| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000031818-ENSMUSG00000041515 |
CGP |
10090 |
8:120668222-120756694  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0000IY_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_0000IY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000131143' => 'cytochrome c oxidase subunit IV isoform 1',
'ENSG00000131148' => 'ER membrane protein complex subunit 8',
'ENSG00000140968' => 'interferon regulatory factor 8',
'ENSG00000214259' => null,
'ENSG00000270698' => null,
'ENSG00000274134' => 'microRNA 6774',
'ENSG00000279907' => null,
'ENSMUSG00000031818' => 'cytochrome c oxidase subunit IV isoform 1',
'ENSMUSG00000031819' => 'ER membrane protein complex subunit 8',
'ENSMUSG00000041515' => 'interferon regulatory factor 8',
'ENSMUSG00000088416' => 'predicted gene, 24239',
'ENSMUSG00000097895' => 'predicted gene, 18709'
),
'gene_name_arr' => array(
'ENSG00000131143' => 'COX4I1',
'ENSG00000131148' => 'EMC8',
'ENSG00000140968' => 'IRF8',
'ENSG00000214259' => 'RP11-568J23.1',
'ENSG00000270698' => 'RP11-568J23.7',
'ENSG00000274134' => 'MIR6774',
'ENSG00000279907' => 'RP11-568J23.2',
'ENSMUSG00000031818' => 'Cox4i1',
'ENSMUSG00000031819' => 'Emc8',
'ENSMUSG00000041515' => 'Irf8',
'ENSMUSG00000088416' => 'Gm24239',
'ENSMUSG00000097895' => 'Gm18709'
),
'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) 8 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 16 => 'Brain',
(int) 23 => 'Breast',
(int) 33 => 'Colon',
(int) 39 => 'Heart',
(int) 48 => 'Kidney',
(int) 55 => 'Liver',
(int) 61 => 'Lung',
(int) 66 => 'Muscle',
(int) 72 => 'Ovary',
(int) 83 => 'Placenta',
(int) 88 => '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) 63,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000253452' => array(
'start' => '85799684',
'end' => '85807002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-001'
),
'ENST00000561569' => array(
'start' => '85799697',
'end' => '85807002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-009'
),
'ENST00000562336' => array(
'start' => '85799693',
'end' => '85807044',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-016'
),
'ENST00000562929' => array(
'start' => '85805069',
'end' => '85807031',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'COX4I1-017'
),
'ENST00000563774' => array(
'start' => '85799696',
'end' => '85805350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-008'
),
'ENST00000564544' => array(
'start' => '85799708',
'end' => '85806975',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'COX4I1-015'
),
'ENST00000564648' => array(
'start' => '85801202',
'end' => '85806967',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-005'
),
'ENST00000564903' => array(
'start' => '85801202',
'end' => '85806968',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-004'
),
'ENST00000565078' => array(
'start' => '85798633',
'end' => '85804992',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-006'
),
'ENST00000566115' => array(
'start' => '85799638',
'end' => '85805096',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'COX4I1-010'
),
'ENST00000566405' => array(
'start' => '85799698',
'end' => '85806802',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-013'
),
'ENST00000566617' => array(
'start' => '85799760',
'end' => '85805309',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-007'
),
'ENST00000567241' => array(
'start' => '85799654',
'end' => '85805328',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-012'
),
'ENST00000567266' => array(
'start' => '85799697',
'end' => '85805426',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-019'
),
'ENST00000568339' => array(
'start' => '85799622',
'end' => '85807002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-003'
),
'ENST00000568794' => array(
'start' => '85799683',
'end' => '85806805',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-011'
),
'ENST00000569997' => array(
'start' => '85803057',
'end' => '85807002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-002'
),
'ENST00000570123' => array(
'start' => '85799612',
'end' => '85805742',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'COX4I1-014'
),
'ENST00000253457' => array(
'start' => '85778624',
'end' => '85799540',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EMC8-001'
),
'ENST00000435200' => array(
'start' => '85778624',
'end' => '85799608',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EMC8-002'
),
'ENST00000595980' => array(
'start' => '85771758',
'end' => '85781258',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'EMC8-003'
),
'ENST00000596852' => array(
'start' => '85788897',
'end' => '85799396',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-006'
),
'ENST00000597291' => array(
'start' => '85779398',
'end' => '85781223',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-005'
),
'ENST00000600807' => array(
'start' => '85779662',
'end' => '85781760',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-004'
),
'ENST00000268638' => array(
'start' => '85898803',
'end' => '85922609',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-001'
),
'ENST00000562492' => array(
'start' => '85914043',
'end' => '85921371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-009'
),
'ENST00000563180' => array(
'start' => '85902689',
'end' => '85909882',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-002'
),
'ENST00000564056' => array(
'start' => '85903131',
'end' => '85913312',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'IRF8-007'
),
'ENST00000564617' => array(
'start' => '85902815',
'end' => '85913160',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-011'
),
'ENST00000564803' => array(
'start' => '85902838',
'end' => '85918800',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-006'
),
'ENST00000565552' => array(
'start' => '85899163',
'end' => '85903156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-004'
),
'ENST00000566369' => array(
'start' => '85908988',
'end' => '85922296',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-003'
),
'ENST00000569145' => array(
'start' => '85913974',
'end' => '85918489',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-008'
),
'ENST00000569607' => array(
'start' => '85914313',
'end' => '85921274',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-010'
),
'ENST00000570088' => array(
'start' => '85899188',
'end' => '85903531',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'IRF8-005'
),
'ENST00000484096' => array(
