| Source ID |
Type |
Tax ID |
Position |
| hs1164 |
VISTA |
9606 |
2:59478396-60080410  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007XW_0001 [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_0007XW_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000200101' => 'RNA, U6 small nuclear 508, pseudogene',
'ENSG00000233891' => null,
'ENSG00000252455' => null,
'ENSG00000252726' => 'RNA, 5S ribosomal pseudogene 94',
'ENSG00000270447' => null,
'ENSG00000275742' => null,
'ENSMUSG00000073103' => 'predicted gene 10466',
'ENSMUSG00000080631' => 'predicted gene, 25507',
'ENSMUSG00000081767' => 'predicted gene 12067',
'ENSMUSG00000086892' => 'RIKEN cDNA 4933430M04 gene',
'ENSMUSG00000087085' => 'predicted gene 12068',
'ENSMUSG00000087145' => 'predicted gene 12665',
'ENSMUSG00000088502' => 'predicted gene, 22787'
),
'gene_name_arr' => array(
'ENSG00000200101' => 'RNU6-508P',
'ENSG00000233891' => 'AC007131.2',
'ENSG00000252455' => 'AC007179.2',
'ENSG00000252726' => 'RNA5SP94',
'ENSG00000270447' => 'RP11-569H17.1',
'ENSG00000275742' => 'AC007006.1',
'ENSMUSG00000073103' => 'Gm10466',
'ENSMUSG00000080631' => 'Gm25507',
'ENSMUSG00000081767' => 'Gm12067',
'ENSMUSG00000086892' => '4933430M04Rik',
'ENSMUSG00000087085' => 'Gm12068',
'ENSMUSG00000087145' => 'Gm12665',
'ENSMUSG00000088502' => 'Gm22787'
),
'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 => 'Brain',
(int) 5 => 'Breast',
(int) 6 => 'Muscle',
(int) 8 => 'Ovary',
(int) 12 => 'Placenta',
(int) 14 => '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) 20,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000363231' => array(
'start' => '59647621',
'end' => '59647723',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-508P-201'
),
'ENST00000412409' => array(
'start' => '59240942',
'end' => '59733396',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-007'
),
'ENST00000434611' => array(
'start' => '59295380',
'end' => '59388159',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-005'
),
'ENST00000435557' => array(
'start' => '59669216',
'end' => '59733331',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-006'
),
'ENST00000440521' => array(
'start' => '59238716',
'end' => '59249567',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-003'
),
'ENST00000443306' => array(
'start' => '59238716',
'end' => '59249672',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-001'
),
'ENST00000444001' => array(
'start' => '59238722',
'end' => '59388365',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-004'
),
'ENST00000451416' => array(
'start' => '59238714',
'end' => '59249511',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-002'
),
'ENST00000516646' => array(
'start' => '59532984',
'end' => '59533075',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007179.2-201'
),
'ENST00000516917' => array(
'start' => '59694762',
'end' => '59694869',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP94-201'
),
'ENST00000604976' => array(
'start' => '59514890',
'end' => '59515124',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-569H17.1-001'
),
'ENST00000615857' => array(
'start' => '59565835',
'end' => '59565921',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007006.1-201'
),
'ENSMUST00000101450' => array(
'start' => '24721006',
'end' => '24730722',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm10466-001'
),
'ENSMUST00000116981' => array(
'start' => '24679568',
'end' => '24679711',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25507-201'
),
'ENSMUST00000119755' => array(
'start' => '24552438',
'end' => '24553962',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm12067-001'
),
'ENSMUST00000152726' => array(
'start' => '24481909',
'end' => '24569952',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933430M04Rik-001'
),
'ENSMUST00000153153' => array(
'start' => '24426246',
'end' => '24722646',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12068-001'
),
'ENSMUST00000126063' => array(
'start' => '24903983',
'end' => '24926058',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12665-001'
),
'ENSMUST00000130092' => array(
'start' => '24903983',
'end' => '24926050',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12665-002'
),
'ENSMUST00000157877' => array(
'start' => '24553986',
'end' => '24554058',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm22787-201'
)
),
'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_0007XW_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007XW_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000073103' => array(
[maximum depth reached]
),
'ENSMUSG00000081767' => array(
[maximum depth reached]
),
'ENSMUSG00000086892' => array(
[maximum depth reached]
),
'ENSMUSG00000087085' => array(
[maximum depth reached]
),
'ENSMUSG00000087145' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Ovary',
(int) 2 => 'Placenta',
(int) 3 => 'Brain',
(int) 4 => 'Ovary',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Muscle',
(int) 12 => 'Ovary',
(int) 13 => 'Testis',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000200101' => 'RNA, U6 small nuclear 508, pseudogene',
'ENSG00000233891' => null,
'ENSG00000252455' => null,
