| Source ID |
Type |
Tax ID |
Position |
| ENSG00000102076-ENSG00000268221 |
CGP |
9606 |
X:154144224-154196135  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007GD_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_0007GD_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000044861' => 'opsin 1 (cone pigments), long-wave-sensitive, 2',
'ENSDARG00000044862' => 'opsin 1 (cone pigments), long-wave-sensitive, 1',
'ENSG00000102076' => 'opsin 1 (cone pigments), long-wave-sensitive',
'ENSG00000268221' => 'opsin 1 (cone pigments), medium-wave-sensitive',
'ENSG00000277008' => 'testis expressed 28 pseudogene 2',
'ENSG00000166160' => 'opsin 1 (cone pigments), medium-wave-sensitive 2',
'ENSG00000269433' => 'opsin 1 (cone pigments), medium-wave-sensitive',
'ENSG00000277009' => null,
'ENSG00000278057' => 'testis expressed 28',
'ENSG00000274962' => 'testis expressed 28 pseudogene 1'
),
'gene_name_arr' => array(
'ENSDARG00000044861' => 'opn1lw2',
'ENSDARG00000044862' => 'opn1lw1',
'ENSG00000102076' => 'OPN1LW',
'ENSG00000268221' => 'OPN1MW',
'ENSG00000277008' => 'TEX28P2',
'ENSG00000166160' => 'OPN1MW2',
'ENSG00000269433' => 'OPN1MW',
'ENSG00000277009' => 'CH17-128G5.1',
'ENSG00000278057' => 'TEX28',
'ENSG00000274962' => 'TEX28P1'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Brain',
(int) 2 => 'Heart'
),
'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) 28,
'longest_tissue_len' => (int) 5,
'transcript_data' => array(
'ENSDART00000065940' => array(
'start' => '26414605',
'end' => '26416765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'opn1lw2-001'
),
'ENSDART00000132277' => array(
'start' => '26414666',
'end' => '26416529',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'opn1lw2-004'
),
'ENSDART00000140746' => array(
'start' => '26414674',
'end' => '26415762',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'opn1lw2-002'
),
'ENSDART00000144302' => array(
'start' => '26414666',
'end' => '26415796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'opn1lw2-003'
),
'ENSDART00000065941' => array(
'start' => '26411202',
'end' => '26413596',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'opn1lw1-001'
),
'ENST00000369951' => array(
'start' => '154144224',
'end' => '154159032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1LW-001'
),
'ENST00000442922' => array(
'start' => '154152942',
'end' => '154159023',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1LW-002'
),
'ENST00000463296' => array(
'start' => '154144274',
'end' => '154156397',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1LW-003'
),
'ENST00000595290' => array(
'start' => '154182596',
'end' => '154196105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-001'
),
'ENST00000595330' => array(
'start' => '154182668',
'end' => '154193511',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1MW-003'
),
'ENST00000596998' => array(
'start' => '154190058',
'end' => '154196135',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-002'
),
'ENST00000617764' => array(
'start' => '154159357',
'end' => '154176349',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'TEX28P2-001'
),
'ENST00000369929' => array(
'start' => '154219756',
'end' => '154233286',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW2-001'
),
'ENST00000430419' => array(
'start' => '154227196',
'end' => '154233277',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW2-002'
),
'ENST00000488220' => array(
'start' => '154219797',
'end' => '154230651',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1MW2-003'
),
'ENST00000599405' => array(
'start' => '154257538',
'end' => '154271805',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-001'
),
'ENST00000621631' => array(
'start' => '154233615',
'end' => '154251288',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'CH17-128G5.1-001'
),
'ENST00000610938' => array(
'start' => '154271415',
'end' => '154292117',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-201'
),
'ENST00000617213' => array(
'start' => '154288336',
'end' => '154295853',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TEX28-003'
),
'ENST00000617225' => array(
'start' => '154271267',
'end' => '154295085',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-002'
),
'ENST00000619903' => array(
'start' => '154271265',
'end' => '154295211',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-001'
