| Source ID |
Type |
Tax ID |
Position |
| TOX |
UCNEbase |
7955 |
Zv9_NA363:10903-11223  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007OA_0004 [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_0007OA_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OA_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OA_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000167912' => null,
'ENSG00000198846' => 'thymocyte selection-associated high mobility group box',
'ENSG00000201231' => 'RNA, U4 small nuclear 50, pseudogene',
'ENSG00000201763' => 'RNA, 5S ribosomal pseudogene 267',
'ENSG00000206853' => 'Small nucleolar RNA SNORA51',
'ENSG00000253260' => null,
'ENSG00000253413' => null,
'ENSG00000253723' => null,
'ENSG00000253879' => null,
'ENSG00000254048' => null,
'ENSG00000254150' => null,
'ENSG00000254775' => null,
'ENSG00000278428' => null,
'ENSMUSG00000041272' => 'thymocyte selection-associated high mobility group box',
'ENSMUSG00000082024' => 'predicted gene 11794',
'ENSMUSG00000083023' => 'predicted gene 11804',
'ENSMUSG00000085630' => 'predicted gene 11795',
'ENSMUSG00000086052' => 'predicted gene 11802',
'ENSMUSG00000086070' => 'RIKEN cDNA 8430436N08 gene',
'ENSMUSG00000094771' => 'predicted gene, 23860',
'ENSDARG00000032317' => 'thymocyte selection-associated high mobility group box'
),
'gene_name_arr' => array(
'ENSG00000167912' => 'RP11-25K19.1',
'ENSG00000198846' => 'TOX',
'ENSG00000201231' => 'RNU4-50P',
'ENSG00000201763' => 'RNA5SP267',
'ENSG00000206853' => 'SNORA51',
'ENSG00000253260' => 'RP11-379I19.1',
'ENSG00000253413' => 'RP11-960H2.2',
'ENSG00000253723' => 'RP11-960H2.1',
'ENSG00000253879' => 'RP11-379I19.3',
'ENSG00000254048' => 'RP11-328K2.1',
'ENSG00000254150' => 'RP11-379I19.2',
'ENSG00000254775' => 'RP11-27P7.1',
'ENSG00000278428' => 'RP11-88H1.1',
'ENSMUSG00000041272' => 'Tox',
'ENSMUSG00000082024' => 'Gm11794',
'ENSMUSG00000083023' => 'Gm11804',
'ENSMUSG00000085630' => 'Gm11795',
'ENSMUSG00000086052' => 'Gm11802',
'ENSMUSG00000086070' => '8430436N08Rik',
'ENSMUSG00000094771' => 'Gm23860',
'ENSDARG00000032317' => 'tox'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 13 => 'Brain',
(int) 22 => 'Breast',
(int) 27 => 'Colon',
(int) 32 => 'Heart',
(int) 37 => 'Kidney',
(int) 42 => 'Liver',
(int) 49 => 'Lung',
(int) 52 => 'Muscle',
(int) 59 => 'Ovary',
(int) 65 => 'Placenta',
(int) 71 => '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) 29,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000517898' => array(
'start' => '59119946',
'end' => '59121315',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-002'
),
'ENST00000518993' => array(
'start' => '59119218',
'end' => '59121346',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-001'
),
'ENST00000523683' => array(
'start' => '59119040',
'end' => '59120031',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-003'
),
'ENST00000361421' => array(
'start' => '58805418',
'end' => '59119208',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TOX-001'
),
'ENST00000364361' => array(
'start' => '58814412',
'end' => '58814552',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU4-50P-201'
),
'ENST00000364893' => array(
'start' => '59455885',
'end' => '59456010',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP267-201'
),
'ENST00000384126' => array(
'start' => '59137372',
'end' => '59137502',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORA51.1-205'
),
'ENST00000521456' => array(
'start' => '59561327',
'end' => '59593701',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.1-001'
),
'ENST00000522215' => array(
'start' => '59760047',
'end' => '59760263',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-960H2.2-001'
),
'ENST00000518653' => array(
'start' => '59821124',
'end' => '59821433',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-960H2.1-001'
),
'ENST00000521274' => array(
'start' => '59601404',
'end' => '59613775',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.3-002'
),
'ENST00000522898' => array(
'start' => '59601378',
'end' => '59607005',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.3-001'
),
'ENST00000518011' => array(