'ENSG00000252726' => 'RNA, 5S ribosomal pseudogene 94',
'ENSG00000270447' => null,
'ENSG00000275742' => null,
'ENSMUSG00000073103' => 'predicted gene 10466',
'ENSMUSG00000080631' => 'predicted gene, 25507',
'ENSMUSG00000081767' => 'predicted gene 12067',
'ENSMUSG00000086892' => 'RIKEN cDNA 4933430M04 gene',
'ENSMUSG00000087085' => 'predicted gene 12068',
'ENSMUSG00000087145' => 'predicted gene 12665',
'ENSMUSG00000088502' => 'predicted gene, 22787'
)
$gene_name_arr = array(
'ENSG00000200101' => 'RNU6-508P',
'ENSG00000233891' => 'AC007131.2',
'ENSG00000252455' => 'AC007179.2',
'ENSG00000252726' => 'RNA5SP94',
'ENSG00000270447' => 'RP11-569H17.1',
'ENSG00000275742' => 'AC007006.1',
'ENSMUSG00000073103' => 'Gm10466',
'ENSMUSG00000080631' => 'Gm25507',
'ENSMUSG00000081767' => 'Gm12067',
'ENSMUSG00000086892' => '4933430M04Rik',
'ENSMUSG00000087085' => 'Gm12068',
'ENSMUSG00000087145' => 'Gm12665',
'ENSMUSG00000088502' => 'Gm22787'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007XW_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '59478396',
'seq_end' => '60080410',
'region_length' => '602014',
'region_type' => 'VISTA',
'el_id' => 'hs1164'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007XW_0002',
'tax_id' => '10090',
'chromosome' => '11',
'seq_start' => '24539672',
'seq_end' => '25141740',
'region_length' => '602068',
'region_type' => 'VISTA',
'el_id' => 'hs1164'
)
)
)
$all_tissues = array(
(int) 0 => 'Brain',
(int) 5 => 'Breast',
(int) 6 => 'Muscle',
(int) 8 => 'Ovary',
(int) 12 => 'Placenta',
(int) 14 => '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) 20
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000363231' => array(
'start' => '59647621',
'end' => '59647723',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-508P-201'
),
'ENST00000412409' => array(
'start' => '59240942',
'end' => '59733396',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-007'
),
'ENST00000434611' => array(
'start' => '59295380',
'end' => '59388159',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-005'
),
'ENST00000435557' => array(
'start' => '59669216',
'end' => '59733331',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-006'
),
'ENST00000440521' => array(
'start' => '59238716',
'end' => '59249567',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-003'
),
'ENST00000443306' => array(
'start' => '59238716',
'end' => '59249672',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-001'
),
'ENST00000444001' => array(
'start' => '59238722',
'end' => '59388365',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-004'
),
'ENST00000451416' => array(
'start' => '59238714',
'end' => '59249511',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-002'
),
'ENST00000516646' => array(
'start' => '59532984',
'end' => '59533075',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007179.2-201'
),
'ENST00000516917' => array(
'start' => '59694762',
'end' => '59694869',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP94-201'
),
'ENST00000604976' => array(
'start' => '59514890',
'end' => '59515124',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-569H17.1-001'
),
'ENST00000615857' => array(
'start' => '59565835',
'end' => '59565921',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007006.1-201'
),
'ENSMUST00000101450' => array(
'start' => '24721006',
'end' => '24730722',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm10466-001'
),
'ENSMUST00000116981' => array(
'start' => '24679568',
'end' => '24679711',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25507-201'
),
'ENSMUST00000119755' => array(
'start' => '24552438',
'end' => '24553962',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm12067-001'
),
'ENSMUST00000152726' => array(
'start' => '24481909',
'end' => '24569952',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933430M04Rik-001'
),
'ENSMUST00000153153' => array(
'start' => '24426246',
'end' => '24722646',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12068-001'
),
'ENSMUST00000126063' => array(
'start' => '24903983',
'end' => '24926058',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12665-001'
),
'ENSMUST00000130092' => array(
'start' => '24903983',
'end' => '24926050',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12665-002'
),
'ENSMUST00000157877' => array(
'start' => '24553986',
'end' => '24554058',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm22787-201'
)
)
$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_0007XW_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000073103' => array(
[maximum depth reached]
),
'ENSMUSG00000081767' => array(
[maximum depth reached]
),
'ENSMUSG00000086892' => array(
[maximum depth reached]
),
'ENSMUSG00000087085' => array(
[maximum depth reached]
),
'ENSMUSG00000087145' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Ovary',
(int) 2 => 'Placenta',
(int) 3 => 'Brain',
(int) 4 => 'Ovary',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Muscle',
(int) 12 => 'Ovary',
(int) 13 => 'Testis',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007XW_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '59478396',
'seq_end' => '60080410',
'region_length' => '602014',
