUST00000150356' => array(
'start' => '123254271',
'end' => '123257636',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-006'
),
'ENSMUST00000154450' => array(
'start' => '123254686',
'end' => '123265070',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zfp276-007'
),
'ENSMUST00000156896' => array(
'start' => '123254284',
'end' => '123269743',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-002'
),
'ENSMUST00000035495' => array(
'start' => '123268300',
'end' => '123318576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-001'
),
'ENSMUST00000118395' => array(
'start' => '123302075',
'end' => '123318560',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-005'
),
'ENSMUST00000126834' => array(
'start' => '123271205',
'end' => '123278054',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-009'
),
'ENSMUST00000127904' => array(
'start' => '123286404',
'end' => '123313362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-003'
),
'ENSMUST00000133950' => array(
'start' => '123289361',
'end' => '123291861',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-006'
),
'ENSMUST00000135702' => array(
'start' => '123269290',
'end' => '123274223',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fanca-011'
),
'ENSMUST00000146687' => array(
'start' => '123277856',
'end' => '123282667',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-007'
),
'ENSMUST00000150318' => array(
'start' => '123312283',
'end' => '123318560',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-004'
),
'ENSMUST00000155279' => array(
'start' => '123277416',
'end' => '123281287',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fanca-008'
),
'ENSMUST00000155488' => array(
'start' => '123286189',
'end' => '123318560',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-002'
),
'ENSMUST00000155510' => array(
'start' => '123274158',
'end' => '123276598',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-010'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_000063_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000063_0001' => array(
'genes_in_region' => array(
'ENSG00000075399' => array(
[maximum depth reached]
),
'ENSG00000158805' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Ovary',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Lung',
(int) 25 => 'Brain',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Bladder',
(int) 30 => 'Breast',
(int) 31 => 'Lung',
(int) 32 => 'Bladder',
(int) 33 => 'Muscle',
(int) 34 => 'Adipose',
(int) 35 => 'Bladder',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adrenal',
(int) 46 => 'Bladder',
(int) 47 => 'Colon',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSG00000075399' => 'VPS9 domain containing 1',
'ENSG00000158805' => 'zinc finger protein 276',
'ENSG00000187741' => 'Fanconi anemia, complementation group A',
'ENSMUSG00000001062' => 'VPS9 domain containing 1',
'ENSMUSG00000001065' => 'zinc finger protein (C2H2 type) 276',
'ENSMUSG00000032815' => 'Fanconi anemia, complementation group A'
)
$gene_name_arr = array(
'ENSG00000075399' => 'VPS9D1',
'ENSG00000158805' => 'ZNF276',
'ENSG00000187741' => 'FANCA',
'ENSMUSG00000001062' => 'Vps9d1',
'ENSMUSG00000001065' => 'Zfp276',
'ENSMUSG00000032815' => 'Fanca'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000063_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89720400',
'seq_end' => '89816657',
'region_length' => '96257',
'region_type' => 'CGP',
'el_id' => 'ENSG00000158805-ENSG00000187741'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000063_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123254195',
'seq_end' => '123318576',
'region_length' => '64381',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001065-ENSMUSG00000032815'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 11 => 'Brain',
(int) 15 => 'Breast',
(int) 19 => 'Colon',
(int) 22 => 'Heart',
(int) 25 => 'Kidney',
(int) 28 => 'Liver',
(int) 32 => 'Lung',
(int) 38 => 'Muscle',
(int) 43 => 'Ovary',
(int) 49 => 'Placenta',
(int) 52 => 'Testis'
)
$column_titles = array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
)
$geneviewer = array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
)
$transcript_count = (int) 83
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000389386' => array(
'start' => '89707134',
'end' => '89720986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-002'
),
'ENST00000561976' => array(
'start' => '89707134',
'end' => '89719369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-001'
),
'ENST00000563798' => array(
'start' => '89711393',
'end' => '89720885',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'VPS9D1-003'
),
'ENST00000565023' => array(
'start' => '89707784',
'end' => '89710642',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-007'
),
'ENST00000565452' => array(
'start' => '89710965',
'end' => '89711644',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'VPS9D1-006'
),
'ENST00000567379' => array(
'start' => '89711359',
'end' => '89713040',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS9D1-005'
),
'ENST00000568691' => array(
'start' => '89710933',
'end' => '89713080',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS9D1-004'
),
'ENST00000614968' => array(
'start' => '89707134',
'end' => '89719369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-201'
),
'ENST00000289816' => array(
'start' => '89720985',
'end' => '89740903',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-001'
),
'ENST00000443381' => array(
'start' => '89721544',
'end' => '89738571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-004'
),
'ENST00000561536' => array(
'start' => '89722869',
'end' => '89738589',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-006'
),
'ENST00000562530' => array(
'start' => '89720400',
'end' => '89738281',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-007'
),
'ENST00000563541' => array(
