| Source ID |
Type |
Tax ID |
Position |
| ENSG00000137474-ENSG00000178795 |
CGP |
9606 |
11:77128264-77301687  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0001JF_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_0001JF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000044632' => 'myosin VIIAb',
'ENSDARG00000079293' => 'glycerophosphodiester phosphodiesterase domain containing 4',
'ENSG00000137474' => 'myosin VIIA',
'ENSG00000178795' => 'glycerophosphodiester phosphodiesterase domain containing 4'
),
'gene_name_arr' => array(
'ENSDARG00000044632' => 'myo7ab',
'ENSDARG00000079293' => 'GDPD4 (3 of 3)',
'ENSG00000137474' => 'MYO7A',
'ENSG00000178795' => 'GDPD4'
),
'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) 2 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 7 => 'Brain',
(int) 13 => 'Breast',
(int) 17 => 'Colon',
(int) 19 => 'Heart',
(int) 26 => 'Kidney',
(int) 30 => 'Liver',
(int) 33 => 'Lung',
(int) 37 => 'Muscle',
(int) 41 => 'Ovary',
(int) 46 => 'Placenta',
(int) 51 => '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) 21,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000003181' => array(
'start' => '21189835',
'end' => '21261331',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo7ab-201'
),
'ENSDART00000148019' => array(
'start' => '21190581',
'end' => '21261337',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo7ab-001'
),
'ENSDART00000108701' => array(
'start' => '21263835',
'end' => '21274181',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4 (3 of 3)-201'
),
'ENSDART00000142100' => array(
'start' => '21265123',
'end' => '21276995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4 (3 of 3)-001'
),
'ENST00000409619' => array(
'start' => '77128302',
'end' => '77214954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-009'
),
'ENST00000409709' => array(
'start' => '77128264',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-001'
),
'ENST00000409893' => array(
'start' => '77128270',
'end' => '77184996',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-005'
),
'ENST00000458169' => array(
'start' => '77179825',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-010'
),
'ENST00000458637' => array(
'start' => '77128270',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-002'
),
'ENST00000467137' => array(
'start' => '77184686',
'end' => '77191187',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-007'
),
'ENST00000481328' => array(
'start' => '77179825',
'end' => '77215238',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-003'
),
'ENST00000481532' => array(
'start' => '77212535',
'end' => '77213918',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-008'
),
'ENST00000526863' => array(
'start' => '77210887',
'end' => '77212975',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO7A-011'
),
'ENST00000605744' => array(
'start' => '77203186',
'end' => '77215239',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO7A-004'
),
'ENST00000620575' => array(
'start' => '77128270',
'end' => '77184989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-201'
),
'ENST00000315938' => array(
'start' => '77216558',
'end' => '77287418',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4-001'
),
'ENST00000376217' => array(
'start' => '77216558',
'end' => '77287418',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4-002'
),
'ENST00000527489' => array(
'start' => '77271356',
'end' => '77301649',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GDPD4-005'
),
'ENST00000532155' => array(
'start' => '77270920',
'end' => '77301687',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GDPD4-003'
),
'ENST00000532907' => array(
'start' => '77216862',
'end' => '77224302',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GDPD4-006'
),
'ENST00000534245' => array(
'start' => '77286923',
'end' => '77301666',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GDPD4-004'
)
),
'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_0001JF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0001JF_0001' => array(
'genes_in_region' => array(
'ENSDARG00000044632' => array(
[maximum depth reached]
),
'ENSDARG00000079293' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Brain',
(int) 3 => 'Heart',
(int) 4 => 'Muscle',
(int) 5 => 'Heart',
(int) 6 => 'Muscle',
(int) 7 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000044632' => 'myosin VIIAb',
'ENSDARG00000079293' => 'glycerophosphodiester phosphodiesterase domain containing 4',
'ENSG00000137474' => 'myosin VIIA',
'ENSG00000178795' => 'glycerophosphodiester phosphodiesterase domain containing 4'
)
$gene_name_arr = array(
'ENSDARG00000044632' => 'myo7ab',
'ENSDARG00000079293' => 'GDPD4 (3 of 3)',
'ENSG00000137474' => 'MYO7A',