'start' => '85815873',
'end' => '85816536',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-568J23.1-001'
),
'ENST00000605872' => array(
'start' => '85814425',
'end' => '85815062',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-568J23.7-001'
),
'ENST00000614651' => array(
'start' => '85918347',
'end' => '85918416',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6774-201'
),
'ENST00000624587' => array(
'start' => '85859521',
'end' => '85862012',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-568J23.2-001'
),
'ENSMUST00000034276' => array(
'start' => '120668222',
'end' => '120674207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-001'
),
'ENSMUST00000180856' => array(
'start' => '120668261',
'end' => '120669821',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-003'
),
'ENSMUST00000181026' => array(
'start' => '120673152',
'end' => '120674207',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-006'
),
'ENSMUST00000181172' => array(
'start' => '120672590',
'end' => '120674113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-005'
),
'ENSMUST00000181586' => array(
'start' => '120668222',
'end' => '120674207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-002'
),
'ENSMUST00000181795' => array(
'start' => '120668308',
'end' => '120674032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-007'
),
'ENSMUST00000181847' => array(
'start' => '120668336',
'end' => '120674045',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Cox4i1-004'
),
'ENSMUST00000034277' => array(
'start' => '120653914',
'end' => '120668121',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-001'
),
'ENSMUST00000180417' => array(
'start' => '120657851',
'end' => '120668573',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Emc8-002'
),
'ENSMUST00000180909' => array(
'start' => '120660647',
'end' => '120668113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Emc8-005'
),
'ENSMUST00000181111' => array(
'start' => '120658024',
'end' => '120667763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-006'
),
'ENSMUST00000181334' => array(
'start' => '120659974',
'end' => '120668003',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-004'
),
'ENSMUST00000181402' => array(
'start' => '120655978',
'end' => '120668012',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Emc8-003'
),
'ENSMUST00000181836' => array(
'start' => '120658050',
'end' => '120667836',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-008'
),
'ENSMUST00000181950' => array(
'start' => '120657833',
'end' => '120668087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-007'
),
'ENSMUST00000047737' => array(
'start' => '120736358',
'end' => '120756694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-001'
),
'ENSMUST00000160388' => array(
'start' => '120745480',
'end' => '120753733',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Irf8-006'
),
'ENSMUST00000160594' => array(
'start' => '120752209',
'end' => '120753711',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Irf8-007'
),
'ENSMUST00000160943' => array(
'start' => '120739990',
'end' => '120755204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-004'
),
'ENSMUST00000162001' => array(
'start' => '120738639',
'end' => '120755581',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-003'
),
'ENSMUST00000162658' => array(
'start' => '120736385',
'end' => '120753478',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-005'
),
'ENSMUST00000162775' => array(
'start' => '120736359',
'end' => '120743234',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Irf8-002'
),
'ENSMUST00000157791' => array(
'start' => '120717500',
'end' => '120717754',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm24239-201'
),
'ENSMUST00000180564' => array(
'start' => '120727263',
'end' => '120727943',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm18709-001'
)
),
'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_0000IY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0000IY_0001' => array(
'genes_in_region' => array(
'ENSG00000131143' => array(
[maximum depth reached]
),
'ENSG00000131148' => array(
[maximum depth reached]
),
'ENSG00000140968' => array(
[maximum depth reached]
),
'ENSG00000214259' => array(
[maximum depth reached]
),
'ENSG00000274134' => array(
[maximum depth reached]
),
'ENSG00000279907' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Liver',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Bladder',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Heart',
(int) 29 => 'Ovary',
(int) 30 => 'Heart',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Breast',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Bladder',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Liver',
(int) 49 => 'Muscle',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Kidney',
(int) 54 => 'Lung',
(int) 55 => 'Adipose',
(int) 56 => 'Brain',
(int) 57 => 'Heart',
(int) 58 => 'Kidney',
(int) 59 => 'Breast',
(int) 60 => 'Colon',
(int) 61 => 'Ovary',
(int) 62 => 'Placenta',
(int) 63 => 'Testis',
(int) 64 => 'Ovary',
(int) 65 => 'Testis',
(int) 66 => 'Adipose',
(int) 67 => 'Bladder',
(int) 68 => 'Breast',
(int) 69 => 'Heart',
(int) 70 => 'Kidney',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Bladder',
(int) 75 => 'Liver',
(int) 76 => 'Adipose',
(int) 77 => 'Brain',
(int) 78 => 'Breast',
(int) 79 => 'Colon',
(int) 80 => 'Lung',
(int) 81 => 'Muscle',
(int) 82 => 'Ovary',
(int) 83 => 'Testis',
(int) 84 => 'Adipose',
(int) 85 => 'Adipose',
(int) 86 => 'Adrenal',
(int) 87 => 'Brain',
(int) 88 => 'Breast',
(int) 89 => 'Colon',
(int) 90 => 'Heart',
(int) 91 => 'Kidney',
(int) 92 => 'Liver',
(int) 93 => 'Lung',
(int) 94 => 'Ovary',
(int) 95 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000131143' => 'cytochrome c oxidase subunit IV isoform 1',
'ENSG00000131148' => 'ER membrane protein complex subunit 8',
'ENSG00000140968' => 'interferon regulatory factor 8',
'ENSG00000214259' => null,
'ENSG00000270698' => null,
'ENSG00000274134' => 'microRNA 6774',
'ENSG00000279907' => null,
'ENSMUSG00000031818' => 'cytochrome c oxidase subunit IV isoform 1',
'ENSMUSG00000031819' => 'ER membrane protein complex subunit 8',
'ENSMUSG00000041515' => 'interferon regulatory factor 8',
'ENSMUSG00000088416' => 'predicted gene, 24239',
'ENSMUSG00000097895' => 'predicted gene, 18709'
)
$gene_name_arr = array(
'ENSG00000131143' => 'COX4I1',
'ENSG00000131148' => 'EMC8',
'ENSG00000140968' => 'IRF8',