'start' => '89723489',
'end' => '89733537',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-009'
),
'ENST00000563983' => array(
'start' => '89721160',
'end' => '89739816',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-005'
),
'ENST00000564004' => array(
'start' => '89731526',
'end' => '89738570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-008'
),
'ENST00000568064' => array(
'start' => '89721007',
'end' => '89738520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-002'
),
'ENST00000568295' => array(
'start' => '89721573',
'end' => '89738571',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-003'
),
'ENST00000569426' => array(
'start' => '89723606',
'end' => '89733470',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-010'
),
'ENST00000569582' => array(
'start' => '89733249',
'end' => '89737883',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-011'
),
'ENST00000569901' => array(
'start' => '89737712',
'end' => '89738329',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-012'
),
'ENST00000305699' => array(
'start' => '89739741',
'end' => '89765039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-009'
),
'ENST00000389301' => array(
'start' => '89737549',
'end' => '89816646',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-001'
),
'ENST00000389302' => array(
'start' => '89798374',
'end' => '89816657',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-003'
),
'ENST00000534992' => array(
'start' => '89798919',
'end' => '89816655',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-201'
),
'ENST00000543736' => array(
'start' => '89798919',
'end' => '89816657',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-004'
),
'ENST00000561660' => array(
'start' => '89745027',
'end' => '89765044',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-022'
),
'ENST00000561667' => array(
'start' => '89769915',
'end' => '89770583',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-018'
),
'ENST00000561722' => array(
'start' => '89738493',
'end' => '89740078',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-027'
),
'ENST00000562424' => array(
'start' => '89738495',
'end' => '89739758',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-029'
),
'ENST00000563318' => array(
'start' => '89752161',
'end' => '89767147',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-020'
),
'ENST00000563510' => array(
'start' => '89748764',
'end' => '89764947',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-019'
),
'ENST00000563513' => array(
'start' => '89808311',
'end' => '89816621',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-011'
),
'ENST00000563673' => array(
'start' => '89798385',
'end' => '89816635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-006'
),
'ENST00000563767' => array(
'start' => '89791044',
'end' => '89792011',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-017'
),
'ENST00000564475' => array(
'start' => '89738744',
'end' => '89742894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-028'
),
'ENST00000564870' => array(
'start' => '89738883',
'end' => '89742828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-030'
),
'ENST00000564969' => array(
'start' => '89739363',
'end' => '89745008',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-024'
),
'ENST00000565582' => array(
'start' => '89798991',
'end' => '89815978',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-012'
),
'ENST00000566133' => array(
'start' => '89791563',
'end' => '89792725',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-014'
),
'ENST00000566409' => array(
'start' => '89795906',
'end' => '89799232',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-007'
),
'ENST00000566889' => array(
'start' => '89798354',
'end' => '89816647',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-005'
),
'ENST00000567205' => array(
'start' => '89767142',
'end' => '89770024',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-008'
),
'ENST00000567284' => array(
'start' => '89770430',
'end' => '89778850',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FANCA-031'
),
'ENST00000567510' => array(
'start' => '89773320',
'end' => '89779957',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-016'
),
'ENST00000567621' => array(
'start' => '89791508',
'end' => '89808366',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-013'
),
'ENST00000567879' => array(
'start' => '89738630',
'end' => '89745062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-026'
),
'ENST00000567883' => array(
'start' => '89810572',
'end' => '89816608',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-032'
),
'ENST00000567943' => array(
'start' => '89810985',
'end' => '89816648',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-010'
),
'ENST00000567988' => array(
'start' => '89742902',
'end' => '89765004',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-021'
),
'ENST00000568369' => array(
'start' => '89738403',
'end' => '89816646',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-002'
),
'ENST00000568626' => array(
'start' => '89739282',
'end' => '89749816',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-023'
),
'ENST00000568983' => array(
'start' => '89744687',
'end' => '89749796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-025'
),
'ENSMUST00000117643' => array(
'start' => '123242356',
'end' => '123254176',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-003'
),
'ENSMUST00000118279' => array(
'start' => '123242359',
'end' => '123254092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-007'
),
'ENSMUST00000122363' => array(
'start' => '123242356',
'end' => '123254348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-001'
),
'ENSMUST00000124508' => array(
'start' => '123246857',
'end' => '123248013',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-011'
),
'ENSMUST00000127978' => array(
'start' => '123246516',
