| Source ID |
Type |
Tax ID |
Position |
| hs250 |
VISTA |
10090 |
17:51236358-51837318  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_000816_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_000816_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000182568' => 'SATB homeobox 1',
'ENSG00000213383' => null,
'ENSG00000214286' => 'phosducin-like 3 pseudogene 3',
'ENSG00000226238' => null,
'ENSG00000272477' => null,
'ENSG00000274840' => null,
'ENSMUSG00000023927' => 'special AT-rich sequence binding protein 1'
),
'gene_name_arr' => array(
'ENSG00000182568' => 'SATB1',
'ENSG00000213383' => 'AC104297.1',
'ENSG00000214286' => 'PDCL3P3',
'ENSG00000226238' => 'AC132807.1',
'ENSG00000272477' => 'RP11-158G18.1',
'ENSG00000274840' => 'RP11-320G10.1',
'ENSMUSG00000023927' => 'Satb1'
),
'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) 6 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 21 => 'Brain',
(int) 33 => 'Breast',
(int) 41 => 'Colon',
(int) 51 => 'Heart',
(int) 61 => 'Kidney',
(int) 71 => 'Liver',
(int) 83 => 'Lung',
(int) 93 => 'Muscle',
(int) 102 => 'Ovary',
(int) 109 => 'Placenta',
(int) 117 => '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) 38,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000338745' => array(
'start' => '18345387',
'end' => '18425337',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-001'
),
'ENST00000414509' => array(
'start' => '18416942',
'end' => '18438692',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-011'
),
'ENST00000415069' => array(
'start' => '18416023',
'end' => '18445588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-006'
),
'ENST00000417717' => array(
'start' => '18347940',
'end' => '18424573',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-004'
),
'ENST00000440737' => array(
'start' => '18397256',
'end' => '18444883',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-008'
),
'ENST00000444341' => array(
'start' => '18420756',
'end' => '18435253',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-012'
),
'ENST00000450898' => array(
'start' => '18420944',
'end' => '18425369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-013'
),
'ENST00000452260' => array(
'start' => '18416004',
'end' => '18421388',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-015'
),
'ENST00000454909' => array(
'start' => '18347940',
'end' => '18438773',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-002'
),
'ENST00000457005' => array(
'start' => '18416901',
'end' => '18424740',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-014'
),
'ENST00000467628' => array(
'start' => '18351803',
'end' => '18378327',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-019'
),
'ENST00000475083' => array(
'start' => '18397214',
'end' => '18417510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-016'
),
'ENST00000476178' => array(
'start' => '18349541',
'end' => '18351531',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-007'
),
'ENST00000482788' => array(
'start' => '18414949',
'end' => '18416126',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-018'
),
'ENST00000487699' => array(
'start' => '18420685',
'end' => '18438734',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-010'
),
'ENST00000491519' => array(
'start' => '18410798',
'end' => '18417393',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-017'
),
'ENST00000493952' => array(
'start' => '18417576',
'end' => '18444873',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-009'
),
'ENST00000606296' => array(
'start' => '18348885',
'end' => '18353084',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-003'
),
'ENST00000393779' => array(
'start' => '17871729',
'end' => '17872598',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC104297.1-001'
),
'ENST00000417487' => array(
'start' => '17877455',
'end' => '17878169',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PDCL3P3-001'
),
'ENST00000449613' => array(
'start' => '17990023',
'end' => '17995544',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC132807.1-001'
),
'ENST00000607148' => array(
'start' => '18408680',
'end' => '18409635',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-158G18.1-001'
),
'ENST00000616960' => array(
'start' => '18013226',
'end' => '18041603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-320G10.1-201'
),
'ENST00000624232' => array(
'start' => '18013655',
'end' => '18041541',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-320G10.1-001'
),
'ENSMUST00000124222' => array(
'start' => '51805363',
'end' => '51832019',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-008'
),
'ENSMUST00000129205' => array(
'start' => '51804366',
'end' => '51821091',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-011'
),
'ENSMUST00000129667' => array(
'start' => '51739455',
'end' => '51826566',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-003'
),
'ENSMUST00000133574' => array(
'start' => '51738894',
'end' => '51833290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-005'
),
'ENSMUST00000137697' => array(
'start' => '51739988',
'end' => '51742266',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-009'
),
'ENSMUST00000140727' => array(
'start' => '51802330',
