| Source ID |
Type |
Tax ID |
Position |
| hs303 |
VISTA |
10090 |
3:18413569-19014476  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007VL_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_0007VL_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000213873' => null,
'ENSG00000239261' => 'ribosomal protein L31 pseudogene 41',
'ENSG00000253493' => null,
'ENSG00000254081' => 'long intergenic non-protein coding RNA 1299',
'ENSMUSG00000040217' => 'predicted gene 6369'
),
'gene_name_arr' => array(
'ENSG00000213873' => 'RP11-678D18.1',
'ENSG00000239261' => 'RPL31P41',
'ENSG00000253493' => 'RP11-89A16.1',
'ENSG00000254081' => 'LINC01299',
'ENSMUSG00000040217' => 'Gm6369'
),
'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) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 5 => 'Breast',
(int) 6 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => '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) 5,
'longest_tissue_len' => (int) 7,
'transcript_data' => array(
'ENST00000518241' => array(
'start' => '65377592',
'end' => '65378111',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-678D18.1-001'
),
'ENST00000477967' => array(
'start' => '65155407',
'end' => '65155778',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL31P41-001'
),
'ENST00000520501' => array(
'start' => '64973488',
'end' => '64973848',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-89A16.1-001'
),
'ENST00000520902' => array(
'start' => '65527008',
'end' => '65562780',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01299-001'
),
'ENSMUST00000069626' => array(
'start' => '18533861',
'end' => '18534289',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm6369-201'
)
),
'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_0007VL_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007VL_0001' => array(
'genes_in_region' => array(
'ENSG00000213873' => array(
[maximum depth reached]
),
'ENSG00000239261' => array(
[maximum depth reached]
),
'ENSG00000254081' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Kidney',
(int) 3 => 'Brain',
(int) 4 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 6 => 'Brain',
(int) 7 => 'Breast',
(int) 8 => 'Colon',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000213873' => null,
'ENSG00000239261' => 'ribosomal protein L31 pseudogene 41',
'ENSG00000253493' => null,
'ENSG00000254081' => 'long intergenic non-protein coding RNA 1299',
'ENSMUSG00000040217' => 'predicted gene 6369'
)
$gene_name_arr = array(
'ENSG00000213873' => 'RP11-678D18.1',
'ENSG00000239261' => 'RPL31P41',
'ENSG00000253493' => 'RP11-89A16.1',
'ENSG00000254081' => 'LINC01299',
'ENSMUSG00000040217' => 'Gm6369'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007VL_0001',
'tax_id' => '9606',
'chromosome' => '8',
'seq_start' => '64936692',
'seq_end' => '65537601',
'region_length' => '600909',
'region_type' => 'VISTA',
'el_id' => 'hs303'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007VL_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '18413569',
'seq_end' => '19014476',
'region_length' => '600907',
'region_type' => 'VISTA',
'el_id' => 'hs303'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 5 => 'Breast',
(int) 6 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => '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) 5
$longest_tissue_len = (int) 7
$transcript_data = array(
'ENST00000518241' => array(
'start' => '65377592',
'end' => '65378111',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-678D18.1-001'
),
'ENST00000477967' => array(
'start' => '65155407',
'end' => '65155778',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL31P41-001'
),
'ENST00000520501' => array(
'start' => '64973488',
'end' => '64973848',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-89A16.1-001'
),
'ENST00000520902' => array(
'start' => '65527008',
'end' => '65562780',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01299-001'
),
'ENSMUST00000069626' => array(
'start' => '18533861',
'end' => '18534289',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm6369-201'
)
)
$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_0007VL_0001' => array(
'genes_in_region' => array(
'ENSG00000213873' => array(
[maximum depth reached]
),
'ENSG00000239261' => array(
[maximum depth reached]
),
'ENSG00000254081' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Kidney',
(int) 3 => 'Brain',
(int) 4 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 6 => 'Brain',
(int) 7 => 'Breast',
(int) 8 => 'Colon',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007VL_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '18413569',
'seq_end' => '19014476',
'region_length' => '600907',
'region_type' => 'VISTA',
'el_id' => 'hs303'
)
)
$gene_el = array(
'ENST00000520902' => array(
'Adipose' => array(
'average_FPKM' => '0.049',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.135',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.218',
'stddev_FPKM' => '0.04'
),
'Breast' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.045',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.02'
),
'Ovary' => array(
'average_FPKM' => '0.014',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.01'
)
)
)
$gene_key = 'ENSG00000254081'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.049',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.135',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.218',
'stddev_FPKM' => '0.04'
),
'Breast' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.045',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.02'
),
'Ovary' => array(
'average_FPKM' => '0.014',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.01'