'end' => '123247996',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Vps9d1-012'
),
'ENSMUST00000129591' => array(
'start' => '123249712',
'end' => '123254050',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-008'
),
'ENSMUST00000130275' => array(
'start' => '123244947',
'end' => '123254105',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-006'
),
'ENSMUST00000130965' => array(
'start' => '123248553',
'end' => '123248983',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-010'
),
'ENSMUST00000137569' => array(
'start' => '123248828',
'end' => '123251071',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-009'
),
'ENSMUST00000146136' => array(
'start' => '123242358',
'end' => '123254163',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-004'
),
'ENSMUST00000149490' => array(
'start' => '123242356',
'end' => '123254222',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-002'
),
'ENSMUST00000155853' => array(
'start' => '123245143',
'end' => '123246930',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Vps9d1-013'
),
'ENSMUST00000155869' => array(
'start' => '123242358',
'end' => '123254109',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Vps9d1-005'
),
'ENSMUST00000001092' => array(
'start' => '123254195',
'end' => '123269745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zfp276-001'
),
'ENSMUST00000130333' => array(
'start' => '123264821',
'end' => '123265643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-005'
),
'ENSMUST00000146158' => array(
'start' => '123258328',
'end' => '123268122',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-003'
),
'ENSMUST00000147312' => array(
'start' => '123259460',
'end' => '123267917',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-004'
),
'ENSMUST00000150356' => array(
'start' => '123254271',
'end' => '123257636',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-006'
),
'ENSMUST00000154450' => array(
'start' => '123254686',
'end' => '123265070',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zfp276-007'
),
'ENSMUST00000156896' => array(
'start' => '123254284',
'end' => '123269743',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-002'
),
'ENSMUST00000035495' => array(
'start' => '123268300',
'end' => '123318576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-001'
),
'ENSMUST00000118395' => array(
'start' => '123302075',
'end' => '123318560',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-005'
),
'ENSMUST00000126834' => array(
'start' => '123271205',
'end' => '123278054',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-009'
),
'ENSMUST00000127904' => array(
'start' => '123286404',
'end' => '123313362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-003'
),
'ENSMUST00000133950' => array(
'start' => '123289361',
'end' => '123291861',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-006'
),
'ENSMUST00000135702' => array(
'start' => '123269290',
'end' => '123274223',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fanca-011'
),
'ENSMUST00000146687' => array(
'start' => '123277856',
'end' => '123282667',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-007'
),
'ENSMUST00000150318' => array(
'start' => '123312283',
'end' => '123318560',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-004'
),
'ENSMUST00000155279' => array(
'start' => '123277416',
'end' => '123281287',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fanca-008'
),
'ENSMUST00000155488' => array(
'start' => '123286189',
'end' => '123318560',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-002'
),
'ENSMUST00000155510' => array(
'start' => '123274158',
'end' => '123276598',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-010'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_000063_0001' => array(
'genes_in_region' => array(
'ENSG00000075399' => array(
[maximum depth reached]
),
'ENSG00000158805' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Ovary',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Lung',
(int) 25 => 'Brain',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Bladder',
(int) 30 => 'Breast',
(int) 31 => 'Lung',
(int) 32 => 'Bladder',
(int) 33 => 'Muscle',
(int) 34 => 'Adipose',
(int) 35 => 'Bladder',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adrenal',
(int) 46 => 'Bladder',
(int) 47 => 'Colon',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000063_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123254195',
'seq_end' => '123318576',
'region_length' => '64381',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001065-ENSMUSG00000032815'
)
)
$gene_el = array(
'ENST00000289816' => array(
'Adipose' => array(
'average_FPKM' => '0.965',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '6.200',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '2.623',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '1.451',
'stddev_FPKM' => '0.37'
),
'Heart' => array(
'average_FPKM' => '0.812',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1.352',
'stddev_FPKM' => '1.07'
),
'Liver' => array(
'average_FPKM' => '0.691',
'stddev_FPKM' => '0.39'
),
'Lung' => array(
'average_FPKM' => '0.573',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '3.348',
'stddev_FPKM' => '2.04'
),
'Placenta' => array(
'average_FPKM' => '1.861',
'stddev_FPKM' => '0.28'
)
),
'ENST00000443381' => array(
'Lung' => array(
'average_FPKM' => '1.246',
'stddev_FPKM' => '0.00'
)
),
'ENST00000561536' => array(),
'ENST00000562530' => array(
'Brain' => array(
'average_FPKM' => '2.110',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '5.263',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563541' => array(
'Muscle' => array(
'average_FPKM' => '0.934',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563983' => array(
'Ovary' => array(
'average_FPKM' => '0.367',
'stddev_FPKM' => '0.00'
)
),
'ENST00000564004' => array(
'Bladder' => array(