'end' => '51809132',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Satb1-013'
),
'ENSMUST00000140979' => array(
'start' => '51739476',
'end' => '51812680',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-004'
),
'ENSMUST00000144331' => array(
'start' => '51736187',
'end' => '51832672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-001'
),
'ENSMUST00000146414' => array(
'start' => '51807080',
'end' => '51810919',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-006'
),
'ENSMUST00000148559' => array(
'start' => '51809189',
'end' => '51826588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-010'
),
'ENSMUST00000152830' => array(
'start' => '51739471',
'end' => '51815004',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-002'
),
'ENSMUST00000156051' => array(
'start' => '51824641',
'end' => '51829497',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-007'
),
'ENSMUST00000169480' => array(
'start' => '51736188',
'end' => '51826588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-201'
),
'ENSMUST00000176669' => array(
'start' => '51739452',
'end' => '51810919',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-012'
)
),
'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_000816_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000816_0001' => array(
'genes_in_region' => array(
'ENSG00000182568' => array(
[maximum depth reached]
),
'ENSG00000213383' => array(
[maximum depth reached]
),
'ENSG00000214286' => array(
[maximum depth reached]
),
'ENSG00000272477' => array(
[maximum depth reached]
),
'ENSG00000274840' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Adipose',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 11 => 'Breast',
(int) 12 => 'Colon',
(int) 13 => 'Heart',
(int) 14 => 'Liver',
(int) 15 => 'Lung',
(int) 16 => 'Muscle',
(int) 17 => 'Testis',
(int) 18 => 'Adrenal',
(int) 19 => 'Brain',
(int) 20 => 'Colon',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Testis',
(int) 27 => 'Adrenal',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain',
(int) 48 => 'Colon',
(int) 49 => 'Heart',
(int) 50 => 'Kidney',
(int) 51 => 'Liver',
(int) 52 => 'Lung',
(int) 53 => 'Testis',
(int) 54 => 'Testis',
(int) 55 => 'Colon',
(int) 56 => 'Placenta'
)
)
)
$gene_desc_arr = array(
'ENSG00000182568' => 'SATB homeobox 1',
'ENSG00000213383' => null,
'ENSG00000214286' => 'phosducin-like 3 pseudogene 3',
'ENSG00000226238' => null,
'ENSG00000272477' => null,
'ENSG00000274840' => null,
'ENSMUSG00000023927' => 'special AT-rich sequence binding protein 1'
)
$gene_name_arr = array(
'ENSG00000182568' => 'SATB1',
'ENSG00000213383' => 'AC104297.1',
'ENSG00000214286' => 'PDCL3P3',
'ENSG00000226238' => 'AC132807.1',
'ENSG00000272477' => 'RP11-158G18.1',
'ENSG00000274840' => 'RP11-320G10.1',
'ENSMUSG00000023927' => 'Satb1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000816_0001',
'tax_id' => '9606',
'chromosome' => '3',
'seq_start' => '17827870',
'seq_end' => '18428745',
'region_length' => '600875',
'region_type' => 'VISTA',
'el_id' => 'hs250'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000816_0002',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '51236358',
'seq_end' => '51837318',
'region_length' => '600960',
'region_type' => 'VISTA',
'el_id' => 'hs250'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 21 => 'Brain',
(int) 33 => 'Breast',
(int) 41 => 'Colon',
(int) 51 => 'Heart',
(int) 61 => 'Kidney',
(int) 71 => 'Liver',
(int) 83 => 'Lung',
(int) 93 => 'Muscle',
(int) 102 => 'Ovary',
(int) 109 => 'Placenta',
(int) 117 => '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) 38
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000338745' => array(
'start' => '18345387',
'end' => '18425337',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-001'
),
'ENST00000414509' => array(
'start' => '18416942',
'end' => '18438692',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-011'
),
'ENST00000415069' => array(
'start' => '18416023',
'end' => '18445588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-006'
),
'ENST00000417717' => array(
'start' => '18347940',
'end' => '18424573',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-004'
),
'ENST00000440737' => array(
'start' => '18397256',
'end' => '18444883',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-008'
),
'ENST00000444341' => array(
'start' => '18420756',
'end' => '18435253',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-012'
),
'ENST00000450898' => array(
'start' => '18420944',
'end' => '18425369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-013'
),
'ENST00000452260' => array(
'start' => '18416004',
'end' => '18421388',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-015'
),
'ENST00000454909' => array(
'start' => '18347940',
'end' => '18438773',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-002'
),
'ENST00000457005' => array(
'start' => '18416901',
'end' => '18424740',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-014'
),
'ENST00000467628' => array(
'start' => '18351803',
'end' => '18378327',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-019'
),
'ENST00000475083' => array(
'start' => '18397214',
'end' => '18417510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-016'
),
'ENST00000476178' => array(