)
)
$tran_key = 'ENST00000520902'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007VL_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000213873' => null,
'ENSG00000239261' => 'ribosomal protein L31 pseudogene 41',
'ENSG00000253493' => null,
'ENSG00000254081' => 'long intergenic non-protein coding RNA 1299',
'ENSMUSG00000040217' => 'predicted gene 6369'
),
'gene_name_arr' => array(
'ENSG00000213873' => 'RP11-678D18.1',
'ENSG00000239261' => 'RPL31P41',
'ENSG00000253493' => 'RP11-89A16.1',
'ENSG00000254081' => 'LINC01299',
'ENSMUSG00000040217' => 'Gm6369'
),
'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) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 5 => 'Breast',
(int) 6 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => '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) 5,
'longest_tissue_len' => (int) 7,
'transcript_data' => array(
'ENST00000518241' => array(
'start' => '65377592',
'end' => '65378111',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-678D18.1-001'
),
'ENST00000477967' => array(
'start' => '65155407',
'end' => '65155778',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL31P41-001'
),
'ENST00000520501' => array(
'start' => '64973488',
'end' => '64973848',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-89A16.1-001'
),
'ENST00000520902' => array(
'start' => '65527008',
'end' => '65562780',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01299-001'
),
'ENSMUST00000069626' => array(
'start' => '18533861',
'end' => '18534289',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm6369-201'
)
),
'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_0007VL_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007VL_0001' => array(
'genes_in_region' => array(
'ENSG00000213873' => array(
[maximum depth reached]
),
'ENSG00000239261' => array(
[maximum depth reached]
),
'ENSG00000254081' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Kidney',
(int) 3 => 'Brain',
(int) 4 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 6 => 'Brain',
(int) 7 => 'Breast',
(int) 8 => 'Colon',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000213873' => null,
'ENSG00000239261' => 'ribosomal protein L31 pseudogene 41',
'ENSG00000253493' => null,
'ENSG00000254081' => 'long intergenic non-protein coding RNA 1299',
'ENSMUSG00000040217' => 'predicted gene 6369'
)
$gene_name_arr = array(
'ENSG00000213873' => 'RP11-678D18.1',
'ENSG00000239261' => 'RPL31P41',
'ENSG00000253493' => 'RP11-89A16.1',
'ENSG00000254081' => 'LINC01299',
'ENSMUSG00000040217' => 'Gm6369'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007VL_0001',
'tax_id' => '9606',
'chromosome' => '8',
'seq_start' => '64936692',
'seq_end' => '65537601',
'region_length' => '600909',
'region_type' => 'VISTA',
'el_id' => 'hs303'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007VL_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '18413569',
'seq_end' => '19014476',
'region_length' => '600907',
'region_type' => 'VISTA',
'el_id' => 'hs303'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 5 => 'Breast',
(int) 6 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => '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) 5
$longest_tissue_len = (int) 7
$transcript_data = array(
'ENST00000518241' => array(
'start' => '65377592',
'end' => '65378111',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-678D18.1-001'
),
'ENST00000477967' => array(
'start' => '65155407',
'end' => '65155778',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL31P41-001'
),
'ENST00000520501' => array(
'start' => '64973488',
'end' => '64973848',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-89A16.1-001'
),
'ENST00000520902' => array(
'start' => '65527008',
'end' => '65562780',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01299-001'
),
'ENSMUST00000069626' => array(
'start' => '18533861',
'end' => '18534289',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm6369-201'
)
)
$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_0007VL_0001' => array(
'genes_in_region' => array(
'ENSG00000213873' => array(
[maximum depth reached]
),
'ENSG00000239261' => array(
[maximum depth reached]
),
'ENSG00000254081' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Kidney',
(int) 3 => 'Brain',
(int) 4 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 6 => 'Brain',
(int) 7 => 'Breast',
(int) 8 => 'Colon',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007VL_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '18413569',
'seq_end' => '19014476',
'region_length' => '600907',
'region_type' => 'VISTA',
'el_id' => 'hs303'
)
)
$gene_el = array(
'ENST00000520902' => array(
'Adipose' => array(
'average_FPKM' => '0.049',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.135',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.218',
'stddev_FPKM' => '0.04'
),
'Breast' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.045',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.02'
),
'Ovary' => array(
'average_FPKM' => '0.014',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.01'
)
)
)
$gene_key = 'ENSG00000254081'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.049',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.135',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.218',
'stddev_FPKM' => '0.04'
),
'Breast' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.045',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.02'
),
'Ovary' => array(
'average_FPKM' => '0.014',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.01'
)
)
$tran_key = 'ENST00000520902'
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
(RP11-678D18.1)