| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000001472-ENSMUSG00000074037 |
CGP |
10090 |
8:123373824-123410742  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0006AO_0003 [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_0006AO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000020237' => 'melanocortin 1 receptor',
'ENSDARG00000040861' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000141002' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000198211' => 'tubulin, beta 3 class III',
'ENSG00000258839' => 'melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)',
'ENSG00000259006' => null,
'ENSG00000267048' => null,
'ENSMUSG00000001472' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSMUSG00000074037' => 'melanocortin 1 receptor'
),
'gene_name_arr' => array(
'ENSDARG00000020237' => 'mc1r',
'ENSDARG00000040861' => 'tcf25',
'ENSG00000141002' => 'TCF25',
'ENSG00000198211' => 'TUBB3',
'ENSG00000258839' => 'MC1R',
'ENSG00000259006' => 'RP11-566K11.4',
'ENSG00000267048' => 'RP11-566K11.7',
'ENSMUSG00000001472' => 'Tcf25',
'ENSMUSG00000074037' => 'Mc1r'
),
'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]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 8 => 'Breast',
(int) 11 => 'Colon',
(int) 14 => 'Heart',
(int) 20 => 'Kidney',
(int) 26 => 'Liver',
(int) 30 => 'Lung',
(int) 34 => 'Muscle',
(int) 37 => 'Ovary',
(int) 40 => 'Placenta',
(int) 43 => '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) 39,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000003210' => array(
'start' => '31115011',
'end' => '31116338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mc1r-001'
),
'ENSDART00000059893' => array(
'start' => '31006046',
'end' => '31095381',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tcf25-201'
),
'ENSDART00000138403' => array(
'start' => '31005946',
'end' => '31095255',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tcf25-002'
),
'ENSDART00000148746' => array(
'start' => '31077680',
'end' => '31095196',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'tcf25-006'
),
'ENSDART00000149331' => array(
'start' => '31040528',
'end' => '31041330',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'tcf25-005'
),
'ENST00000263346' => array(
'start' => '89873612',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-001'
),
'ENST00000263347' => array(
'start' => '89873586',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-201'
),
'ENST00000561585' => array(
'start' => '89873592',
'end' => '89884063',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-002'
),
'ENST00000561958' => array(
'start' => '89873606',
'end' => '89893767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-012'
),
'ENST00000562184' => array(
'start' => '89894956',
'end' => '89900793',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-017'
),
'ENST00000562193' => array(
'start' => '89898601',
'end' => '89904975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-023'
),
'ENST00000562256' => array(
'start' => '89884644',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-004'
),
'ENST00000563032' => array(
'start' => '89873643',
'end' => '89874855',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-009'
),
'ENST00000563406' => array(
'start' => '89874550',
'end' => '89884613',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-010'
),
'ENST00000563484' => array(
'start' => '89905009',
'end' => '89909174',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-021'
),
'ENST00000563636' => array(
'start' => '89895115',
'end' => '89901039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-018'
),
'ENST00000564652' => array(
'start' => '89873644',
'end' => '89892247',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TCF25-008'
),
'ENST00000564957' => array(
'start' => '89909840',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-024'
),
'ENST00000565196' => array(
'start' => '89873644',
'end' => '89892275',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-011'
),
'ENST00000565404' => array(
'start' => '89883394',
'end' => '89886130',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-013'
),
'ENST00000565860' => array(
'start' => '89910293',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-026'
),
'ENST00000566158' => array(
'start' => '89895990',
'end' => '89898835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-019'
),
'ENST00000566283' => array(
'start' => '89908966',
'end' => '89911379',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-025'
),
'ENST00000566751' => array(
'start' => '89884642',
'end' => '89895137',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-015'
),
'ENST00000567171' => array(
'start' => '89909428',
'end' => '89911378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-007'
),
'ENST00000568409' => array(
'start' => '89887649',
'end' => '89904183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-016'
),
'ENST00000568412' => array(
'start' => '89873668',
'end' => '89896083',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-014'
),
'ENST00000568870' => array(
'start' => '89892193',
'end' => '89893907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-020'
),
'ENST00000570116' => array(
'start' => '89895990',
'end' => '89911350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-005'