'ENSG00000214259' => 'RP11-568J23.1',
'ENSG00000270698' => 'RP11-568J23.7',
'ENSG00000274134' => 'MIR6774',
'ENSG00000279907' => 'RP11-568J23.2',
'ENSMUSG00000031818' => 'Cox4i1',
'ENSMUSG00000031819' => 'Emc8',
'ENSMUSG00000041515' => 'Irf8',
'ENSMUSG00000088416' => 'Gm24239',
'ENSMUSG00000097895' => 'Gm18709'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000IY_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '85798633',
'seq_end' => '85922609',
'region_length' => '123976',
'region_type' => 'CGP',
'el_id' => 'ENSG00000131143-ENSG00000140968'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000IY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '120668222',
'seq_end' => '120756694',
'region_length' => '88472',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031818-ENSMUSG00000041515'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 16 => 'Brain',
(int) 23 => 'Breast',
(int) 33 => 'Colon',
(int) 39 => 'Heart',
(int) 48 => 'Kidney',
(int) 55 => 'Liver',
(int) 61 => 'Lung',
(int) 66 => 'Muscle',
(int) 72 => 'Ovary',
(int) 83 => 'Placenta',
(int) 88 => '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) 63
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000253452' => array(
'start' => '85799684',
'end' => '85807002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-001'
),
'ENST00000561569' => array(
'start' => '85799697',
'end' => '85807002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-009'
),
'ENST00000562336' => array(
'start' => '85799693',
'end' => '85807044',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-016'
),
'ENST00000562929' => array(
'start' => '85805069',
'end' => '85807031',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'COX4I1-017'
),
'ENST00000563774' => array(
'start' => '85799696',
'end' => '85805350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-008'
),
'ENST00000564544' => array(
'start' => '85799708',
'end' => '85806975',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'COX4I1-015'
),
'ENST00000564648' => array(
'start' => '85801202',
'end' => '85806967',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-005'
),
'ENST00000564903' => array(
'start' => '85801202',
'end' => '85806968',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-004'
),
'ENST00000565078' => array(
'start' => '85798633',
'end' => '85804992',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-006'
),
'ENST00000566115' => array(
'start' => '85799638',
'end' => '85805096',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'COX4I1-010'
),
'ENST00000566405' => array(
'start' => '85799698',
'end' => '85806802',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-013'
),
'ENST00000566617' => array(
'start' => '85799760',
'end' => '85805309',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-007'
),
'ENST00000567241' => array(
'start' => '85799654',
'end' => '85805328',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-012'
),
'ENST00000567266' => array(
'start' => '85799697',
'end' => '85805426',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-019'
),
'ENST00000568339' => array(
'start' => '85799622',
'end' => '85807002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-003'
),
'ENST00000568794' => array(
'start' => '85799683',
'end' => '85806805',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-011'
),
'ENST00000569997' => array(
'start' => '85803057',
'end' => '85807002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-002'
),
'ENST00000570123' => array(
'start' => '85799612',
'end' => '85805742',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'COX4I1-014'
),
'ENST00000253457' => array(
'start' => '85778624',
'end' => '85799540',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EMC8-001'
),
'ENST00000435200' => array(
'start' => '85778624',
'end' => '85799608',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EMC8-002'
),
'ENST00000595980' => array(
'start' => '85771758',
'end' => '85781258',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'EMC8-003'
),
'ENST00000596852' => array(
'start' => '85788897',
'end' => '85799396',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-006'
),
'ENST00000597291' => array(
'start' => '85779398',
'end' => '85781223',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-005'
),
'ENST00000600807' => array(
'start' => '85779662',
'end' => '85781760',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-004'
),
'ENST00000268638' => array(
'start' => '85898803',
'end' => '85922609',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-001'
),
'ENST00000562492' => array(
'start' => '85914043',
'end' => '85921371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-009'
),
'ENST00000563180' => array(
'start' => '85902689',
'end' => '85909882',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-002'
),
'ENST00000564056' => array(
'start' => '85903131',
'end' => '85913312',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'IRF8-007'
),
'ENST00000564617' => array(
'start' => '85902815',
'end' => '85913160',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-011'
),
'ENST00000564803' => array(
'start' => '85902838',
'end' => '85918800',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-006'
),
'ENST00000565552' => array(
'start' => '85899163',
'end' => '85903156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-004'
),
'ENST00000566369' => array(
'start' => '85908988',
'end' => '85922296',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-003'
),
'ENST00000569145' => array(
'start' => '85913974',
'end' => '85918489',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-008'
),
'ENST00000569607' => array(
'start' => '85914313',
'end' => '85921274',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-010'
),
'ENST00000570088' => array(
'start' => '85899188',
'end' => '85903531',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'IRF8-005'
),
'ENST00000484096' => array(
'start' => '85815873',
'end' => '85816536',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-568J23.1-001'
),
'ENST00000605872' => array(
'start' => '85814425',
'end' => '85815062',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-568J23.7-001'
),
'ENST00000614651' => array(
'start' => '85918347',
'end' => '85918416',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6774-201'
),
'ENST00000624587' => array(
'start' => '85859521',
'end' => '85862012',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-568J23.2-001'
),
'ENSMUST00000034276' => array(