'ENSG00000178795' => 'GDPD4'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0001JF_0001',
'tax_id' => '7955',
'chromosome' => '21',
'seq_start' => '21189835',
'seq_end' => '21276995',
'region_length' => '87160',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000044632-ENSDARG00000079293'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0001JF_0002',
'tax_id' => '9606',
'chromosome' => '11',
'seq_start' => '77128264',
'seq_end' => '77301687',
'region_length' => '173423',
'region_type' => 'CGP',
'el_id' => 'ENSG00000137474-ENSG00000178795'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 7 => 'Brain',
(int) 13 => 'Breast',
(int) 17 => 'Colon',
(int) 19 => 'Heart',
(int) 26 => 'Kidney',
(int) 30 => 'Liver',
(int) 33 => 'Lung',
(int) 37 => 'Muscle',
(int) 41 => 'Ovary',
(int) 46 => 'Placenta',
(int) 51 => '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) 21
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000003181' => array(
'start' => '21189835',
'end' => '21261331',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo7ab-201'
),
'ENSDART00000148019' => array(
'start' => '21190581',
'end' => '21261337',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo7ab-001'
),
'ENSDART00000108701' => array(
'start' => '21263835',
'end' => '21274181',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4 (3 of 3)-201'
),
'ENSDART00000142100' => array(
'start' => '21265123',
'end' => '21276995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4 (3 of 3)-001'
),
'ENST00000409619' => array(
'start' => '77128302',
'end' => '77214954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-009'
),
'ENST00000409709' => array(
'start' => '77128264',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-001'
),
'ENST00000409893' => array(
'start' => '77128270',
'end' => '77184996',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-005'
),
'ENST00000458169' => array(
'start' => '77179825',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-010'
),
'ENST00000458637' => array(
'start' => '77128270',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-002'
),
'ENST00000467137' => array(
'start' => '77184686',
'end' => '77191187',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-007'
),
'ENST00000481328' => array(
'start' => '77179825',
'end' => '77215238',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-003'
),
'ENST00000481532' => array(
'start' => '77212535',
'end' => '77213918',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-008'
),
'ENST00000526863' => array(
'start' => '77210887',
'end' => '77212975',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO7A-011'
),
'ENST00000605744' => array(
'start' => '77203186',
'end' => '77215239',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO7A-004'
),
'ENST00000620575' => array(
'start' => '77128270',
'end' => '77184989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-201'
),
'ENST00000315938' => array(
'start' => '77216558',
'end' => '77287418',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4-001'
),
'ENST00000376217' => array(
'start' => '77216558',
'end' => '77287418',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4-002'
),
'ENST00000527489' => array(
'start' => '77271356',
'end' => '77301649',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GDPD4-005'
),
'ENST00000532155' => array(
'start' => '77270920',
'end' => '77301687',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GDPD4-003'
),
'ENST00000532907' => array(
'start' => '77216862',
'end' => '77224302',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GDPD4-006'
),
'ENST00000534245' => array(
'start' => '77286923',
'end' => '77301666',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GDPD4-004'
)
)
$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_0001JF_0001' => array(
'genes_in_region' => array(
'ENSDARG00000044632' => array(
[maximum depth reached]
),
'ENSDARG00000079293' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Brain',
(int) 3 => 'Heart',
(int) 4 => 'Muscle',
(int) 5 => 'Heart',
(int) 6 => 'Muscle',
(int) 7 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0001JF_0002',
'tax_id' => '9606',
'chromosome' => '11',
'seq_start' => '77128264',
'seq_end' => '77301687',
'region_length' => '173423',
'region_type' => 'CGP',
'el_id' => 'ENSG00000137474-ENSG00000178795'
)
)
$gene_el = array(
'ENSDART00000108701' => array(
'Heart' => array(
'average_FPKM' => '0.983',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.156',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000142100' => array(
'Heart' => array(