'average_FPKM' => '0.368',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '1.605',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '2.222',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568064' => array(),
'ENST00000568295' => array(),
'ENST00000569426' => array(
'Bladder' => array(
'average_FPKM' => '1.930',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '10.704',
'stddev_FPKM' => '0.00'
)
),
'ENST00000569582' => array(),
'ENST00000569901' => array()
)
$gene_key = 'ENSG00000158805'
$is_first = false
$tran_el = array()
$tran_key = 'ENST00000569901'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_000063_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000075399' => 'VPS9 domain containing 1',
'ENSG00000158805' => 'zinc finger protein 276',
'ENSG00000187741' => 'Fanconi anemia, complementation group A',
'ENSMUSG00000001062' => 'VPS9 domain containing 1',
'ENSMUSG00000001065' => 'zinc finger protein (C2H2 type) 276',
'ENSMUSG00000032815' => 'Fanconi anemia, complementation group A'
),
'gene_name_arr' => array(
'ENSG00000075399' => 'VPS9D1',
'ENSG00000158805' => 'ZNF276',
'ENSG00000187741' => 'FANCA',
'ENSMUSG00000001062' => 'Vps9d1',
'ENSMUSG00000001065' => 'Zfp276',
'ENSMUSG00000032815' => 'Fanca'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 11 => 'Brain',
(int) 15 => 'Breast',
(int) 19 => 'Colon',
(int) 22 => 'Heart',
(int) 25 => 'Kidney',
(int) 28 => 'Liver',
(int) 32 => 'Lung',
(int) 38 => 'Muscle',
(int) 43 => 'Ovary',
(int) 49 => 'Placenta',
(int) 52 => 'Testis'
),
'column_titles' => array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
),
'geneviewer' => array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
),
'transcript_count' => (int) 83,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000389386' => array(
'start' => '89707134',
'end' => '89720986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-002'
),
'ENST00000561976' => array(
'start' => '89707134',
'end' => '89719369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-001'
),
'ENST00000563798' => array(
'start' => '89711393',
'end' => '89720885',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'VPS9D1-003'
),
'ENST00000565023' => array(
'start' => '89707784',
'end' => '89710642',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-007'
),
'ENST00000565452' => array(
'start' => '89710965',
'end' => '89711644',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'VPS9D1-006'
),
'ENST00000567379' => array(
'start' => '89711359',
'end' => '89713040',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS9D1-005'
),
'ENST00000568691' => array(
'start' => '89710933',
'end' => '89713080',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS9D1-004'
),
'ENST00000614968' => array(
'start' => '89707134',
'end' => '89719369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-201'
),
'ENST00000289816' => array(
'start' => '89720985',
'end' => '89740903',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-001'
),
'ENST00000443381' => array(
'start' => '89721544',
'end' => '89738571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-004'
),
'ENST00000561536' => array(
'start' => '89722869',
'end' => '89738589',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-006'
),
'ENST00000562530' => array(
'start' => '89720400',
'end' => '89738281',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-007'
),
'ENST00000563541' => array(
'start' => '89723489',
'end' => '89733537',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-009'
),
'ENST00000563983' => array(
'start' => '89721160',
'end' => '89739816',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-005'
),
'ENST00000564004' => array(
'start' => '89731526',
'end' => '89738570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-008'
),
'ENST00000568064' => array(
'start' => '89721007',
'end' => '89738520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-002'
),
'ENST00000568295' => array(
'start' => '89721573',
'end' => '89738571',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-003'
),
'ENST00000569426' => array(
'start' => '89723606',
'end' => '89733470',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-010'
),
'ENST00000569582' => array(
'start' => '89733249',
'end' => '89737883',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-011'
),
'ENST00000569901' => array(
'start' => '89737712',
'end' => '89738329',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-012'
),
'ENST00000305699' => array(
'start' => '89739741',
'end' => '89765039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-009'
),
'ENST00000389301' => array(
'start' => '89737549',
'end' => '89816646',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-001'
),
'ENST00000389302' => array(
'start' => '89798374',
'end' => '89816657',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-003'
),
'ENST00000534992' => array(
'start' => '89798919',
'end' => '89816655',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-201'
),
'ENST00000543736' => array(
'start' => '89798919',
'end' => '89816657',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-004'
),
'ENST00000561660' => array(
'start' => '89745027',
'end' => '89765044',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-022'
),
'ENST00000561667' => array(
'start' => '89769915',
'end' => '89770583',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-018'
),
'ENST00000561722' => array(
'start' => '89738493',
'end' => '89740078',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-027'
),
'ENST00000562424' => array(
'start' => '89738495',
'end' => '89739758',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-029'
),
'ENST00000563318' => array(
'start' => '89752161',
'end' => '89767147',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-020'
),
'ENST00000563510' => array(
'start' => '89748764',
'end' => '89764947',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-019'