),
'ENST00000613479' => array(
'start' => '154196471',
'end' => '154213487',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'TEX28P1-001'
)
),
'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_0007GD_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007GD_0001' => array(
'genes_in_region' => array(
'ENSDARG00000044861' => array(
[maximum depth reached]
),
'ENSDARG00000044862' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Heart',
(int) 3 => 'Brain'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000044861' => 'opsin 1 (cone pigments), long-wave-sensitive, 2',
'ENSDARG00000044862' => 'opsin 1 (cone pigments), long-wave-sensitive, 1',
'ENSG00000102076' => 'opsin 1 (cone pigments), long-wave-sensitive',
'ENSG00000268221' => 'opsin 1 (cone pigments), medium-wave-sensitive',
'ENSG00000277008' => 'testis expressed 28 pseudogene 2',
'ENSG00000166160' => 'opsin 1 (cone pigments), medium-wave-sensitive 2',
'ENSG00000269433' => 'opsin 1 (cone pigments), medium-wave-sensitive',
'ENSG00000277009' => null,
'ENSG00000278057' => 'testis expressed 28',
'ENSG00000274962' => 'testis expressed 28 pseudogene 1'
)
$gene_name_arr = array(
'ENSDARG00000044861' => 'opn1lw2',
'ENSDARG00000044862' => 'opn1lw1',
'ENSG00000102076' => 'OPN1LW',
'ENSG00000268221' => 'OPN1MW',
'ENSG00000277008' => 'TEX28P2',
'ENSG00000166160' => 'OPN1MW2',
'ENSG00000269433' => 'OPN1MW',
'ENSG00000277009' => 'CH17-128G5.1',
'ENSG00000278057' => 'TEX28',
'ENSG00000274962' => 'TEX28P1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0001',
'tax_id' => '7955',
'chromosome' => '11',
'seq_start' => '26411202',
'seq_end' => '26416765',
'region_length' => '5563',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000044862-ENSDARG00000044861'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0002',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '154144224',
'seq_end' => '154196135',
'region_length' => '51911',
'region_type' => 'CGP',
'el_id' => 'ENSG00000102076-ENSG00000268221'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0003',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '154219756',
'seq_end' => '154271805',
'region_length' => '52049',
'region_type' => 'CGP',
'el_id' => 'ENSG00000166160-ENSG00000269433'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0004',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '154182596',
'seq_end' => '154233286',
'region_length' => '50690',
'region_type' => 'CGP',
'el_id' => 'ENSG00000268221-ENSG00000166160'
)
)
)
$all_tissues = array(
(int) 0 => 'Brain',
(int) 2 => 'Heart'
)
$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) 28
$longest_tissue_len = (int) 5
$transcript_data = array(
'ENSDART00000065940' => array(
'start' => '26414605',
'end' => '26416765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'opn1lw2-001'
),
'ENSDART00000132277' => array(
'start' => '26414666',
'end' => '26416529',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'opn1lw2-004'
),
'ENSDART00000140746' => array(
'start' => '26414674',
'end' => '26415762',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'opn1lw2-002'
),
'ENSDART00000144302' => array(
'start' => '26414666',
'end' => '26415796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'opn1lw2-003'
),
'ENSDART00000065941' => array(
'start' => '26411202',
'end' => '26413596',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'opn1lw1-001'
),
'ENST00000369951' => array(
'start' => '154144224',
'end' => '154159032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1LW-001'
),
'ENST00000442922' => array(
'start' => '154152942',
'end' => '154159023',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1LW-002'
),
'ENST00000463296' => array(
'start' => '154144274',
'end' => '154156397',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1LW-003'
),
'ENST00000595290' => array(
'start' => '154182596',
'end' => '154196105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-001'
),
'ENST00000595330' => array(
'start' => '154182668',
'end' => '154193511',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1MW-003'
),
'ENST00000596998' => array(
'start' => '154190058',
'end' => '154196135',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-002'
),
'ENST00000617764' => array(
'start' => '154159357',
'end' => '154176349',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'TEX28P2-001'