'average_FPKM' => '1.590',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000079293'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '1.590',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000142100'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0001JF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000044632' => 'myosin VIIAb',
'ENSDARG00000079293' => 'glycerophosphodiester phosphodiesterase domain containing 4',
'ENSG00000137474' => 'myosin VIIA',
'ENSG00000178795' => 'glycerophosphodiester phosphodiesterase domain containing 4'
),
'gene_name_arr' => array(
'ENSDARG00000044632' => 'myo7ab',
'ENSDARG00000079293' => 'GDPD4 (3 of 3)',
'ENSG00000137474' => 'MYO7A',
'ENSG00000178795' => 'GDPD4'
),
'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) 2 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 7 => 'Brain',
(int) 13 => 'Breast',
(int) 17 => 'Colon',
(int) 19 => 'Heart',
(int) 26 => 'Kidney',
(int) 30 => 'Liver',
(int) 33 => 'Lung',
(int) 37 => 'Muscle',
(int) 41 => 'Ovary',
(int) 46 => 'Placenta',
(int) 51 => '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) 21,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000003181' => array(
'start' => '21189835',
'end' => '21261331',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo7ab-201'
),
'ENSDART00000148019' => array(
'start' => '21190581',
'end' => '21261337',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo7ab-001'
),
'ENSDART00000108701' => array(
'start' => '21263835',
'end' => '21274181',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4 (3 of 3)-201'
),
'ENSDART00000142100' => array(
'start' => '21265123',
'end' => '21276995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4 (3 of 3)-001'
),
'ENST00000409619' => array(
'start' => '77128302',
'end' => '77214954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-009'
),
'ENST00000409709' => array(
'start' => '77128264',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-001'
),
'ENST00000409893' => array(
'start' => '77128270',
'end' => '77184996',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-005'
),
'ENST00000458169' => array(
'start' => '77179825',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-010'
),
'ENST00000458637' => array(
'start' => '77128270',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-002'
),
'ENST00000467137' => array(
'start' => '77184686',
'end' => '77191187',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-007'
),
'ENST00000481328' => array(
'start' => '77179825',
'end' => '77215238',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-003'
),
'ENST00000481532' => array(
'start' => '77212535',
'end' => '77213918',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-008'
),
'ENST00000526863' => array(
'start' => '77210887',
'end' => '77212975',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO7A-011'
),
'ENST00000605744' => array(
'start' => '77203186',
'end' => '77215239',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO7A-004'
),
'ENST00000620575' => array(
'start' => '77128270',
'end' => '77184989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-201'
),
'ENST00000315938' => array(
'start' => '77216558',
'end' => '77287418',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4-001'
),
'ENST00000376217' => array(
'start' => '77216558',
'end' => '77287418',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4-002'
),
'ENST00000527489' => array(
'start' => '77271356',
'end' => '77301649',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GDPD4-005'
),
'ENST00000532155' => array(
'start' => '77270920',
'end' => '77301687',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GDPD4-003'
),
'ENST00000532907' => array(
'start' => '77216862',
'end' => '77224302',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GDPD4-006'
),
'ENST00000534245' => array(
'start' => '77286923',
'end' => '77301666',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GDPD4-004'
)
),
'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_0001JF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0001JF_0001' => array(
'genes_in_region' => array(
'ENSDARG00000044632' => array(
[maximum depth reached]
),
'ENSDARG00000079293' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Brain',
(int) 3 => 'Heart',
(int) 4 => 'Muscle',
(int) 5 => 'Heart',
(int) 6 => 'Muscle',
(int) 7 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000044632' => 'myosin VIIAb',
'ENSDARG00000079293' => 'glycerophosphodiester phosphodiesterase domain containing 4',
'ENSG00000137474' => 'myosin VIIA',
'ENSG00000178795' => 'glycerophosphodiester phosphodiesterase domain containing 4'
)
$gene_name_arr = array(
'ENSDARG00000044632' => 'myo7ab',
'ENSDARG00000079293' => 'GDPD4 (3 of 3)',
'ENSG00000137474' => 'MYO7A',
'ENSG00000178795' => 'GDPD4'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0001JF_0001',
'tax_id' => '7955',
'chromosome' => '21',