'start' => '18349541',
'end' => '18351531',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-007'
),
'ENST00000482788' => array(
'start' => '18414949',
'end' => '18416126',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-018'
),
'ENST00000487699' => array(
'start' => '18420685',
'end' => '18438734',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-010'
),
'ENST00000491519' => array(
'start' => '18410798',
'end' => '18417393',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-017'
),
'ENST00000493952' => array(
'start' => '18417576',
'end' => '18444873',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-009'
),
'ENST00000606296' => array(
'start' => '18348885',
'end' => '18353084',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-003'
),
'ENST00000393779' => array(
'start' => '17871729',
'end' => '17872598',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC104297.1-001'
),
'ENST00000417487' => array(
'start' => '17877455',
'end' => '17878169',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PDCL3P3-001'
),
'ENST00000449613' => array(
'start' => '17990023',
'end' => '17995544',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC132807.1-001'
),
'ENST00000607148' => array(
'start' => '18408680',
'end' => '18409635',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-158G18.1-001'
),
'ENST00000616960' => array(
'start' => '18013226',
'end' => '18041603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-320G10.1-201'
),
'ENST00000624232' => array(
'start' => '18013655',
'end' => '18041541',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-320G10.1-001'
),
'ENSMUST00000124222' => array(
'start' => '51805363',
'end' => '51832019',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-008'
),
'ENSMUST00000129205' => array(
'start' => '51804366',
'end' => '51821091',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-011'
),
'ENSMUST00000129667' => array(
'start' => '51739455',
'end' => '51826566',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-003'
),
'ENSMUST00000133574' => array(
'start' => '51738894',
'end' => '51833290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-005'
),
'ENSMUST00000137697' => array(
'start' => '51739988',
'end' => '51742266',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-009'
),
'ENSMUST00000140727' => array(
'start' => '51802330',
'end' => '51809132',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Satb1-013'
),
'ENSMUST00000140979' => array(
'start' => '51739476',
'end' => '51812680',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-004'
),
'ENSMUST00000144331' => array(
'start' => '51736187',
'end' => '51832672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-001'
),
'ENSMUST00000146414' => array(
'start' => '51807080',
'end' => '51810919',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-006'
),
'ENSMUST00000148559' => array(
'start' => '51809189',
'end' => '51826588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-010'
),
'ENSMUST00000152830' => array(
'start' => '51739471',
'end' => '51815004',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-002'
),
'ENSMUST00000156051' => array(
'start' => '51824641',
'end' => '51829497',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-007'
),
'ENSMUST00000169480' => array(
'start' => '51736188',
'end' => '51826588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-201'
),
'ENSMUST00000176669' => array(
'start' => '51739452',
'end' => '51810919',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-012'
)
)
$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_000816_0001' => array(
'genes_in_region' => array(
'ENSG00000182568' => array(
[maximum depth reached]
),
'ENSG00000213383' => array(
[maximum depth reached]
),
'ENSG00000214286' => array(
[maximum depth reached]
),
'ENSG00000272477' => array(
[maximum depth reached]
),
'ENSG00000274840' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Adipose',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 11 => 'Breast',
(int) 12 => 'Colon',
(int) 13 => 'Heart',
(int) 14 => 'Liver',
(int) 15 => 'Lung',
(int) 16 => 'Muscle',
(int) 17 => 'Testis',
(int) 18 => 'Adrenal',
(int) 19 => 'Brain',
(int) 20 => 'Colon',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Testis',
(int) 27 => 'Adrenal',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain',
(int) 48 => 'Colon',
(int) 49 => 'Heart',
(int) 50 => 'Kidney',
(int) 51 => 'Liver',
(int) 52 => 'Lung',
(int) 53 => 'Testis',
(int) 54 => 'Testis',
(int) 55 => 'Colon',
(int) 56 => 'Placenta'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000816_0002',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '51236358',
'seq_end' => '51837318',
'region_length' => '600960',
'region_type' => 'VISTA',
'el_id' => 'hs250'
)
)
$gene_el = array(
'ENST00000616960' => array(
'Testis' => array(
'average_FPKM' => '0.041',
'stddev_FPKM' => '0.00'
)
),
'ENST00000624232' => array(
'Colon' => array(
'average_FPKM' => '0.049',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.207',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000274840'
$is_first = false
$tran_el = array(
'Colon' => array(