'region_type' => 'VISTA',
'el_id' => 'hs1164'
)
)
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007XW_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000200101' => 'RNA, U6 small nuclear 508, pseudogene',
'ENSG00000233891' => null,
'ENSG00000252455' => null,
'ENSG00000252726' => 'RNA, 5S ribosomal pseudogene 94',
'ENSG00000270447' => null,
'ENSG00000275742' => null,
'ENSMUSG00000073103' => 'predicted gene 10466',
'ENSMUSG00000080631' => 'predicted gene, 25507',
'ENSMUSG00000081767' => 'predicted gene 12067',
'ENSMUSG00000086892' => 'RIKEN cDNA 4933430M04 gene',
'ENSMUSG00000087085' => 'predicted gene 12068',
'ENSMUSG00000087145' => 'predicted gene 12665',
'ENSMUSG00000088502' => 'predicted gene, 22787'
),
'gene_name_arr' => array(
'ENSG00000200101' => 'RNU6-508P',
'ENSG00000233891' => 'AC007131.2',
'ENSG00000252455' => 'AC007179.2',
'ENSG00000252726' => 'RNA5SP94',
'ENSG00000270447' => 'RP11-569H17.1',
'ENSG00000275742' => 'AC007006.1',
'ENSMUSG00000073103' => 'Gm10466',
'ENSMUSG00000080631' => 'Gm25507',
'ENSMUSG00000081767' => 'Gm12067',
'ENSMUSG00000086892' => '4933430M04Rik',
'ENSMUSG00000087085' => 'Gm12068',
'ENSMUSG00000087145' => 'Gm12665',
'ENSMUSG00000088502' => 'Gm22787'
),
'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 => 'Brain',
(int) 5 => 'Breast',
(int) 6 => 'Muscle',
(int) 8 => 'Ovary',
(int) 12 => 'Placenta',
(int) 14 => '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) 20,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000363231' => array(
'start' => '59647621',
'end' => '59647723',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-508P-201'
),
'ENST00000412409' => array(
'start' => '59240942',
'end' => '59733396',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-007'
),
'ENST00000434611' => array(
'start' => '59295380',
'end' => '59388159',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-005'
),
'ENST00000435557' => array(
'start' => '59669216',
'end' => '59733331',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-006'
),
'ENST00000440521' => array(
'start' => '59238716',
'end' => '59249567',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-003'
),
'ENST00000443306' => array(
'start' => '59238716',
'end' => '59249672',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-001'
),
'ENST00000444001' => array(
'start' => '59238722',
'end' => '59388365',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-004'
),
'ENST00000451416' => array(
'start' => '59238714',
'end' => '59249511',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-002'
),
'ENST00000516646' => array(
'start' => '59532984',
'end' => '59533075',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007179.2-201'
),
'ENST00000516917' => array(
'start' => '59694762',
'end' => '59694869',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP94-201'
),
'ENST00000604976' => array(
'start' => '59514890',
'end' => '59515124',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-569H17.1-001'
),
'ENST00000615857' => array(
'start' => '59565835',
'end' => '59565921',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007006.1-201'
),
'ENSMUST00000101450' => array(
'start' => '24721006',
'end' => '24730722',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm10466-001'
),
'ENSMUST00000116981' => array(
'start' => '24679568',
'end' => '24679711',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25507-201'
),
'ENSMUST00000119755' => array(
'start' => '24552438',
'end' => '24553962',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm12067-001'
),
'ENSMUST00000152726' => array(
'start' => '24481909',
'end' => '24569952',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933430M04Rik-001'
),
'ENSMUST00000153153' => array(
'start' => '24426246',
'end' => '24722646',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12068-001'
),
'ENSMUST00000126063' => array(
'start' => '24903983',
'end' => '24926058',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12665-001'
),
'ENSMUST00000130092' => array(
'start' => '24903983',
'end' => '24926050',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12665-002'
),
'ENSMUST00000157877' => array(
'start' => '24553986',
'end' => '24554058',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm22787-201'
)
),
'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_0007XW_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007XW_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000073103' => array(
[maximum depth reached]
),
'ENSMUSG00000081767' => array(
[maximum depth reached]
),
'ENSMUSG00000086892' => array(
[maximum depth reached]
),
'ENSMUSG00000087085' => array(
[maximum depth reached]
),
'ENSMUSG00000087145' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Ovary',
(int) 2 => 'Placenta',
(int) 3 => 'Brain',
(int) 4 => 'Ovary',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Muscle',
(int) 12 => 'Ovary',
(int) 13 => 'Testis',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000200101' => 'RNA, U6 small nuclear 508, pseudogene',
'ENSG00000233891' => null,
'ENSG00000252455' => null,
'ENSG00000252726' => 'RNA, 5S ribosomal pseudogene 94',
'ENSG00000270447' => null,
'ENSG00000275742' => null,