),
'ENST00000614813' => array(
'start' => '89873641',
'end' => '89890633',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-027'
),
'ENST00000556922' => array(
'start' => '89919165',
'end' => '89936092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TUBB3-001'
),
'ENST00000539976' => array(
'start' => '89912119',
'end' => '89915168',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MC1R-003'
),
'ENST00000555147' => array(
'start' => '89917879',
'end' => '89920977',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MC1R-001'
),
'ENST00000555427' => array(
'start' => '89913418',
'end' => '89920973',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MC1R-002'
),
'ENST00000554623' => array(
'start' => '89919827',
'end' => '89922662',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-566K11.4-001'
),
'ENST00000570217' => array(
'start' => '89906157',
'end' => '89918233',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RP11-566K11.7-001'
),
'ENSMUST00000057934' => array(
'start' => '123373824',
'end' => '123401892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-201'
),
'ENSMUST00000108840' => array(
'start' => '123373835',
'end' => '123404173',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-202'
),
'ENSMUST00000098324' => array(
'start' => '123407082',
'end' => '123410742',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mc1r-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_0006AO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0006AO_0001' => array(
'genes_in_region' => array(
'ENSDARG00000020237' => array(
[maximum depth reached]
),
'ENSDARG00000040861' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Brain',
(int) 3 => 'Kidney',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney'
)
),
'CIL_0006AO_0002' => array(
'genes_in_region' => array(
'ENSG00000141002' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Heart',
(int) 14 => 'Lung',
(int) 15 => 'Heart',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Placenta',
(int) 34 => 'Breast'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000020237' => 'melanocortin 1 receptor',
'ENSDARG00000040861' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000141002' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000198211' => 'tubulin, beta 3 class III',
'ENSG00000258839' => 'melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)',
'ENSG00000259006' => null,
'ENSG00000267048' => null,
'ENSMUSG00000001472' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSMUSG00000074037' => 'melanocortin 1 receptor'
)
$gene_name_arr = array(
'ENSDARG00000020237' => 'mc1r',
'ENSDARG00000040861' => 'tcf25',
'ENSG00000141002' => 'TCF25',
'ENSG00000198211' => 'TUBB3',
'ENSG00000258839' => 'MC1R',
'ENSG00000259006' => 'RP11-566K11.4',
'ENSG00000267048' => 'RP11-566K11.7',
'ENSMUSG00000001472' => 'Tcf25',
'ENSMUSG00000074037' => 'Mc1r'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AO_0001',
'tax_id' => '7955',
'chromosome' => '18',
'seq_start' => '31005946',
'seq_end' => '31116338',
'region_length' => '110392',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000040861-ENSDARG00000020237'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AO_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89873586',
'seq_end' => '89920977',
'region_length' => '47391',
'region_type' => 'CGP',
'el_id' => 'ENSG00000141002-ENSG00000258839'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AO_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123373824',
'seq_end' => '123410742',
'region_length' => '36918',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001472-ENSMUSG00000074037'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 8 => 'Breast',
(int) 11 => 'Colon',
(int) 14 => 'Heart',
(int) 20 => 'Kidney',
(int) 26 => 'Liver',
(int) 30 => 'Lung',
(int) 34 => 'Muscle',
(int) 37 => 'Ovary',
(int) 40 => 'Placenta',
(int) 43 => '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) 39
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000003210' => array(
'start' => '31115011',
'end' => '31116338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mc1r-001'
),
'ENSDART00000059893' => array(
'start' => '31006046',
'end' => '31095381',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tcf25-201'
),
'ENSDART00000138403' => array(
'start' => '31005946',
'end' => '31095255',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tcf25-002'
),
'ENSDART00000148746' => array(
'start' => '31077680',
'end' => '31095196',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'tcf25-006'
),
'ENSDART00000149331' => array(
'start' => '31040528',
'end' => '31041330',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'tcf25-005'
),
'ENST00000263346' => array(
'start' => '89873612',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-001'
),
'ENST00000263347' => array(
'start' => '89873586',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-201'
),
'ENST00000561585' => array(
'start' => '89873592',
'end' => '89884063',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-002'
),
'ENST00000561958' => array(
'start' => '89873606',
'end' => '89893767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-012'
),
'ENST00000562184' => array(
'start' => '89894956',