'average_FPKM' => '0.049',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.207',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000624232'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_000816_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000182568' => 'SATB homeobox 1',
'ENSG00000213383' => null,
'ENSG00000214286' => 'phosducin-like 3 pseudogene 3',
'ENSG00000226238' => null,
'ENSG00000272477' => null,
'ENSG00000274840' => null,
'ENSMUSG00000023927' => 'special AT-rich sequence binding protein 1'
),
'gene_name_arr' => array(
'ENSG00000182568' => 'SATB1',
'ENSG00000213383' => 'AC104297.1',
'ENSG00000214286' => 'PDCL3P3',
'ENSG00000226238' => 'AC132807.1',
'ENSG00000272477' => 'RP11-158G18.1',
'ENSG00000274840' => 'RP11-320G10.1',
'ENSMUSG00000023927' => 'Satb1'
),
'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) 6 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 21 => 'Brain',
(int) 33 => 'Breast',
(int) 41 => 'Colon',
(int) 51 => 'Heart',
(int) 61 => 'Kidney',
(int) 71 => 'Liver',
(int) 83 => 'Lung',
(int) 93 => 'Muscle',
(int) 102 => 'Ovary',
(int) 109 => 'Placenta',
(int) 117 => '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) 38,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000338745' => array(
'start' => '18345387',
'end' => '18425337',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-001'
),
'ENST00000414509' => array(
'start' => '18416942',
'end' => '18438692',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-011'
),
'ENST00000415069' => array(
'start' => '18416023',
'end' => '18445588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-006'
),
'ENST00000417717' => array(
'start' => '18347940',
'end' => '18424573',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-004'
),
'ENST00000440737' => array(
'start' => '18397256',
'end' => '18444883',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-008'
),
'ENST00000444341' => array(
'start' => '18420756',
'end' => '18435253',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-012'
),
'ENST00000450898' => array(
'start' => '18420944',
'end' => '18425369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-013'
),
'ENST00000452260' => array(
'start' => '18416004',
'end' => '18421388',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-015'
),
'ENST00000454909' => array(
'start' => '18347940',
'end' => '18438773',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-002'
),
'ENST00000457005' => array(
'start' => '18416901',
'end' => '18424740',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-014'
),
'ENST00000467628' => array(
'start' => '18351803',
'end' => '18378327',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-019'
),
'ENST00000475083' => array(
'start' => '18397214',
'end' => '18417510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-016'
),
'ENST00000476178' => array(
'start' => '18349541',
'end' => '18351531',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-007'
),
'ENST00000482788' => array(
'start' => '18414949',
'end' => '18416126',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-018'
),
'ENST00000487699' => array(
'start' => '18420685',
'end' => '18438734',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-010'
),
'ENST00000491519' => array(
'start' => '18410798',
'end' => '18417393',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-017'
),
'ENST00000493952' => array(
'start' => '18417576',
'end' => '18444873',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-009'
),
'ENST00000606296' => array(
'start' => '18348885',
'end' => '18353084',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-003'
),
'ENST00000393779' => array(
'start' => '17871729',
'end' => '17872598',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC104297.1-001'
),
'ENST00000417487' => array(
'start' => '17877455',
'end' => '17878169',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PDCL3P3-001'
),
'ENST00000449613' => array(
'start' => '17990023',
'end' => '17995544',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC132807.1-001'
),
'ENST00000607148' => array(
'start' => '18408680',
'end' => '18409635',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-158G18.1-001'
),
'ENST00000616960' => array(
'start' => '18013226',
'end' => '18041603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-320G10.1-201'
),
'ENST00000624232' => array(
'start' => '18013655',
'end' => '18041541',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-320G10.1-001'
),
'ENSMUST00000124222' => array(
'start' => '51805363',
'end' => '51832019',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-008'
),
'ENSMUST00000129205' => array(
'start' => '51804366',
'end' => '51821091',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-011'
),
'ENSMUST00000129667' => array(
'start' => '51739455',
'end' => '51826566',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-003'
),
'ENSMUST00000133574' => array(
'start' => '51738894',
'end' => '51833290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-005'
),
'ENSMUST00000137697' => array(
'start' => '51739988',
'end' => '51742266',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-009'
),
'ENSMUST00000140727' => array(
'start' => '51802330',
'end' => '51809132',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Satb1-013'
),
'ENSMUST00000140979' => array(
'start' => '51739476',