'ENSMUSG00000073103' => 'predicted gene 10466',
'ENSMUSG00000080631' => 'predicted gene, 25507',
'ENSMUSG00000081767' => 'predicted gene 12067',
'ENSMUSG00000086892' => 'RIKEN cDNA 4933430M04 gene',
'ENSMUSG00000087085' => 'predicted gene 12068',
'ENSMUSG00000087145' => 'predicted gene 12665',
'ENSMUSG00000088502' => 'predicted gene, 22787'
)
$gene_name_arr = array(
'ENSG00000200101' => 'RNU6-508P',
'ENSG00000233891' => 'AC007131.2',
'ENSG00000252455' => 'AC007179.2',
'ENSG00000252726' => 'RNA5SP94',
'ENSG00000270447' => 'RP11-569H17.1',
'ENSG00000275742' => 'AC007006.1',
'ENSMUSG00000073103' => 'Gm10466',
'ENSMUSG00000080631' => 'Gm25507',
'ENSMUSG00000081767' => 'Gm12067',
'ENSMUSG00000086892' => '4933430M04Rik',
'ENSMUSG00000087085' => 'Gm12068',
'ENSMUSG00000087145' => 'Gm12665',
'ENSMUSG00000088502' => 'Gm22787'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007XW_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '59478396',
'seq_end' => '60080410',
'region_length' => '602014',
'region_type' => 'VISTA',
'el_id' => 'hs1164'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007XW_0002',
'tax_id' => '10090',
'chromosome' => '11',
'seq_start' => '24539672',
'seq_end' => '25141740',
'region_length' => '602068',
'region_type' => 'VISTA',
'el_id' => 'hs1164'
)
)
)
$all_tissues = array(
(int) 0 => 'Brain',
(int) 5 => 'Breast',
(int) 6 => 'Muscle',
(int) 8 => 'Ovary',
(int) 12 => 'Placenta',
(int) 14 => '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) 20
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000363231' => array(
'start' => '59647621',
'end' => '59647723',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-508P-201'
),
'ENST00000412409' => array(
'start' => '59240942',
'end' => '59733396',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-007'
),
'ENST00000434611' => array(
'start' => '59295380',
'end' => '59388159',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-005'
),
'ENST00000435557' => array(
'start' => '59669216',
'end' => '59733331',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-006'
),
'ENST00000440521' => array(
'start' => '59238716',
'end' => '59249567',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-003'
),
'ENST00000443306' => array(
'start' => '59238716',
'end' => '59249672',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-001'
),
'ENST00000444001' => array(
'start' => '59238722',
'end' => '59388365',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-004'
),
'ENST00000451416' => array(
'start' => '59238714',
'end' => '59249511',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007131.2-002'
),
'ENST00000516646' => array(
'start' => '59532984',
'end' => '59533075',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007179.2-201'
),
'ENST00000516917' => array(
'start' => '59694762',
'end' => '59694869',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP94-201'
),
'ENST00000604976' => array(
'start' => '59514890',
'end' => '59515124',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-569H17.1-001'
),
'ENST00000615857' => array(
'start' => '59565835',
'end' => '59565921',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007006.1-201'
),
'ENSMUST00000101450' => array(
'start' => '24721006',
'end' => '24730722',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm10466-001'
),
'ENSMUST00000116981' => array(
'start' => '24679568',
'end' => '24679711',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25507-201'
),
'ENSMUST00000119755' => array(
'start' => '24552438',
'end' => '24553962',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm12067-001'
),
'ENSMUST00000152726' => array(
'start' => '24481909',
'end' => '24569952',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933430M04Rik-001'
),
'ENSMUST00000153153' => array(
'start' => '24426246',
'end' => '24722646',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12068-001'
),
'ENSMUST00000126063' => array(
'start' => '24903983',
'end' => '24926058',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12665-001'
),
'ENSMUST00000130092' => array(
'start' => '24903983',
'end' => '24926050',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12665-002'
),
'ENSMUST00000157877' => array(
'start' => '24553986',
'end' => '24554058',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm22787-201'
)
)
$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_0007XW_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000073103' => array(
[maximum depth reached]
),
'ENSMUSG00000081767' => array(
[maximum depth reached]
),
'ENSMUSG00000086892' => array(
[maximum depth reached]
),
'ENSMUSG00000087085' => array(
[maximum depth reached]
),
'ENSMUSG00000087145' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Ovary',
(int) 2 => 'Placenta',
(int) 3 => 'Brain',
(int) 4 => 'Ovary',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Muscle',
(int) 12 => 'Ovary',
(int) 13 => 'Testis',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007XW_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '59478396',
'seq_end' => '60080410',
'region_length' => '602014',
'region_type' => 'VISTA',
'el_id' => 'hs1164'
)
)
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
(Gm10466)