'end' => '89900793',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-017'
),
'ENST00000562193' => array(
'start' => '89898601',
'end' => '89904975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-023'
),
'ENST00000562256' => array(
'start' => '89884644',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-004'
),
'ENST00000563032' => array(
'start' => '89873643',
'end' => '89874855',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-009'
),
'ENST00000563406' => array(
'start' => '89874550',
'end' => '89884613',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-010'
),
'ENST00000563484' => array(
'start' => '89905009',
'end' => '89909174',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-021'
),
'ENST00000563636' => array(
'start' => '89895115',
'end' => '89901039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-018'
),
'ENST00000564652' => array(
'start' => '89873644',
'end' => '89892247',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TCF25-008'
),
'ENST00000564957' => array(
'start' => '89909840',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-024'
),
'ENST00000565196' => array(
'start' => '89873644',
'end' => '89892275',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-011'
),
'ENST00000565404' => array(
'start' => '89883394',
'end' => '89886130',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-013'
),
'ENST00000565860' => array(
'start' => '89910293',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-026'
),
'ENST00000566158' => array(
'start' => '89895990',
'end' => '89898835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-019'
),
'ENST00000566283' => array(
'start' => '89908966',
'end' => '89911379',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-025'
),
'ENST00000566751' => array(
'start' => '89884642',
'end' => '89895137',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-015'
),
'ENST00000567171' => array(
'start' => '89909428',
'end' => '89911378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-007'
),
'ENST00000568409' => array(
'start' => '89887649',
'end' => '89904183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-016'
),
'ENST00000568412' => array(
'start' => '89873668',
'end' => '89896083',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-014'
),
'ENST00000568870' => array(
'start' => '89892193',
'end' => '89893907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-020'
),
'ENST00000570116' => array(
'start' => '89895990',
'end' => '89911350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-005'
),
'ENST00000614813' => array(
'start' => '89873641',
'end' => '89890633',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-027'
),
'ENST00000556922' => array(
'start' => '89919165',
'end' => '89936092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TUBB3-001'
),
'ENST00000539976' => array(
'start' => '89912119',
'end' => '89915168',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MC1R-003'
),
'ENST00000555147' => array(
'start' => '89917879',
'end' => '89920977',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MC1R-001'
),
'ENST00000555427' => array(
'start' => '89913418',
'end' => '89920973',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MC1R-002'
),
'ENST00000554623' => array(
'start' => '89919827',
'end' => '89922662',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-566K11.4-001'
),
'ENST00000570217' => array(
'start' => '89906157',
'end' => '89918233',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RP11-566K11.7-001'
),
'ENSMUST00000057934' => array(
'start' => '123373824',
'end' => '123401892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-201'
),
'ENSMUST00000108840' => array(
'start' => '123373835',
'end' => '123404173',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-202'
),
'ENSMUST00000098324' => array(
'start' => '123407082',
'end' => '123410742',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mc1r-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_0006AO_0001' => array(
'genes_in_region' => array(
'ENSDARG00000020237' => array(
[maximum depth reached]
),
'ENSDARG00000040861' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Brain',
(int) 3 => 'Kidney',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney'
)
),
'CIL_0006AO_0002' => array(
'genes_in_region' => array(
'ENSG00000141002' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Heart',
(int) 14 => 'Lung',
(int) 15 => 'Heart',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Placenta',
(int) 34 => 'Breast'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AO_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123373824',
'seq_end' => '123410742',
'region_length' => '36918',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001472-ENSMUSG00000074037'
)
)
$gene_el = array(
'ENST00000263346' => array(
'Adipose' => array(
'average_FPKM' => '46.143',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '56.031',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '32.502',
'stddev_FPKM' => '23.07'
),
'Breast' => array(
'average_FPKM' => '51.269',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '13.994',
'stddev_FPKM' => '9.54'
),
'Heart' => array(
'average_FPKM' => '12.697',
'stddev_FPKM' => '11.73'
),
'Kidney' => array(
'average_FPKM' => '17.130',
'stddev_FPKM' => '13.61'
),