'start' => '120668222',
'end' => '120674207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-001'
),
'ENSMUST00000180856' => array(
'start' => '120668261',
'end' => '120669821',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-003'
),
'ENSMUST00000181026' => array(
'start' => '120673152',
'end' => '120674207',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-006'
),
'ENSMUST00000181172' => array(
'start' => '120672590',
'end' => '120674113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-005'
),
'ENSMUST00000181586' => array(
'start' => '120668222',
'end' => '120674207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-002'
),
'ENSMUST00000181795' => array(
'start' => '120668308',
'end' => '120674032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-007'
),
'ENSMUST00000181847' => array(
'start' => '120668336',
'end' => '120674045',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Cox4i1-004'
),
'ENSMUST00000034277' => array(
'start' => '120653914',
'end' => '120668121',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-001'
),
'ENSMUST00000180417' => array(
'start' => '120657851',
'end' => '120668573',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Emc8-002'
),
'ENSMUST00000180909' => array(
'start' => '120660647',
'end' => '120668113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Emc8-005'
),
'ENSMUST00000181111' => array(
'start' => '120658024',
'end' => '120667763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-006'
),
'ENSMUST00000181334' => array(
'start' => '120659974',
'end' => '120668003',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-004'
),
'ENSMUST00000181402' => array(
'start' => '120655978',
'end' => '120668012',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Emc8-003'
),
'ENSMUST00000181836' => array(
'start' => '120658050',
'end' => '120667836',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-008'
),
'ENSMUST00000181950' => array(
'start' => '120657833',
'end' => '120668087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-007'
),
'ENSMUST00000047737' => array(
'start' => '120736358',
'end' => '120756694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-001'
),
'ENSMUST00000160388' => array(
'start' => '120745480',
'end' => '120753733',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Irf8-006'
),
'ENSMUST00000160594' => array(
'start' => '120752209',
'end' => '120753711',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Irf8-007'
),
'ENSMUST00000160943' => array(
'start' => '120739990',
'end' => '120755204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-004'
),
'ENSMUST00000162001' => array(
'start' => '120738639',
'end' => '120755581',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-003'
),
'ENSMUST00000162658' => array(
'start' => '120736385',
'end' => '120753478',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-005'
),
'ENSMUST00000162775' => array(
'start' => '120736359',
'end' => '120743234',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Irf8-002'
),
'ENSMUST00000157791' => array(
'start' => '120717500',
'end' => '120717754',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm24239-201'
),
'ENSMUST00000180564' => array(
'start' => '120727263',
'end' => '120727943',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm18709-001'
)
)
$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_0000IY_0001' => array(
'genes_in_region' => array(
'ENSG00000131143' => array(
[maximum depth reached]
),
'ENSG00000131148' => array(
[maximum depth reached]
),
'ENSG00000140968' => array(
[maximum depth reached]
),
'ENSG00000214259' => array(
[maximum depth reached]
),
'ENSG00000274134' => array(
[maximum depth reached]
),
'ENSG00000279907' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Liver',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Bladder',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Heart',
(int) 29 => 'Ovary',
(int) 30 => 'Heart',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Breast',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Bladder',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Liver',
(int) 49 => 'Muscle',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Kidney',
(int) 54 => 'Lung',
(int) 55 => 'Adipose',
(int) 56 => 'Brain',
(int) 57 => 'Heart',
(int) 58 => 'Kidney',
(int) 59 => 'Breast',
(int) 60 => 'Colon',
(int) 61 => 'Ovary',
(int) 62 => 'Placenta',
(int) 63 => 'Testis',
(int) 64 => 'Ovary',
(int) 65 => 'Testis',
(int) 66 => 'Adipose',
(int) 67 => 'Bladder',
(int) 68 => 'Breast',
(int) 69 => 'Heart',
(int) 70 => 'Kidney',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Bladder',
(int) 75 => 'Liver',
(int) 76 => 'Adipose',
(int) 77 => 'Brain',
(int) 78 => 'Breast',
(int) 79 => 'Colon',
(int) 80 => 'Lung',
(int) 81 => 'Muscle',
(int) 82 => 'Ovary',
(int) 83 => 'Testis',
(int) 84 => 'Adipose',
(int) 85 => 'Adipose',
(int) 86 => 'Adrenal',
(int) 87 => 'Brain',
(int) 88 => 'Breast',
(int) 89 => 'Colon',
(int) 90 => 'Heart',
(int) 91 => 'Kidney',
(int) 92 => 'Liver',
(int) 93 => 'Lung',
(int) 94 => 'Ovary',
(int) 95 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0000IY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '120668222',
'seq_end' => '120756694',
'region_length' => '88472',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031818-ENSMUSG00000041515'
)
)
$gene_el = array(
'ENST00000624587' => array(
'Adipose' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.070',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.124',
'stddev_FPKM' => '0.08'
),
'Colon' => array(
'average_FPKM' => '0.040',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.041',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.053',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.143',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.032',
'stddev_FPKM' => '0.01'
),
'Testis' => array(
'average_FPKM' => '0.079',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000279907'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.070',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.124',
'stddev_FPKM' => '0.08'
),
'Colon' => array(
'average_FPKM' => '0.040',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.041',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.053',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.143',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.032',
'stddev_FPKM' => '0.01'
),
'Testis' => array(