'end' => '51812680',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-004'
),
'ENSMUST00000144331' => array(
'start' => '51736187',
'end' => '51832672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-001'
),
'ENSMUST00000146414' => array(
'start' => '51807080',
'end' => '51810919',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-006'
),
'ENSMUST00000148559' => array(
'start' => '51809189',
'end' => '51826588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-010'
),
'ENSMUST00000152830' => array(
'start' => '51739471',
'end' => '51815004',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-002'
),
'ENSMUST00000156051' => array(
'start' => '51824641',
'end' => '51829497',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-007'
),
'ENSMUST00000169480' => array(
'start' => '51736188',
'end' => '51826588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-201'
),
'ENSMUST00000176669' => array(
'start' => '51739452',
'end' => '51810919',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-012'
)
),
'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_000816_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000816_0001' => array(
'genes_in_region' => array(
'ENSG00000182568' => array(
[maximum depth reached]
),
'ENSG00000213383' => array(
[maximum depth reached]
),
'ENSG00000214286' => array(
[maximum depth reached]
),
'ENSG00000272477' => array(
[maximum depth reached]
),
'ENSG00000274840' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Adipose',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 11 => 'Breast',
(int) 12 => 'Colon',
(int) 13 => 'Heart',
(int) 14 => 'Liver',
(int) 15 => 'Lung',
(int) 16 => 'Muscle',
(int) 17 => 'Testis',
(int) 18 => 'Adrenal',
(int) 19 => 'Brain',
(int) 20 => 'Colon',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Testis',
(int) 27 => 'Adrenal',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain',
(int) 48 => 'Colon',
(int) 49 => 'Heart',
(int) 50 => 'Kidney',
(int) 51 => 'Liver',
(int) 52 => 'Lung',
(int) 53 => 'Testis',
(int) 54 => 'Testis',
(int) 55 => 'Colon',
(int) 56 => 'Placenta'
)
)
)
$gene_desc_arr = array(
'ENSG00000182568' => 'SATB homeobox 1',
'ENSG00000213383' => null,
'ENSG00000214286' => 'phosducin-like 3 pseudogene 3',
'ENSG00000226238' => null,
'ENSG00000272477' => null,
'ENSG00000274840' => null,
'ENSMUSG00000023927' => 'special AT-rich sequence binding protein 1'
)
$gene_name_arr = array(
'ENSG00000182568' => 'SATB1',
'ENSG00000213383' => 'AC104297.1',
'ENSG00000214286' => 'PDCL3P3',
'ENSG00000226238' => 'AC132807.1',
'ENSG00000272477' => 'RP11-158G18.1',
'ENSG00000274840' => 'RP11-320G10.1',
'ENSMUSG00000023927' => 'Satb1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000816_0001',
'tax_id' => '9606',
'chromosome' => '3',
'seq_start' => '17827870',
'seq_end' => '18428745',
'region_length' => '600875',
'region_type' => 'VISTA',
'el_id' => 'hs250'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000816_0002',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '51236358',
'seq_end' => '51837318',
'region_length' => '600960',
'region_type' => 'VISTA',
'el_id' => 'hs250'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 21 => 'Brain',
(int) 33 => 'Breast',
(int) 41 => 'Colon',
(int) 51 => 'Heart',
(int) 61 => 'Kidney',
(int) 71 => 'Liver',
(int) 83 => 'Lung',
(int) 93 => 'Muscle',
(int) 102 => 'Ovary',
(int) 109 => 'Placenta',
(int) 117 => '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) 38
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000338745' => array(
'start' => '18345387',
'end' => '18425337',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-001'
),
'ENST00000414509' => array(
'start' => '18416942',
'end' => '18438692',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-011'
),
'ENST00000415069' => array(
'start' => '18416023',
'end' => '18445588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-006'
),
'ENST00000417717' => array(
'start' => '18347940',
'end' => '18424573',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-004'
),
'ENST00000440737' => array(
'start' => '18397256',
'end' => '18444883',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-008'
),
'ENST00000444341' => array(
'start' => '18420756',
'end' => '18435253',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-012'
),
'ENST00000450898' => array(
'start' => '18420944',
'end' => '18425369',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-013'
),
'ENST00000452260' => array(
'start' => '18416004',
'end' => '18421388',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-015'
),
'ENST00000454909' => array(
'start' => '18347940',
'end' => '18438773',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-002'
),
'ENST00000457005' => array(
'start' => '18416901',
'end' => '18424740',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-014'
),
'ENST00000467628' => array(
'start' => '18351803',
'end' => '18378327',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-019'
),
'ENST00000475083' => array(
'start' => '18397214',
'end' => '18417510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-016'
),
'ENST00000476178' => array(
'start' => '18349541',
'end' => '18351531',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-007'
),