'Liver' => array(
'average_FPKM' => '11.167',
'stddev_FPKM' => '7.96'
),
'Lung' => array(
'average_FPKM' => '49.309',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '44.566',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '42.471',
'stddev_FPKM' => '39.56'
),
'Placenta' => array(
'average_FPKM' => '57.591',
'stddev_FPKM' => '12.08'
),
'Testis' => array(
'average_FPKM' => '47.123',
'stddev_FPKM' => '7.52'
)
),
'ENST00000263347' => array(
'Heart' => array(
'average_FPKM' => '0.750',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '2.367',
'stddev_FPKM' => '0.00'
)
),
'ENST00000561585' => array(),
'ENST00000561958' => array(
'Heart' => array(
'average_FPKM' => '2.819',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '13.869',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '5.764',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '3.996',
'stddev_FPKM' => '0.00'
)
),
'ENST00000562184' => array(),
'ENST00000562193' => array(),
'ENST00000562256' => array(
'Colon' => array(
'average_FPKM' => '14.630',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '16.324',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563032' => array(),
'ENST00000563406' => array(),
'ENST00000563484' => array(),
'ENST00000563636' => array(),
'ENST00000564652' => array(),
'ENST00000564957' => array(),
'ENST00000565196' => array(
'Bladder' => array(
'average_FPKM' => '22.641',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '15.855',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '4.755',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '23.923',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '1.415',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '15.987',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '3.888',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '15.205',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '8.042',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '7.348',
'stddev_FPKM' => '0.40'
),
'Placenta' => array(
'average_FPKM' => '35.656',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '72.323',
'stddev_FPKM' => '0.00'
)
),
'ENST00000565404' => array(
'Placenta' => array(
'average_FPKM' => '46.837',
'stddev_FPKM' => '0.00'
)
),
'ENST00000565860' => array(),
'ENST00000566158' => array(),
'ENST00000566283' => array(),
'ENST00000566751' => array(),
'ENST00000567171' => array(),
'ENST00000568409' => array(),
'ENST00000568412' => array(
'Breast' => array(
'average_FPKM' => '7.102',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568870' => array(),
'ENST00000570116' => array(),
'ENST00000614813' => array()
)
$gene_key = 'ENSG00000141002'
$is_first = false
$tran_el = array()
$tran_key = 'ENST00000614813'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0006AO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000020237' => 'melanocortin 1 receptor',
'ENSDARG00000040861' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000141002' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000198211' => 'tubulin, beta 3 class III',
'ENSG00000258839' => 'melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)',
'ENSG00000259006' => null,
'ENSG00000267048' => null,
'ENSMUSG00000001472' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSMUSG00000074037' => 'melanocortin 1 receptor'
),
'gene_name_arr' => array(
'ENSDARG00000020237' => 'mc1r',
'ENSDARG00000040861' => 'tcf25',
'ENSG00000141002' => 'TCF25',
'ENSG00000198211' => 'TUBB3',
'ENSG00000258839' => 'MC1R',
'ENSG00000259006' => 'RP11-566K11.4',
'ENSG00000267048' => 'RP11-566K11.7',
'ENSMUSG00000001472' => 'Tcf25',
'ENSMUSG00000074037' => 'Mc1r'
),
'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]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 8 => 'Breast',
(int) 11 => 'Colon',
(int) 14 => 'Heart',
(int) 20 => 'Kidney',
(int) 26 => 'Liver',
(int) 30 => 'Lung',
(int) 34 => 'Muscle',
(int) 37 => 'Ovary',
(int) 40 => 'Placenta',
(int) 43 => '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) 39,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000003210' => array(
'start' => '31115011',
'end' => '31116338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mc1r-001'
),
'ENSDART00000059893' => array(
'start' => '31006046',
'end' => '31095381',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tcf25-201'
),
'ENSDART00000138403' => array(
'start' => '31005946',
'end' => '31095255',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tcf25-002'
),
'ENSDART00000148746' => array(
'start' => '31077680',
'end' => '31095196',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'tcf25-006'
),
'ENSDART00000149331' => array(
'start' => '31040528',
'end' => '31041330',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'tcf25-005'
),
'ENST00000263346' => array(
'start' => '89873612',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-001'
),
'ENST00000263347' => array(
'start' => '89873586',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-201'
),
'ENST00000561585' => array(
'start' => '89873592',
'end' => '89884063',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-002'
),
'ENST00000561958' => array(
'start' => '89873606',
'end' => '89893767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-012'
),
'ENST00000562184' => array(
'start' => '89894956',