),
'ENST00000563513' => array(
'start' => '89808311',
'end' => '89816621',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-011'
),
'ENST00000563673' => array(
'start' => '89798385',
'end' => '89816635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-006'
),
'ENST00000563767' => array(
'start' => '89791044',
'end' => '89792011',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-017'
),
'ENST00000564475' => array(
'start' => '89738744',
'end' => '89742894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-028'
),
'ENST00000564870' => array(
'start' => '89738883',
'end' => '89742828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-030'
),
'ENST00000564969' => array(
'start' => '89739363',
'end' => '89745008',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-024'
),
'ENST00000565582' => array(
'start' => '89798991',
'end' => '89815978',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-012'
),
'ENST00000566133' => array(
'start' => '89791563',
'end' => '89792725',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-014'
),
'ENST00000566409' => array(
'start' => '89795906',
'end' => '89799232',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-007'
),
'ENST00000566889' => array(
'start' => '89798354',
'end' => '89816647',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-005'
),
'ENST00000567205' => array(
'start' => '89767142',
'end' => '89770024',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-008'
),
'ENST00000567284' => array(
'start' => '89770430',
'end' => '89778850',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FANCA-031'
),
'ENST00000567510' => array(
'start' => '89773320',
'end' => '89779957',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-016'
),
'ENST00000567621' => array(
'start' => '89791508',
'end' => '89808366',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-013'
),
'ENST00000567879' => array(
'start' => '89738630',
'end' => '89745062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-026'
),
'ENST00000567883' => array(
'start' => '89810572',
'end' => '89816608',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-032'
),
'ENST00000567943' => array(
'start' => '89810985',
'end' => '89816648',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-010'
),
'ENST00000567988' => array(
'start' => '89742902',
'end' => '89765004',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-021'
),
'ENST00000568369' => array(
'start' => '89738403',
'end' => '89816646',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-002'
),
'ENST00000568626' => array(
'start' => '89739282',
'end' => '89749816',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-023'
),
'ENST00000568983' => array(
'start' => '89744687',
'end' => '89749796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-025'
),
'ENSMUST00000117643' => array(
'start' => '123242356',
'end' => '123254176',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-003'
),
'ENSMUST00000118279' => array(
'start' => '123242359',
'end' => '123254092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-007'
),
'ENSMUST00000122363' => array(
'start' => '123242356',
'end' => '123254348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-001'
),
'ENSMUST00000124508' => array(
'start' => '123246857',
'end' => '123248013',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-011'
),
'ENSMUST00000127978' => array(
'start' => '123246516',
'end' => '123247996',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Vps9d1-012'
),
'ENSMUST00000129591' => array(
'start' => '123249712',
'end' => '123254050',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-008'
),
'ENSMUST00000130275' => array(
'start' => '123244947',
'end' => '123254105',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-006'
),
'ENSMUST00000130965' => array(
'start' => '123248553',
'end' => '123248983',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-010'
),
'ENSMUST00000137569' => array(
'start' => '123248828',
'end' => '123251071',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-009'
),
'ENSMUST00000146136' => array(
'start' => '123242358',
'end' => '123254163',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-004'
),
'ENSMUST00000149490' => array(
'start' => '123242356',
'end' => '123254222',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-002'
),
'ENSMUST00000155853' => array(
'start' => '123245143',
'end' => '123246930',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Vps9d1-013'
),
'ENSMUST00000155869' => array(
'start' => '123242358',
'end' => '123254109',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Vps9d1-005'
),
'ENSMUST00000001092' => array(
'start' => '123254195',
'end' => '123269745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zfp276-001'
),
'ENSMUST00000130333' => array(
'start' => '123264821',
'end' => '123265643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-005'
),
'ENSMUST00000146158' => array(
'start' => '123258328',
'end' => '123268122',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-003'
),
'ENSMUST00000147312' => array(
'start' => '123259460',
'end' => '123267917',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-004'
),
'ENSMUST00000150356' => array(
'start' => '123254271',
'end' => '123257636',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-006'
),
'ENSMUST00000154450' => array(
'start' => '123254686',
'end' => '123265070',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zfp276-007'
),
'ENSMUST00000156896' => array(
'start' => '123254284',
'end' => '123269743',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-002'
),
'ENSMUST00000035495' => array(
'start' => '123268300',
'end' => '123318576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-001'
),
'ENSMUST00000118395' => array(
'start' => '123302075',
'end' => '123318560',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-005'
),