'average_FPKM' => '0.079',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000624587'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0000IY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000131143' => 'cytochrome c oxidase subunit IV isoform 1',
'ENSG00000131148' => 'ER membrane protein complex subunit 8',
'ENSG00000140968' => 'interferon regulatory factor 8',
'ENSG00000214259' => null,
'ENSG00000270698' => null,
'ENSG00000274134' => 'microRNA 6774',
'ENSG00000279907' => null,
'ENSMUSG00000031818' => 'cytochrome c oxidase subunit IV isoform 1',
'ENSMUSG00000031819' => 'ER membrane protein complex subunit 8',
'ENSMUSG00000041515' => 'interferon regulatory factor 8',
'ENSMUSG00000088416' => 'predicted gene, 24239',
'ENSMUSG00000097895' => 'predicted gene, 18709'
),
'gene_name_arr' => array(
'ENSG00000131143' => 'COX4I1',
'ENSG00000131148' => 'EMC8',
'ENSG00000140968' => 'IRF8',
'ENSG00000214259' => 'RP11-568J23.1',
'ENSG00000270698' => 'RP11-568J23.7',
'ENSG00000274134' => 'MIR6774',
'ENSG00000279907' => 'RP11-568J23.2',
'ENSMUSG00000031818' => 'Cox4i1',
'ENSMUSG00000031819' => 'Emc8',
'ENSMUSG00000041515' => 'Irf8',
'ENSMUSG00000088416' => 'Gm24239',
'ENSMUSG00000097895' => 'Gm18709'
),
'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) 8 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 16 => 'Brain',
(int) 23 => 'Breast',
(int) 33 => 'Colon',
(int) 39 => 'Heart',
(int) 48 => 'Kidney',
(int) 55 => 'Liver',
(int) 61 => 'Lung',
(int) 66 => 'Muscle',
(int) 72 => 'Ovary',
(int) 83 => 'Placenta',
(int) 88 => '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) 63,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000253452' => array(
'start' => '85799684',
'end' => '85807002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-001'
),
'ENST00000561569' => array(
'start' => '85799697',
'end' => '85807002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-009'
),
'ENST00000562336' => array(
'start' => '85799693',
'end' => '85807044',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-016'
),
'ENST00000562929' => array(
'start' => '85805069',
'end' => '85807031',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'COX4I1-017'
),
'ENST00000563774' => array(
'start' => '85799696',
'end' => '85805350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-008'
),
'ENST00000564544' => array(
'start' => '85799708',
'end' => '85806975',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'COX4I1-015'
),
'ENST00000564648' => array(
'start' => '85801202',
'end' => '85806967',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-005'
),
'ENST00000564903' => array(
'start' => '85801202',
'end' => '85806968',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-004'
),
'ENST00000565078' => array(
'start' => '85798633',
'end' => '85804992',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-006'
),
'ENST00000566115' => array(
'start' => '85799638',
'end' => '85805096',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'COX4I1-010'
),
'ENST00000566405' => array(
'start' => '85799698',
'end' => '85806802',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-013'
),
'ENST00000566617' => array(
'start' => '85799760',
'end' => '85805309',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-007'
),
'ENST00000567241' => array(
'start' => '85799654',
'end' => '85805328',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-012'
),
'ENST00000567266' => array(
'start' => '85799697',
'end' => '85805426',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-019'
),
'ENST00000568339' => array(
'start' => '85799622',
'end' => '85807002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-003'
),
'ENST00000568794' => array(
'start' => '85799683',
'end' => '85806805',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-011'
),
'ENST00000569997' => array(
'start' => '85803057',
'end' => '85807002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-002'
),
'ENST00000570123' => array(
'start' => '85799612',
'end' => '85805742',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'COX4I1-014'
),
'ENST00000253457' => array(
'start' => '85778624',
'end' => '85799540',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EMC8-001'
),
'ENST00000435200' => array(
'start' => '85778624',
'end' => '85799608',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EMC8-002'
),
'ENST00000595980' => array(
'start' => '85771758',
'end' => '85781258',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'EMC8-003'
),
'ENST00000596852' => array(
'start' => '85788897',
'end' => '85799396',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-006'
),
'ENST00000597291' => array(
'start' => '85779398',
'end' => '85781223',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-005'
),
'ENST00000600807' => array(
'start' => '85779662',
'end' => '85781760',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-004'
),
'ENST00000268638' => array(
'start' => '85898803',
'end' => '85922609',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-001'
),
'ENST00000562492' => array(
'start' => '85914043',
'end' => '85921371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-009'
),
'ENST00000563180' => array(
'start' => '85902689',
'end' => '85909882',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-002'
),
'ENST00000564056' => array(
'start' => '85903131',
'end' => '85913312',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'IRF8-007'
),
'ENST00000564617' => array(
'start' => '85902815',
'end' => '85913160',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-011'
),
'ENST00000564803' => array(
'start' => '85902838',
'end' => '85918800',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-006'
),
'ENST00000565552' => array(
'start' => '85899163',
'end' => '85903156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-004'
),
'ENST00000566369' => array(
'start' => '85908988',
'end' => '85922296',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-003'
),
'ENST00000569145' => array(
'start' => '85913974',
'end' => '85918489',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-008'
),
'ENST00000569607' => array(
'start' => '85914313',
'end' => '85921274',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-010'
),
'ENST00000570088' => array(
'start' => '85899188',
'end' => '85903531',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'IRF8-005'
),
'ENST00000484096' => array(
'start' => '85815873',
'end' => '85816536',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-568J23.1-001'
),
'ENST00000605872' => array(