'ENST00000482788' => array(
'start' => '18414949',
'end' => '18416126',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-018'
),
'ENST00000487699' => array(
'start' => '18420685',
'end' => '18438734',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-010'
),
'ENST00000491519' => array(
'start' => '18410798',
'end' => '18417393',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-017'
),
'ENST00000493952' => array(
'start' => '18417576',
'end' => '18444873',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB1-009'
),
'ENST00000606296' => array(
'start' => '18348885',
'end' => '18353084',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB1-003'
),
'ENST00000393779' => array(
'start' => '17871729',
'end' => '17872598',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC104297.1-001'
),
'ENST00000417487' => array(
'start' => '17877455',
'end' => '17878169',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PDCL3P3-001'
),
'ENST00000449613' => array(
'start' => '17990023',
'end' => '17995544',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC132807.1-001'
),
'ENST00000607148' => array(
'start' => '18408680',
'end' => '18409635',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-158G18.1-001'
),
'ENST00000616960' => array(
'start' => '18013226',
'end' => '18041603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-320G10.1-201'
),
'ENST00000624232' => array(
'start' => '18013655',
'end' => '18041541',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-320G10.1-001'
),
'ENSMUST00000124222' => array(
'start' => '51805363',
'end' => '51832019',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-008'
),
'ENSMUST00000129205' => array(
'start' => '51804366',
'end' => '51821091',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-011'
),
'ENSMUST00000129667' => array(
'start' => '51739455',
'end' => '51826566',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-003'
),
'ENSMUST00000133574' => array(
'start' => '51738894',
'end' => '51833290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-005'
),
'ENSMUST00000137697' => array(
'start' => '51739988',
'end' => '51742266',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-009'
),
'ENSMUST00000140727' => array(
'start' => '51802330',
'end' => '51809132',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Satb1-013'
),
'ENSMUST00000140979' => array(
'start' => '51739476',
'end' => '51812680',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-004'
),
'ENSMUST00000144331' => array(
'start' => '51736187',
'end' => '51832672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-001'
),
'ENSMUST00000146414' => array(
'start' => '51807080',
'end' => '51810919',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-006'
),
'ENSMUST00000148559' => array(
'start' => '51809189',
'end' => '51826588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-010'
),
'ENSMUST00000152830' => array(
'start' => '51739471',
'end' => '51815004',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-002'
),
'ENSMUST00000156051' => array(
'start' => '51824641',
'end' => '51829497',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Satb1-007'
),
'ENSMUST00000169480' => array(
'start' => '51736188',
'end' => '51826588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-201'
),
'ENSMUST00000176669' => array(
'start' => '51739452',
'end' => '51810919',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb1-012'
)
)
$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_000816_0001' => array(
'genes_in_region' => array(
'ENSG00000182568' => array(
[maximum depth reached]
),
'ENSG00000213383' => array(
[maximum depth reached]
),
'ENSG00000214286' => array(
[maximum depth reached]
),
'ENSG00000272477' => array(
[maximum depth reached]
),
'ENSG00000274840' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Adipose',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 11 => 'Breast',
(int) 12 => 'Colon',
(int) 13 => 'Heart',
(int) 14 => 'Liver',
(int) 15 => 'Lung',
(int) 16 => 'Muscle',
(int) 17 => 'Testis',
(int) 18 => 'Adrenal',
(int) 19 => 'Brain',
(int) 20 => 'Colon',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Testis',
(int) 27 => 'Adrenal',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain',
(int) 48 => 'Colon',
(int) 49 => 'Heart',
(int) 50 => 'Kidney',
(int) 51 => 'Liver',
(int) 52 => 'Lung',
(int) 53 => 'Testis',
(int) 54 => 'Testis',
(int) 55 => 'Colon',
(int) 56 => 'Placenta'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000816_0002',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '51236358',
'seq_end' => '51837318',
'region_length' => '600960',
'region_type' => 'VISTA',
'el_id' => 'hs250'
)
)
$gene_el = array(
'ENST00000616960' => array(
'Testis' => array(
'average_FPKM' => '0.041',
'stddev_FPKM' => '0.00'
)
),
'ENST00000624232' => array(
'Colon' => array(
'average_FPKM' => '0.049',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.207',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000274840'
$is_first = false
$tran_el = array(
'Colon' => array(
'average_FPKM' => '0.049',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.207',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000624232'
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
(SATB1)