'end' => '89900793',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-017'
),
'ENST00000562193' => array(
'start' => '89898601',
'end' => '89904975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-023'
),
'ENST00000562256' => array(
'start' => '89884644',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-004'
),
'ENST00000563032' => array(
'start' => '89873643',
'end' => '89874855',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-009'
),
'ENST00000563406' => array(
'start' => '89874550',
'end' => '89884613',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-010'
),
'ENST00000563484' => array(
'start' => '89905009',
'end' => '89909174',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-021'
),
'ENST00000563636' => array(
'start' => '89895115',
'end' => '89901039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-018'
),
'ENST00000564652' => array(
'start' => '89873644',
'end' => '89892247',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TCF25-008'
),
'ENST00000564957' => array(
'start' => '89909840',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-024'
),
'ENST00000565196' => array(
'start' => '89873644',
'end' => '89892275',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-011'
),
'ENST00000565404' => array(
'start' => '89883394',
'end' => '89886130',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-013'
),
'ENST00000565860' => array(
'start' => '89910293',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-026'
),
'ENST00000566158' => array(
'start' => '89895990',
'end' => '89898835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-019'
),
'ENST00000566283' => array(
'start' => '89908966',
'end' => '89911379',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-025'
),
'ENST00000566751' => array(
'start' => '89884642',
'end' => '89895137',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-015'
),
'ENST00000567171' => array(
'start' => '89909428',
'end' => '89911378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-007'
),
'ENST00000568409' => array(
'start' => '89887649',
'end' => '89904183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-016'
),
'ENST00000568412' => array(
'start' => '89873668',
'end' => '89896083',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-014'
),
'ENST00000568870' => array(
'start' => '89892193',
'end' => '89893907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-020'
),
'ENST00000570116' => array(
'start' => '89895990',
'end' => '89911350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-005'
),
'ENST00000614813' => array(
'start' => '89873641',
'end' => '89890633',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-027'
),
'ENST00000556922' => array(
'start' => '89919165',
'end' => '89936092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TUBB3-001'
),
'ENST00000539976' => array(
'start' => '89912119',
'end' => '89915168',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MC1R-003'
),
'ENST00000555147' => array(
'start' => '89917879',
'end' => '89920977',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MC1R-001'
),
'ENST00000555427' => array(
'start' => '89913418',
'end' => '89920973',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MC1R-002'
),
'ENST00000554623' => array(
'start' => '89919827',
'end' => '89922662',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-566K11.4-001'
),
'ENST00000570217' => array(
'start' => '89906157',
'end' => '89918233',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RP11-566K11.7-001'
),
'ENSMUST00000057934' => array(
'start' => '123373824',
'end' => '123401892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-201'
),
'ENSMUST00000108840' => array(
'start' => '123373835',
'end' => '123404173',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-202'
),
'ENSMUST00000098324' => array(
'start' => '123407082',
'end' => '123410742',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mc1r-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_0006AO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0006AO_0001' => array(
'genes_in_region' => array(
'ENSDARG00000020237' => array(
[maximum depth reached]
),
'ENSDARG00000040861' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Brain',
(int) 3 => 'Kidney',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney'
)
),
'CIL_0006AO_0002' => array(
'genes_in_region' => array(
'ENSG00000141002' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Heart',
(int) 14 => 'Lung',
(int) 15 => 'Heart',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Placenta',
(int) 34 => 'Breast'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000020237' => 'melanocortin 1 receptor',
'ENSDARG00000040861' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000141002' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000198211' => 'tubulin, beta 3 class III',
'ENSG00000258839' => 'melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)',
'ENSG00000259006' => null,
'ENSG00000267048' => null,
'ENSMUSG00000001472' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSMUSG00000074037' => 'melanocortin 1 receptor'
)
$gene_name_arr = array(
'ENSDARG00000020237' => 'mc1r',
'ENSDARG00000040861' => 'tcf25',
'ENSG00000141002' => 'TCF25',
'ENSG00000198211' => 'TUBB3',
'ENSG00000258839' => 'MC1R',