'start' => '85814425',
'end' => '85815062',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-568J23.7-001'
),
'ENST00000614651' => array(
'start' => '85918347',
'end' => '85918416',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6774-201'
),
'ENST00000624587' => array(
'start' => '85859521',
'end' => '85862012',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-568J23.2-001'
),
'ENSMUST00000034276' => array(
'start' => '120668222',
'end' => '120674207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-001'
),
'ENSMUST00000180856' => array(
'start' => '120668261',
'end' => '120669821',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-003'
),
'ENSMUST00000181026' => array(
'start' => '120673152',
'end' => '120674207',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-006'
),
'ENSMUST00000181172' => array(
'start' => '120672590',
'end' => '120674113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-005'
),
'ENSMUST00000181586' => array(
'start' => '120668222',
'end' => '120674207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-002'
),
'ENSMUST00000181795' => array(
'start' => '120668308',
'end' => '120674032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-007'
),
'ENSMUST00000181847' => array(
'start' => '120668336',
'end' => '120674045',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Cox4i1-004'
),
'ENSMUST00000034277' => array(
'start' => '120653914',
'end' => '120668121',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-001'
),
'ENSMUST00000180417' => array(
'start' => '120657851',
'end' => '120668573',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Emc8-002'
),
'ENSMUST00000180909' => array(
'start' => '120660647',
'end' => '120668113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Emc8-005'
),
'ENSMUST00000181111' => array(
'start' => '120658024',
'end' => '120667763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-006'
),
'ENSMUST00000181334' => array(
'start' => '120659974',
'end' => '120668003',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-004'
),
'ENSMUST00000181402' => array(
'start' => '120655978',
'end' => '120668012',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Emc8-003'
),
'ENSMUST00000181836' => array(
'start' => '120658050',
'end' => '120667836',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-008'
),
'ENSMUST00000181950' => array(
'start' => '120657833',
'end' => '120668087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-007'
),
'ENSMUST00000047737' => array(
'start' => '120736358',
'end' => '120756694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-001'
),
'ENSMUST00000160388' => array(
'start' => '120745480',
'end' => '120753733',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Irf8-006'
),
'ENSMUST00000160594' => array(
'start' => '120752209',
'end' => '120753711',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Irf8-007'
),
'ENSMUST00000160943' => array(
'start' => '120739990',
'end' => '120755204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-004'
),
'ENSMUST00000162001' => array(
'start' => '120738639',
'end' => '120755581',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-003'
),
'ENSMUST00000162658' => array(
'start' => '120736385',
'end' => '120753478',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-005'
),
'ENSMUST00000162775' => array(
'start' => '120736359',
'end' => '120743234',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Irf8-002'
),
'ENSMUST00000157791' => array(
'start' => '120717500',
'end' => '120717754',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm24239-201'
),
'ENSMUST00000180564' => array(
'start' => '120727263',
'end' => '120727943',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm18709-001'
)
),
'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_0000IY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0000IY_0001' => array(
'genes_in_region' => array(
'ENSG00000131143' => array(
[maximum depth reached]
),
'ENSG00000131148' => array(
[maximum depth reached]
),
'ENSG00000140968' => array(
[maximum depth reached]
),
'ENSG00000214259' => array(
[maximum depth reached]
),
'ENSG00000274134' => array(
[maximum depth reached]
),
'ENSG00000279907' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Liver',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Bladder',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Heart',
(int) 29 => 'Ovary',
(int) 30 => 'Heart',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Breast',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Bladder',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Liver',
(int) 49 => 'Muscle',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Kidney',
(int) 54 => 'Lung',
(int) 55 => 'Adipose',
(int) 56 => 'Brain',
(int) 57 => 'Heart',
(int) 58 => 'Kidney',
(int) 59 => 'Breast',
(int) 60 => 'Colon',
(int) 61 => 'Ovary',
(int) 62 => 'Placenta',
(int) 63 => 'Testis',
(int) 64 => 'Ovary',
(int) 65 => 'Testis',
(int) 66 => 'Adipose',
(int) 67 => 'Bladder',
(int) 68 => 'Breast',
(int) 69 => 'Heart',
(int) 70 => 'Kidney',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Bladder',
(int) 75 => 'Liver',
(int) 76 => 'Adipose',
(int) 77 => 'Brain',
(int) 78 => 'Breast',
(int) 79 => 'Colon',
(int) 80 => 'Lung',
(int) 81 => 'Muscle',
(int) 82 => 'Ovary',
(int) 83 => 'Testis',
(int) 84 => 'Adipose',
(int) 85 => 'Adipose',
(int) 86 => 'Adrenal',
(int) 87 => 'Brain',
(int) 88 => 'Breast',
(int) 89 => 'Colon',
(int) 90 => 'Heart',
(int) 91 => 'Kidney',
(int) 92 => 'Liver',
(int) 93 => 'Lung',
(int) 94 => 'Ovary',
(int) 95 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000131143' => 'cytochrome c oxidase subunit IV isoform 1',
'ENSG00000131148' => 'ER membrane protein complex subunit 8',
'ENSG00000140968' => 'interferon regulatory factor 8',
'ENSG00000214259' => null,
'ENSG00000270698' => null,
'ENSG00000274134' => 'microRNA 6774',
'ENSG00000279907' => null,
'ENSMUSG00000031818' => 'cytochrome c oxidase subunit IV isoform 1',
'ENSMUSG00000031819' => 'ER membrane protein complex subunit 8',
'ENSMUSG00000041515' => 'interferon regulatory factor 8',
'ENSMUSG00000088416' => 'predicted gene, 24239',
'ENSMUSG00000097895' => 'predicted gene, 18709'
)
$gene_name_arr = array(
'ENSG00000131143' => 'COX4I1',
'ENSG00000131148' => 'EMC8',
'ENSG00000140968' => 'IRF8',
'ENSG00000214259' => 'RP11-568J23.1',
'ENSG00000270698' => 'RP11-568J23.7',
'ENSG00000274134' => 'MIR6774',
'ENSG00000279907' => 'RP11-568J23.2',