'ENSMUST00000126834' => array(
'start' => '123271205',
'end' => '123278054',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-009'
),
'ENSMUST00000127904' => array(
'start' => '123286404',
'end' => '123313362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-003'
),
'ENSMUST00000133950' => array(
'start' => '123289361',
'end' => '123291861',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-006'
),
'ENSMUST00000135702' => array(
'start' => '123269290',
'end' => '123274223',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fanca-011'
),
'ENSMUST00000146687' => array(
'start' => '123277856',
'end' => '123282667',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-007'
),
'ENSMUST00000150318' => array(
'start' => '123312283',
'end' => '123318560',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-004'
),
'ENSMUST00000155279' => array(
'start' => '123277416',
'end' => '123281287',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fanca-008'
),
'ENSMUST00000155488' => array(
'start' => '123286189',
'end' => '123318560',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-002'
),
'ENSMUST00000155510' => array(
'start' => '123274158',
'end' => '123276598',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-010'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_000063_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000063_0001' => array(
'genes_in_region' => array(
'ENSG00000075399' => array(
[maximum depth reached]
),
'ENSG00000158805' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Ovary',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Lung',
(int) 25 => 'Brain',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Bladder',
(int) 30 => 'Breast',
(int) 31 => 'Lung',
(int) 32 => 'Bladder',
(int) 33 => 'Muscle',
(int) 34 => 'Adipose',
(int) 35 => 'Bladder',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adrenal',
(int) 46 => 'Bladder',
(int) 47 => 'Colon',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSG00000075399' => 'VPS9 domain containing 1',
'ENSG00000158805' => 'zinc finger protein 276',
'ENSG00000187741' => 'Fanconi anemia, complementation group A',
'ENSMUSG00000001062' => 'VPS9 domain containing 1',
'ENSMUSG00000001065' => 'zinc finger protein (C2H2 type) 276',
'ENSMUSG00000032815' => 'Fanconi anemia, complementation group A'
)
$gene_name_arr = array(
'ENSG00000075399' => 'VPS9D1',
'ENSG00000158805' => 'ZNF276',
'ENSG00000187741' => 'FANCA',
'ENSMUSG00000001062' => 'Vps9d1',
'ENSMUSG00000001065' => 'Zfp276',
'ENSMUSG00000032815' => 'Fanca'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000063_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89720400',
'seq_end' => '89816657',
'region_length' => '96257',
'region_type' => 'CGP',
'el_id' => 'ENSG00000158805-ENSG00000187741'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000063_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123254195',
'seq_end' => '123318576',
'region_length' => '64381',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001065-ENSMUSG00000032815'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 11 => 'Brain',
(int) 15 => 'Breast',
(int) 19 => 'Colon',
(int) 22 => 'Heart',
(int) 25 => 'Kidney',
(int) 28 => 'Liver',
(int) 32 => 'Lung',
(int) 38 => 'Muscle',
(int) 43 => 'Ovary',
(int) 49 => 'Placenta',
(int) 52 => 'Testis'
)
$column_titles = array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
)
$geneviewer = array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
)
$transcript_count = (int) 83
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000389386' => array(
'start' => '89707134',
'end' => '89720986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-002'
),
'ENST00000561976' => array(
'start' => '89707134',
'end' => '89719369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-001'
),
'ENST00000563798' => array(
'start' => '89711393',
'end' => '89720885',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'VPS9D1-003'
),
'ENST00000565023' => array(
'start' => '89707784',
'end' => '89710642',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-007'
),
'ENST00000565452' => array(
'start' => '89710965',
'end' => '89711644',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'VPS9D1-006'
),
'ENST00000567379' => array(
'start' => '89711359',
'end' => '89713040',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS9D1-005'
),
'ENST00000568691' => array(
'start' => '89710933',
'end' => '89713080',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS9D1-004'
),
'ENST00000614968' => array(
'start' => '89707134',
'end' => '89719369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS9D1-201'
),
'ENST00000289816' => array(
'start' => '89720985',
'end' => '89740903',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-001'
),
'ENST00000443381' => array(
'start' => '89721544',
'end' => '89738571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-004'
),
'ENST00000561536' => array(
'start' => '89722869',
'end' => '89738589',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-006'
),
'ENST00000562530' => array(
'start' => '89720400',
'end' => '89738281',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-007'
),
'ENST00000563541' => array(
'start' => '89723489',
'end' => '89733537',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-009'
),
'ENST00000563983' => array(
'start' => '89721160',
'end' => '89739816',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-005'
),
'ENST00000564004' => array(
'start' => '89731526',
'end' => '89738570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-008'
),
'ENST00000568064' => array(
'start' => '89721007',
'end' => '89738520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZNF276-002'
),
'ENST00000568295' => array(
'start' => '89721573',
'end' => '89738571',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZNF276-003'
),
'ENST00000569426' => array(
'start' => '89723606',