'ENSG00000259006' => 'RP11-566K11.4',
'ENSG00000267048' => 'RP11-566K11.7',
'ENSMUSG00000001472' => 'Tcf25',
'ENSMUSG00000074037' => 'Mc1r'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AO_0001',
'tax_id' => '7955',
'chromosome' => '18',
'seq_start' => '31005946',
'seq_end' => '31116338',
'region_length' => '110392',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000040861-ENSDARG00000020237'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AO_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89873586',
'seq_end' => '89920977',
'region_length' => '47391',
'region_type' => 'CGP',
'el_id' => 'ENSG00000141002-ENSG00000258839'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AO_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123373824',
'seq_end' => '123410742',
'region_length' => '36918',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001472-ENSMUSG00000074037'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 8 => 'Breast',
(int) 11 => 'Colon',
(int) 14 => 'Heart',
(int) 20 => 'Kidney',
(int) 26 => 'Liver',
(int) 30 => 'Lung',
(int) 34 => 'Muscle',
(int) 37 => 'Ovary',
(int) 40 => 'Placenta',
(int) 43 => '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) 39
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000003210' => array(
'start' => '31115011',
'end' => '31116338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mc1r-001'
),
'ENSDART00000059893' => array(
'start' => '31006046',
'end' => '31095381',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tcf25-201'
),
'ENSDART00000138403' => array(
'start' => '31005946',
'end' => '31095255',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tcf25-002'
),
'ENSDART00000148746' => array(
'start' => '31077680',
'end' => '31095196',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'tcf25-006'
),
'ENSDART00000149331' => array(
'start' => '31040528',
'end' => '31041330',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'tcf25-005'
),
'ENST00000263346' => array(
'start' => '89873612',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-001'
),
'ENST00000263347' => array(
'start' => '89873586',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-201'
),
'ENST00000561585' => array(
'start' => '89873592',
'end' => '89884063',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-002'
),
'ENST00000561958' => array(
'start' => '89873606',
'end' => '89893767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-012'
),
'ENST00000562184' => array(
'start' => '89894956',
'end' => '89900793',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-017'
),
'ENST00000562193' => array(
'start' => '89898601',
'end' => '89904975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-023'
),
'ENST00000562256' => array(
'start' => '89884644',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-004'
),
'ENST00000563032' => array(
'start' => '89873643',
'end' => '89874855',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-009'
),
'ENST00000563406' => array(
'start' => '89874550',
'end' => '89884613',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-010'
),
'ENST00000563484' => array(
'start' => '89905009',
'end' => '89909174',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-021'
),
'ENST00000563636' => array(
'start' => '89895115',
'end' => '89901039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-018'
),
'ENST00000564652' => array(
'start' => '89873644',
'end' => '89892247',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TCF25-008'
),
'ENST00000564957' => array(
'start' => '89909840',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-024'
),
'ENST00000565196' => array(
'start' => '89873644',
'end' => '89892275',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-011'
),
'ENST00000565404' => array(
'start' => '89883394',
'end' => '89886130',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-013'
),
'ENST00000565860' => array(
'start' => '89910293',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-026'
),
'ENST00000566158' => array(
'start' => '89895990',
'end' => '89898835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-019'
),
'ENST00000566283' => array(
'start' => '89908966',
'end' => '89911379',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-025'
),
'ENST00000566751' => array(
'start' => '89884642',
'end' => '89895137',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-015'
),
'ENST00000567171' => array(
'start' => '89909428',
'end' => '89911378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-007'
),
'ENST00000568409' => array(
'start' => '89887649',
'end' => '89904183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-016'
),
'ENST00000568412' => array(
'start' => '89873668',
'end' => '89896083',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-014'
),
'ENST00000568870' => array(
'start' => '89892193',
'end' => '89893907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-020'
),
'ENST00000570116' => array(
'start' => '89895990',
'end' => '89911350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-005'
),
'ENST00000614813' => array(
'start' => '89873641',
'end' => '89890633',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-027'
),
'ENST00000556922' => array(
'start' => '89919165',
'end' => '89936092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TUBB3-001'