'ENSMUSG00000031818' => 'Cox4i1',
'ENSMUSG00000031819' => 'Emc8',
'ENSMUSG00000041515' => 'Irf8',
'ENSMUSG00000088416' => 'Gm24239',
'ENSMUSG00000097895' => 'Gm18709'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000IY_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '85798633',
'seq_end' => '85922609',
'region_length' => '123976',
'region_type' => 'CGP',
'el_id' => 'ENSG00000131143-ENSG00000140968'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000IY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '120668222',
'seq_end' => '120756694',
'region_length' => '88472',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031818-ENSMUSG00000041515'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 16 => 'Brain',
(int) 23 => 'Breast',
(int) 33 => 'Colon',
(int) 39 => 'Heart',
(int) 48 => 'Kidney',
(int) 55 => 'Liver',
(int) 61 => 'Lung',
(int) 66 => 'Muscle',
(int) 72 => 'Ovary',
(int) 83 => 'Placenta',
(int) 88 => '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) 63
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000253452' => array(
'start' => '85799684',
'end' => '85807002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-001'
),
'ENST00000561569' => array(
'start' => '85799697',
'end' => '85807002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-009'
),
'ENST00000562336' => array(
'start' => '85799693',
'end' => '85807044',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-016'
),
'ENST00000562929' => array(
'start' => '85805069',
'end' => '85807031',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'COX4I1-017'
),
'ENST00000563774' => array(
'start' => '85799696',
'end' => '85805350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-008'
),
'ENST00000564544' => array(
'start' => '85799708',
'end' => '85806975',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'COX4I1-015'
),
'ENST00000564648' => array(
'start' => '85801202',
'end' => '85806967',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-005'
),
'ENST00000564903' => array(
'start' => '85801202',
'end' => '85806968',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-004'
),
'ENST00000565078' => array(
'start' => '85798633',
'end' => '85804992',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-006'
),
'ENST00000566115' => array(
'start' => '85799638',
'end' => '85805096',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'COX4I1-010'
),
'ENST00000566405' => array(
'start' => '85799698',
'end' => '85806802',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-013'
),
'ENST00000566617' => array(
'start' => '85799760',
'end' => '85805309',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-007'
),
'ENST00000567241' => array(
'start' => '85799654',
'end' => '85805328',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-012'
),
'ENST00000567266' => array(
'start' => '85799697',
'end' => '85805426',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-019'
),
'ENST00000568339' => array(
'start' => '85799622',
'end' => '85807002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-003'
),
'ENST00000568794' => array(
'start' => '85799683',
'end' => '85806805',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COX4I1-011'
),
'ENST00000569997' => array(
'start' => '85803057',
'end' => '85807002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'COX4I1-002'
),
'ENST00000570123' => array(
'start' => '85799612',
'end' => '85805742',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'COX4I1-014'
),
'ENST00000253457' => array(
'start' => '85778624',
'end' => '85799540',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EMC8-001'
),
'ENST00000435200' => array(
'start' => '85778624',
'end' => '85799608',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EMC8-002'
),
'ENST00000595980' => array(
'start' => '85771758',
'end' => '85781258',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'EMC8-003'
),
'ENST00000596852' => array(
'start' => '85788897',
'end' => '85799396',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-006'
),
'ENST00000597291' => array(
'start' => '85779398',
'end' => '85781223',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-005'
),
'ENST00000600807' => array(
'start' => '85779662',
'end' => '85781760',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EMC8-004'
),
'ENST00000268638' => array(
'start' => '85898803',
'end' => '85922609',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-001'
),
'ENST00000562492' => array(
'start' => '85914043',
'end' => '85921371',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-009'
),
'ENST00000563180' => array(
'start' => '85902689',
'end' => '85909882',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-002'
),
'ENST00000564056' => array(
'start' => '85903131',
'end' => '85913312',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'IRF8-007'
),
'ENST00000564617' => array(
'start' => '85902815',
'end' => '85913160',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-011'
),
'ENST00000564803' => array(
'start' => '85902838',
'end' => '85918800',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-006'
),
'ENST00000565552' => array(
'start' => '85899163',
'end' => '85903156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-004'
),
'ENST00000566369' => array(
'start' => '85908988',
'end' => '85922296',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-003'
),
'ENST00000569145' => array(
'start' => '85913974',
'end' => '85918489',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-008'
),
'ENST00000569607' => array(
'start' => '85914313',
'end' => '85921274',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'IRF8-010'
),
'ENST00000570088' => array(
'start' => '85899188',
'end' => '85903531',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'IRF8-005'
),
'ENST00000484096' => array(
'start' => '85815873',
'end' => '85816536',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-568J23.1-001'
),
'ENST00000605872' => array(
'start' => '85814425',
'end' => '85815062',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-568J23.7-001'
),
'ENST00000614651' => array(
'start' => '85918347',
'end' => '85918416',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6774-201'
),
'ENST00000624587' => array(
'start' => '85859521',
'end' => '85862012',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-568J23.2-001'
),
'ENSMUST00000034276' => array(
'start' => '120668222',
'end' => '120674207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-001'
),
'ENSMUST00000180856' => array(