),
'ENST00000369929' => array(
'start' => '154219756',
'end' => '154233286',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW2-001'
),
'ENST00000430419' => array(
'start' => '154227196',
'end' => '154233277',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW2-002'
),
'ENST00000488220' => array(
'start' => '154219797',
'end' => '154230651',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1MW2-003'
),
'ENST00000599405' => array(
'start' => '154257538',
'end' => '154271805',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-001'
),
'ENST00000621631' => array(
'start' => '154233615',
'end' => '154251288',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'CH17-128G5.1-001'
),
'ENST00000610938' => array(
'start' => '154271415',
'end' => '154292117',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-201'
),
'ENST00000617213' => array(
'start' => '154288336',
'end' => '154295853',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TEX28-003'
),
'ENST00000617225' => array(
'start' => '154271267',
'end' => '154295085',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-002'
),
'ENST00000619903' => array(
'start' => '154271265',
'end' => '154295211',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-001'
),
'ENST00000613479' => array(
'start' => '154196471',
'end' => '154213487',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'TEX28P1-001'
)
)
$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_0007GD_0001' => array(
'genes_in_region' => array(
'ENSDARG00000044861' => array(
[maximum depth reached]
),
'ENSDARG00000044862' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Heart',
(int) 3 => 'Brain'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0002',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '154144224',
'seq_end' => '154196135',
'region_length' => '51911',
'region_type' => 'CGP',
'el_id' => 'ENSG00000102076-ENSG00000268221'
)
)
$gene_el = array(
'ENSDART00000065941' => array(
'Brain' => array(
'average_FPKM' => '0.167',
'stddev_FPKM' => '0.09'
)
)
)
$gene_key = 'ENSDARG00000044862'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '0.167',
'stddev_FPKM' => '0.09'
)
)
$tran_key = 'ENSDART00000065941'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007GD_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000044861' => 'opsin 1 (cone pigments), long-wave-sensitive, 2',
'ENSDARG00000044862' => 'opsin 1 (cone pigments), long-wave-sensitive, 1',
'ENSG00000102076' => 'opsin 1 (cone pigments), long-wave-sensitive',
'ENSG00000268221' => 'opsin 1 (cone pigments), medium-wave-sensitive',
'ENSG00000277008' => 'testis expressed 28 pseudogene 2',
'ENSG00000166160' => 'opsin 1 (cone pigments), medium-wave-sensitive 2',
'ENSG00000269433' => 'opsin 1 (cone pigments), medium-wave-sensitive',
'ENSG00000277009' => null,
'ENSG00000278057' => 'testis expressed 28',
'ENSG00000274962' => 'testis expressed 28 pseudogene 1'
),
'gene_name_arr' => array(
'ENSDARG00000044861' => 'opn1lw2',
'ENSDARG00000044862' => 'opn1lw1',
'ENSG00000102076' => 'OPN1LW',
'ENSG00000268221' => 'OPN1MW',
'ENSG00000277008' => 'TEX28P2',
'ENSG00000166160' => 'OPN1MW2',
'ENSG00000269433' => 'OPN1MW',
'ENSG00000277009' => 'CH17-128G5.1',
'ENSG00000278057' => 'TEX28',
'ENSG00000274962' => 'TEX28P1'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Brain',
(int) 2 => 'Heart'
),
'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) 28,
'longest_tissue_len' => (int) 5,
'transcript_data' => array(
'ENSDART00000065940' => array(
'start' => '26414605',
'end' => '26416765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'opn1lw2-001'
),
'ENSDART00000132277' => array(
'start' => '26414666',
'end' => '26416529',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'opn1lw2-004'
),
'ENSDART00000140746' => array(
'start' => '26414674',
'end' => '26415762',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'opn1lw2-002'
),
'ENSDART00000144302' => array(
'start' => '26414666',
'end' => '26415796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'opn1lw2-003'
),
'ENSDART00000065941' => array(
'start' => '26411202',
'end' => '26413596',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'opn1lw1-001'
),
'ENST00000369951' => array(
'start' => '154144224',
'end' => '154159032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1LW-001'