),
'ENST00000539976' => array(
'start' => '89912119',
'end' => '89915168',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MC1R-003'
),
'ENST00000555147' => array(
'start' => '89917879',
'end' => '89920977',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MC1R-001'
),
'ENST00000555427' => array(
'start' => '89913418',
'end' => '89920973',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MC1R-002'
),
'ENST00000554623' => array(
'start' => '89919827',
'end' => '89922662',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-566K11.4-001'
),
'ENST00000570217' => array(
'start' => '89906157',
'end' => '89918233',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RP11-566K11.7-001'
),
'ENSMUST00000057934' => array(
'start' => '123373824',
'end' => '123401892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-201'
),
'ENSMUST00000108840' => array(
'start' => '123373835',
'end' => '123404173',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-202'
),
'ENSMUST00000098324' => array(
'start' => '123407082',
'end' => '123410742',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mc1r-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_0006AO_0001' => array(
'genes_in_region' => array(
'ENSDARG00000020237' => array(
[maximum depth reached]
),
'ENSDARG00000040861' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Brain',
(int) 3 => 'Kidney',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney'
)
),
'CIL_0006AO_0002' => array(
'genes_in_region' => array(
'ENSG00000141002' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Heart',
(int) 14 => 'Lung',
(int) 15 => 'Heart',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Placenta',
(int) 34 => 'Breast'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AO_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123373824',
'seq_end' => '123410742',
'region_length' => '36918',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001472-ENSMUSG00000074037'
)
)
$gene_el = array(
'ENST00000263346' => array(
'Adipose' => array(
'average_FPKM' => '46.143',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '56.031',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '32.502',
'stddev_FPKM' => '23.07'
),
'Breast' => array(
'average_FPKM' => '51.269',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '13.994',
'stddev_FPKM' => '9.54'
),
'Heart' => array(
'average_FPKM' => '12.697',
'stddev_FPKM' => '11.73'
),
'Kidney' => array(
'average_FPKM' => '17.130',
'stddev_FPKM' => '13.61'
),
'Liver' => array(
'average_FPKM' => '11.167',
'stddev_FPKM' => '7.96'
),
'Lung' => array(
'average_FPKM' => '49.309',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '44.566',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '42.471',
'stddev_FPKM' => '39.56'
),
'Placenta' => array(
'average_FPKM' => '57.591',
'stddev_FPKM' => '12.08'
),
'Testis' => array(
'average_FPKM' => '47.123',
'stddev_FPKM' => '7.52'
)
),
'ENST00000263347' => array(
'Heart' => array(
'average_FPKM' => '0.750',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '2.367',
'stddev_FPKM' => '0.00'
)
),
'ENST00000561585' => array(),
'ENST00000561958' => array(
'Heart' => array(
'average_FPKM' => '2.819',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '13.869',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '5.764',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '3.996',
'stddev_FPKM' => '0.00'
)
),
'ENST00000562184' => array(),
'ENST00000562193' => array(),
'ENST00000562256' => array(
'Colon' => array(
'average_FPKM' => '14.630',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '16.324',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563032' => array(),
'ENST00000563406' => array(),
'ENST00000563484' => array(),
'ENST00000563636' => array(),
'ENST00000564652' => array(),
'ENST00000564957' => array(),
'ENST00000565196' => array(
'Bladder' => array(
'average_FPKM' => '22.641',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '15.855',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '4.755',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '23.923',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '1.415',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '15.987',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '3.888',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '15.205',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '8.042',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '7.348',
'stddev_FPKM' => '0.40'
),
'Placenta' => array(
'average_FPKM' => '35.656',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '72.323',
'stddev_FPKM' => '0.00'
)
),
'ENST00000565404' => array(
'Placenta' => array(
'average_FPKM' => '46.837',
'stddev_FPKM' => '0.00'
)
),
'ENST00000565860' => array(),
'ENST00000566158' => array(),
'ENST00000566283' => array(),
'ENST00000566751' => array(),
'ENST00000567171' => array(),
'ENST00000568409' => array(),
'ENST00000568412' => array(
'Breast' => array(
'average_FPKM' => '7.102',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568870' => array(),
'ENST00000570116' => array(),
'ENST00000614813' => array()
)
$gene_key = 'ENSG00000141002'
$is_first = false
$tran_el = array()
$tran_key = 'ENST00000614813'
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
(mc1r)