'end' => '89733470',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-010'
),
'ENST00000569582' => array(
'start' => '89733249',
'end' => '89737883',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-011'
),
'ENST00000569901' => array(
'start' => '89737712',
'end' => '89738329',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZNF276-012'
),
'ENST00000305699' => array(
'start' => '89739741',
'end' => '89765039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-009'
),
'ENST00000389301' => array(
'start' => '89737549',
'end' => '89816646',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-001'
),
'ENST00000389302' => array(
'start' => '89798374',
'end' => '89816657',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-003'
),
'ENST00000534992' => array(
'start' => '89798919',
'end' => '89816655',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-201'
),
'ENST00000543736' => array(
'start' => '89798919',
'end' => '89816657',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-004'
),
'ENST00000561660' => array(
'start' => '89745027',
'end' => '89765044',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-022'
),
'ENST00000561667' => array(
'start' => '89769915',
'end' => '89770583',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-018'
),
'ENST00000561722' => array(
'start' => '89738493',
'end' => '89740078',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-027'
),
'ENST00000562424' => array(
'start' => '89738495',
'end' => '89739758',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-029'
),
'ENST00000563318' => array(
'start' => '89752161',
'end' => '89767147',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-020'
),
'ENST00000563510' => array(
'start' => '89748764',
'end' => '89764947',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-019'
),
'ENST00000563513' => array(
'start' => '89808311',
'end' => '89816621',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-011'
),
'ENST00000563673' => array(
'start' => '89798385',
'end' => '89816635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-006'
),
'ENST00000563767' => array(
'start' => '89791044',
'end' => '89792011',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-017'
),
'ENST00000564475' => array(
'start' => '89738744',
'end' => '89742894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-028'
),
'ENST00000564870' => array(
'start' => '89738883',
'end' => '89742828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-030'
),
'ENST00000564969' => array(
'start' => '89739363',
'end' => '89745008',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-024'
),
'ENST00000565582' => array(
'start' => '89798991',
'end' => '89815978',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-012'
),
'ENST00000566133' => array(
'start' => '89791563',
'end' => '89792725',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-014'
),
'ENST00000566409' => array(
'start' => '89795906',
'end' => '89799232',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-007'
),
'ENST00000566889' => array(
'start' => '89798354',
'end' => '89816647',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-005'
),
'ENST00000567205' => array(
'start' => '89767142',
'end' => '89770024',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-008'
),
'ENST00000567284' => array(
'start' => '89770430',
'end' => '89778850',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FANCA-031'
),
'ENST00000567510' => array(
'start' => '89773320',
'end' => '89779957',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-016'
),
'ENST00000567621' => array(
'start' => '89791508',
'end' => '89808366',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-013'
),
'ENST00000567879' => array(
'start' => '89738630',
'end' => '89745062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-026'
),
'ENST00000567883' => array(
'start' => '89810572',
'end' => '89816608',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-032'
),
'ENST00000567943' => array(
'start' => '89810985',
'end' => '89816648',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-010'
),
'ENST00000567988' => array(
'start' => '89742902',
'end' => '89765004',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-021'
),
'ENST00000568369' => array(
'start' => '89738403',
'end' => '89816646',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FANCA-002'
),
'ENST00000568626' => array(
'start' => '89739282',
'end' => '89749816',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FANCA-023'
),
'ENST00000568983' => array(
'start' => '89744687',
'end' => '89749796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FANCA-025'
),
'ENSMUST00000117643' => array(
'start' => '123242356',
'end' => '123254176',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-003'
),
'ENSMUST00000118279' => array(
'start' => '123242359',
'end' => '123254092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-007'
),
'ENSMUST00000122363' => array(
'start' => '123242356',
'end' => '123254348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps9d1-001'
),
'ENSMUST00000124508' => array(
'start' => '123246857',
'end' => '123248013',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-011'
),
'ENSMUST00000127978' => array(
'start' => '123246516',
'end' => '123247996',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Vps9d1-012'
),
'ENSMUST00000129591' => array(
'start' => '123249712',
'end' => '123254050',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-008'
),
'ENSMUST00000130275' => array(
'start' => '123244947',
'end' => '123254105',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-006'
),
'ENSMUST00000130965' => array(
'start' => '123248553',
'end' => '123248983',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-010'
),
'ENSMUST00000137569' => array(
'start' => '123248828',
'end' => '123251071',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-009'
),