'start' => '120668261',
'end' => '120669821',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-003'
),
'ENSMUST00000181026' => array(
'start' => '120673152',
'end' => '120674207',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-006'
),
'ENSMUST00000181172' => array(
'start' => '120672590',
'end' => '120674113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cox4i1-005'
),
'ENSMUST00000181586' => array(
'start' => '120668222',
'end' => '120674207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-002'
),
'ENSMUST00000181795' => array(
'start' => '120668308',
'end' => '120674032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cox4i1-007'
),
'ENSMUST00000181847' => array(
'start' => '120668336',
'end' => '120674045',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Cox4i1-004'
),
'ENSMUST00000034277' => array(
'start' => '120653914',
'end' => '120668121',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-001'
),
'ENSMUST00000180417' => array(
'start' => '120657851',
'end' => '120668573',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Emc8-002'
),
'ENSMUST00000180909' => array(
'start' => '120660647',
'end' => '120668113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Emc8-005'
),
'ENSMUST00000181111' => array(
'start' => '120658024',
'end' => '120667763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-006'
),
'ENSMUST00000181334' => array(
'start' => '120659974',
'end' => '120668003',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-004'
),
'ENSMUST00000181402' => array(
'start' => '120655978',
'end' => '120668012',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Emc8-003'
),
'ENSMUST00000181836' => array(
'start' => '120658050',
'end' => '120667836',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-008'
),
'ENSMUST00000181950' => array(
'start' => '120657833',
'end' => '120668087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Emc8-007'
),
'ENSMUST00000047737' => array(
'start' => '120736358',
'end' => '120756694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-001'
),
'ENSMUST00000160388' => array(
'start' => '120745480',
'end' => '120753733',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Irf8-006'
),
'ENSMUST00000160594' => array(
'start' => '120752209',
'end' => '120753711',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Irf8-007'
),
'ENSMUST00000160943' => array(
'start' => '120739990',
'end' => '120755204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-004'
),
'ENSMUST00000162001' => array(
'start' => '120738639',
'end' => '120755581',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-003'
),
'ENSMUST00000162658' => array(
'start' => '120736385',
'end' => '120753478',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Irf8-005'
),
'ENSMUST00000162775' => array(
'start' => '120736359',
'end' => '120743234',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Irf8-002'
),
'ENSMUST00000157791' => array(
'start' => '120717500',
'end' => '120717754',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm24239-201'
),
'ENSMUST00000180564' => array(
'start' => '120727263',
'end' => '120727943',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm18709-001'
)
)
$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_0000IY_0001' => array(
'genes_in_region' => array(
'ENSG00000131143' => array(
[maximum depth reached]
),
'ENSG00000131148' => array(
[maximum depth reached]
),
'ENSG00000140968' => array(
[maximum depth reached]
),
'ENSG00000214259' => array(
[maximum depth reached]
),
'ENSG00000274134' => array(
[maximum depth reached]
),
'ENSG00000279907' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Liver',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Bladder',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Heart',
(int) 29 => 'Ovary',
(int) 30 => 'Heart',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Breast',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Bladder',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Liver',
(int) 49 => 'Muscle',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Kidney',
(int) 54 => 'Lung',
(int) 55 => 'Adipose',
(int) 56 => 'Brain',
(int) 57 => 'Heart',
(int) 58 => 'Kidney',
(int) 59 => 'Breast',
(int) 60 => 'Colon',
(int) 61 => 'Ovary',
(int) 62 => 'Placenta',
(int) 63 => 'Testis',
(int) 64 => 'Ovary',
(int) 65 => 'Testis',
(int) 66 => 'Adipose',
(int) 67 => 'Bladder',
(int) 68 => 'Breast',
(int) 69 => 'Heart',
(int) 70 => 'Kidney',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Bladder',
(int) 75 => 'Liver',
(int) 76 => 'Adipose',
(int) 77 => 'Brain',
(int) 78 => 'Breast',
(int) 79 => 'Colon',
(int) 80 => 'Lung',
(int) 81 => 'Muscle',
(int) 82 => 'Ovary',
(int) 83 => 'Testis',
(int) 84 => 'Adipose',
(int) 85 => 'Adipose',
(int) 86 => 'Adrenal',
(int) 87 => 'Brain',
(int) 88 => 'Breast',
(int) 89 => 'Colon',
(int) 90 => 'Heart',
(int) 91 => 'Kidney',
(int) 92 => 'Liver',
(int) 93 => 'Lung',
(int) 94 => 'Ovary',
(int) 95 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0000IY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '120668222',
'seq_end' => '120756694',
'region_length' => '88472',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031818-ENSMUSG00000041515'
)
)
$gene_el = array(
'ENST00000624587' => array(
'Adipose' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.070',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.124',
'stddev_FPKM' => '0.08'
),
'Colon' => array(
'average_FPKM' => '0.040',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.041',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.053',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.143',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.032',
'stddev_FPKM' => '0.01'
),
'Testis' => array(
'average_FPKM' => '0.079',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000279907'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.070',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.124',
'stddev_FPKM' => '0.08'
),
'Colon' => array(
'average_FPKM' => '0.040',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.041',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.053',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.143',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.032',
'stddev_FPKM' => '0.01'
),
'Testis' => array(
'average_FPKM' => '0.079',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000624587'
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
(COX4I1)