),
'ENST00000442922' => array(
'start' => '154152942',
'end' => '154159023',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1LW-002'
),
'ENST00000463296' => array(
'start' => '154144274',
'end' => '154156397',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1LW-003'
),
'ENST00000595290' => array(
'start' => '154182596',
'end' => '154196105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-001'
),
'ENST00000595330' => array(
'start' => '154182668',
'end' => '154193511',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1MW-003'
),
'ENST00000596998' => array(
'start' => '154190058',
'end' => '154196135',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-002'
),
'ENST00000617764' => array(
'start' => '154159357',
'end' => '154176349',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'TEX28P2-001'
),
'ENST00000369929' => array(
'start' => '154219756',
'end' => '154233286',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW2-001'
),
'ENST00000430419' => array(
'start' => '154227196',
'end' => '154233277',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW2-002'
),
'ENST00000488220' => array(
'start' => '154219797',
'end' => '154230651',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1MW2-003'
),
'ENST00000599405' => array(
'start' => '154257538',
'end' => '154271805',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-001'
),
'ENST00000621631' => array(
'start' => '154233615',
'end' => '154251288',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'CH17-128G5.1-001'
),
'ENST00000610938' => array(
'start' => '154271415',
'end' => '154292117',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-201'
),
'ENST00000617213' => array(
'start' => '154288336',
'end' => '154295853',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TEX28-003'
),
'ENST00000617225' => array(
'start' => '154271267',
'end' => '154295085',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-002'
),
'ENST00000619903' => array(
'start' => '154271265',
'end' => '154295211',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-001'
),
'ENST00000613479' => array(
'start' => '154196471',
'end' => '154213487',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'TEX28P1-001'
)
),
'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_0007GD_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007GD_0001' => array(
'genes_in_region' => array(
'ENSDARG00000044861' => array(
[maximum depth reached]
),
'ENSDARG00000044862' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Heart',
(int) 3 => 'Brain'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000044861' => 'opsin 1 (cone pigments), long-wave-sensitive, 2',
'ENSDARG00000044862' => 'opsin 1 (cone pigments), long-wave-sensitive, 1',
'ENSG00000102076' => 'opsin 1 (cone pigments), long-wave-sensitive',
'ENSG00000268221' => 'opsin 1 (cone pigments), medium-wave-sensitive',
'ENSG00000277008' => 'testis expressed 28 pseudogene 2',
'ENSG00000166160' => 'opsin 1 (cone pigments), medium-wave-sensitive 2',
'ENSG00000269433' => 'opsin 1 (cone pigments), medium-wave-sensitive',
'ENSG00000277009' => null,
'ENSG00000278057' => 'testis expressed 28',
'ENSG00000274962' => 'testis expressed 28 pseudogene 1'
)
$gene_name_arr = array(
'ENSDARG00000044861' => 'opn1lw2',
'ENSDARG00000044862' => 'opn1lw1',
'ENSG00000102076' => 'OPN1LW',
'ENSG00000268221' => 'OPN1MW',
'ENSG00000277008' => 'TEX28P2',
'ENSG00000166160' => 'OPN1MW2',
'ENSG00000269433' => 'OPN1MW',
'ENSG00000277009' => 'CH17-128G5.1',
'ENSG00000278057' => 'TEX28',
'ENSG00000274962' => 'TEX28P1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0001',
'tax_id' => '7955',
'chromosome' => '11',
'seq_start' => '26411202',
'seq_end' => '26416765',
'region_length' => '5563',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000044862-ENSDARG00000044861'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0002',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '154144224',
'seq_end' => '154196135',
'region_length' => '51911',
'region_type' => 'CGP',
'el_id' => 'ENSG00000102076-ENSG00000268221'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0003',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '154219756',
'seq_end' => '154271805',
'region_length' => '52049',
'region_type' => 'CGP',