'seq_start' => '21189835',
'seq_end' => '21276995',
'region_length' => '87160',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000044632-ENSDARG00000079293'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0001JF_0002',
'tax_id' => '9606',
'chromosome' => '11',
'seq_start' => '77128264',
'seq_end' => '77301687',
'region_length' => '173423',
'region_type' => 'CGP',
'el_id' => 'ENSG00000137474-ENSG00000178795'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 7 => 'Brain',
(int) 13 => 'Breast',
(int) 17 => 'Colon',
(int) 19 => 'Heart',
(int) 26 => 'Kidney',
(int) 30 => 'Liver',
(int) 33 => 'Lung',
(int) 37 => 'Muscle',
(int) 41 => 'Ovary',
(int) 46 => 'Placenta',
(int) 51 => '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) 21
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000003181' => array(
'start' => '21189835',
'end' => '21261331',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo7ab-201'
),
'ENSDART00000148019' => array(
'start' => '21190581',
'end' => '21261337',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo7ab-001'
),
'ENSDART00000108701' => array(
'start' => '21263835',
'end' => '21274181',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4 (3 of 3)-201'
),
'ENSDART00000142100' => array(
'start' => '21265123',
'end' => '21276995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4 (3 of 3)-001'
),
'ENST00000409619' => array(
'start' => '77128302',
'end' => '77214954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-009'
),
'ENST00000409709' => array(
'start' => '77128264',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-001'
),
'ENST00000409893' => array(
'start' => '77128270',
'end' => '77184996',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-005'
),
'ENST00000458169' => array(
'start' => '77179825',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-010'
),
'ENST00000458637' => array(
'start' => '77128270',
'end' => '77215238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-002'
),
'ENST00000467137' => array(
'start' => '77184686',
'end' => '77191187',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-007'
),
'ENST00000481328' => array(
'start' => '77179825',
'end' => '77215238',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-003'
),
'ENST00000481532' => array(
'start' => '77212535',
'end' => '77213918',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO7A-008'
),
'ENST00000526863' => array(
'start' => '77210887',
'end' => '77212975',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO7A-011'
),
'ENST00000605744' => array(
'start' => '77203186',
'end' => '77215239',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO7A-004'
),
'ENST00000620575' => array(
'start' => '77128270',
'end' => '77184989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO7A-201'
),
'ENST00000315938' => array(
'start' => '77216558',
'end' => '77287418',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4-001'
),
'ENST00000376217' => array(
'start' => '77216558',
'end' => '77287418',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GDPD4-002'
),
'ENST00000527489' => array(
'start' => '77271356',
'end' => '77301649',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GDPD4-005'
),
'ENST00000532155' => array(
'start' => '77270920',
'end' => '77301687',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GDPD4-003'
),
'ENST00000532907' => array(
'start' => '77216862',
'end' => '77224302',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GDPD4-006'
),
'ENST00000534245' => array(
'start' => '77286923',
'end' => '77301666',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GDPD4-004'
)
)
$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_0001JF_0001' => array(
'genes_in_region' => array(
'ENSDARG00000044632' => array(
[maximum depth reached]
),
'ENSDARG00000079293' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Brain',
(int) 3 => 'Heart',
(int) 4 => 'Muscle',
(int) 5 => 'Heart',
(int) 6 => 'Muscle',
(int) 7 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0001JF_0002',
'tax_id' => '9606',
'chromosome' => '11',
'seq_start' => '77128264',
'seq_end' => '77301687',
'region_length' => '173423',
'region_type' => 'CGP',
'el_id' => 'ENSG00000137474-ENSG00000178795'
)
)
$gene_el = array(
'ENSDART00000108701' => array(
'Heart' => array(
'average_FPKM' => '0.983',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.156',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000142100' => array(
'Heart' => array(
'average_FPKM' => '1.590',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000079293'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '1.590',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000142100'
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
(myo7ab)