'ENSMUST00000146136' => array(
'start' => '123242358',
'end' => '123254163',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-004'
),
'ENSMUST00000149490' => array(
'start' => '123242356',
'end' => '123254222',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps9d1-002'
),
'ENSMUST00000155853' => array(
'start' => '123245143',
'end' => '123246930',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Vps9d1-013'
),
'ENSMUST00000155869' => array(
'start' => '123242358',
'end' => '123254109',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Vps9d1-005'
),
'ENSMUST00000001092' => array(
'start' => '123254195',
'end' => '123269745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zfp276-001'
),
'ENSMUST00000130333' => array(
'start' => '123264821',
'end' => '123265643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-005'
),
'ENSMUST00000146158' => array(
'start' => '123258328',
'end' => '123268122',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-003'
),
'ENSMUST00000147312' => array(
'start' => '123259460',
'end' => '123267917',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-004'
),
'ENSMUST00000150356' => array(
'start' => '123254271',
'end' => '123257636',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-006'
),
'ENSMUST00000154450' => array(
'start' => '123254686',
'end' => '123265070',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zfp276-007'
),
'ENSMUST00000156896' => array(
'start' => '123254284',
'end' => '123269743',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zfp276-002'
),
'ENSMUST00000035495' => array(
'start' => '123268300',
'end' => '123318576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-001'
),
'ENSMUST00000118395' => array(
'start' => '123302075',
'end' => '123318560',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-005'
),
'ENSMUST00000126834' => array(
'start' => '123271205',
'end' => '123278054',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-009'
),
'ENSMUST00000127904' => array(
'start' => '123286404',
'end' => '123313362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-003'
),
'ENSMUST00000133950' => array(
'start' => '123289361',
'end' => '123291861',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-006'
),
'ENSMUST00000135702' => array(
'start' => '123269290',
'end' => '123274223',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fanca-011'
),
'ENSMUST00000146687' => array(
'start' => '123277856',
'end' => '123282667',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-007'
),
'ENSMUST00000150318' => array(
'start' => '123312283',
'end' => '123318560',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-004'
),
'ENSMUST00000155279' => array(
'start' => '123277416',
'end' => '123281287',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fanca-008'
),
'ENSMUST00000155488' => array(
'start' => '123286189',
'end' => '123318560',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fanca-002'
),
'ENSMUST00000155510' => array(
'start' => '123274158',
'end' => '123276598',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fanca-010'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_000063_0001' => array(
'genes_in_region' => array(
'ENSG00000075399' => array(
[maximum depth reached]
),
'ENSG00000158805' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Ovary',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Lung',
(int) 25 => 'Brain',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Bladder',
(int) 30 => 'Breast',
(int) 31 => 'Lung',
(int) 32 => 'Bladder',
(int) 33 => 'Muscle',
(int) 34 => 'Adipose',
(int) 35 => 'Bladder',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adrenal',
(int) 46 => 'Bladder',
(int) 47 => 'Colon',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000063_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123254195',
'seq_end' => '123318576',
'region_length' => '64381',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001065-ENSMUSG00000032815'
)
)
$gene_el = array(
'ENST00000289816' => array(
'Adipose' => array(
'average_FPKM' => '0.965',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '6.200',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '2.623',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '1.451',
'stddev_FPKM' => '0.37'
),
'Heart' => array(
'average_FPKM' => '0.812',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1.352',
'stddev_FPKM' => '1.07'
),
'Liver' => array(
'average_FPKM' => '0.691',
'stddev_FPKM' => '0.39'
),
'Lung' => array(
'average_FPKM' => '0.573',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '3.348',
'stddev_FPKM' => '2.04'
),
'Placenta' => array(
'average_FPKM' => '1.861',
'stddev_FPKM' => '0.28'
)
),
'ENST00000443381' => array(
'Lung' => array(
'average_FPKM' => '1.246',
'stddev_FPKM' => '0.00'
)
),
'ENST00000561536' => array(),
'ENST00000562530' => array(
'Brain' => array(
'average_FPKM' => '2.110',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '5.263',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563541' => array(
'Muscle' => array(
'average_FPKM' => '0.934',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563983' => array(
'Ovary' => array(
'average_FPKM' => '0.367',
'stddev_FPKM' => '0.00'
)
),
'ENST00000564004' => array(
'Bladder' => array(
'average_FPKM' => '0.368',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '1.605',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '2.222',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568064' => array(),
'ENST00000568295' => array(),
'ENST00000569426' => array(
'Bladder' => array(
'average_FPKM' => '1.930',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '10.704',
'stddev_FPKM' => '0.00'
)
),
'ENST00000569582' => array(),
'ENST00000569901' => array()
)
$gene_key = 'ENSG00000158805'
$is_first = false
$tran_el = array()
$tran_key = 'ENST00000569901'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
(VPS9D1)