'el_id' => 'ENSG00000166160-ENSG00000269433'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0004',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '154182596',
'seq_end' => '154233286',
'region_length' => '50690',
'region_type' => 'CGP',
'el_id' => 'ENSG00000268221-ENSG00000166160'
)
)
)
$all_tissues = array(
(int) 0 => 'Brain',
(int) 2 => 'Heart'
)
$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) 28
$longest_tissue_len = (int) 5
$transcript_data = array(
'ENSDART00000065940' => array(
'start' => '26414605',
'end' => '26416765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'opn1lw2-001'
),
'ENSDART00000132277' => array(
'start' => '26414666',
'end' => '26416529',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'opn1lw2-004'
),
'ENSDART00000140746' => array(
'start' => '26414674',
'end' => '26415762',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'opn1lw2-002'
),
'ENSDART00000144302' => array(
'start' => '26414666',
'end' => '26415796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'opn1lw2-003'
),
'ENSDART00000065941' => array(
'start' => '26411202',
'end' => '26413596',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'opn1lw1-001'
),
'ENST00000369951' => array(
'start' => '154144224',
'end' => '154159032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1LW-001'
),
'ENST00000442922' => array(
'start' => '154152942',
'end' => '154159023',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1LW-002'
),
'ENST00000463296' => array(
'start' => '154144274',
'end' => '154156397',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1LW-003'
),
'ENST00000595290' => array(
'start' => '154182596',
'end' => '154196105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-001'
),
'ENST00000595330' => array(
'start' => '154182668',
'end' => '154193511',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1MW-003'
),
'ENST00000596998' => array(
'start' => '154190058',
'end' => '154196135',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-002'
),
'ENST00000617764' => array(
'start' => '154159357',
'end' => '154176349',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'TEX28P2-001'
),
'ENST00000369929' => array(
'start' => '154219756',
'end' => '154233286',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW2-001'
),
'ENST00000430419' => array(
'start' => '154227196',
'end' => '154233277',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW2-002'
),
'ENST00000488220' => array(
'start' => '154219797',
'end' => '154230651',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'OPN1MW2-003'
),
'ENST00000599405' => array(
'start' => '154257538',
'end' => '154271805',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OPN1MW-001'
),
'ENST00000621631' => array(
'start' => '154233615',
'end' => '154251288',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'CH17-128G5.1-001'
),
'ENST00000610938' => array(
'start' => '154271415',
'end' => '154292117',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-201'
),
'ENST00000617213' => array(
'start' => '154288336',
'end' => '154295853',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TEX28-003'
),
'ENST00000617225' => array(
'start' => '154271267',
'end' => '154295085',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-002'
),
'ENST00000619903' => array(
'start' => '154271265',
'end' => '154295211',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TEX28-001'
),
'ENST00000613479' => array(
'start' => '154196471',
'end' => '154213487',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'TEX28P1-001'
)
)
$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_0007GD_0001' => array(
'genes_in_region' => array(
'ENSDARG00000044861' => array(
[maximum depth reached]
),
'ENSDARG00000044862' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Heart',
(int) 3 => 'Brain'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007GD_0002',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '154144224',
'seq_end' => '154196135',
'region_length' => '51911',
'region_type' => 'CGP',
'el_id' => 'ENSG00000102076-ENSG00000268221'
)
)
$gene_el = array(
'ENSDART00000065941' => array(
'Brain' => array(
'average_FPKM' => '0.167',
'stddev_FPKM' => '0.09'
)
)
)
$gene_key = 'ENSDARG00000044862'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '0.167',
'stddev_FPKM' => '0.09'
)
)
$tran_key = 'ENSDART00000065941'
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
(opn1lw2)