'start' => '58991720',
'end' => '58992938',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-328K2.1-001'
),
'ENST00000524110' => array(
'start' => '59557528',
'end' => '59557855',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-379I19.2-001'
),
'ENST00000531077' => array(
'start' => '60049587',
'end' => '60074715',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-27P7.1-001'
),
'ENST00000615967' => array(
'start' => '59893856',
'end' => '59893942',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'RP11-88H1.1-001'
),
'ENSMUST00000039987' => array(
'start' => '6686353',
'end' => '6990799',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tox-001'
),
'ENSMUST00000125974' => array(
'start' => '6688046',
'end' => '6689351',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tox-003'
),
'ENSMUST00000147657' => array(
'start' => '6740230',
'end' => '6991557',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tox-002'
),
'ENSMUST00000150082' => array(
'start' => '6820694',
'end' => '6990483',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tox-004'
),
'ENSMUST00000119446' => array(
'start' => '7763264',
'end' => '7763500',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11794-001'
),
'ENSMUST00000121663' => array(
'start' => '7039047',
'end' => '7039514',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11804-001'
),
'ENSMUST00000127180' => array(
'start' => '7759670',
'end' => '7763930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm11795-001'
),
'ENSMUST00000137749' => array(
'start' => '6688169',
'end' => '6704160',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm11802-001'
),
'ENSMUST00000129988' => array(
'start' => '7560688',
'end' => '7573801',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '8430436N08Rik-001'
),
'ENSMUST00000179446' => array(
'start' => '7820916',
'end' => '7821047',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23860-201'
),
'ENSDART00000044371' => array(
'start' => '21779436',
'end' => '21901778',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-001'
),
'ENSDART00000132039' => array(
'start' => '21839268',
'end' => '21867729',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-002'
),
'ENSDART00000134912' => array(
'start' => '21779508',
'end' => '21867594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-003'
)
),
'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_0007OA_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OA_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OA_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007OA_0001' => array(
'genes_in_region' => array(
'ENSG00000167912' => array(
[maximum depth reached]
),
'ENSG00000198846' => array(
[maximum depth reached]
),
'ENSG00000253260' => array(
[maximum depth reached]
),
'ENSG00000253413' => array(
[maximum depth reached]
),
'ENSG00000253879' => array(
[maximum depth reached]
),
'ENSG00000254048' => array(
[maximum depth reached]
),
'ENSG00000254775' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Liver',
(int) 2 => 'Ovary',
(int) 3 => 'Adrenal',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Colon',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Testis',
(int) 26 => 'Liver',
(int) 27 => 'Testis',
(int) 28 => 'Adrenal',
(int) 29 => 'Brain',
(int) 30 => 'Breast',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Testis',
(int) 35 => 'Brain',
(int) 36 => 'Ovary',
(int) 37 => 'Testis',
(int) 38 => 'Testis'
)
),
'CIL_0007OA_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000041272' => array(
[maximum depth reached]
),
'ENSMUSG00000082024' => array(
[maximum depth reached]
),
'ENSMUSG00000083023' => array(
[maximum depth reached]
),
'ENSMUSG00000085630' => array(
[maximum depth reached]
),
'ENSMUSG00000086052' => array(
[maximum depth reached]
),
'ENSMUSG00000086070' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Muscle',
(int) 15 => 'Testis',
(int) 16 => 'Muscle',
(int) 17 => 'Brain',
(int) 18 => 'Liver',
(int) 19 => 'Muscle',
(int) 20 => 'Brain',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Breast',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta',
(int) 38 => 'Testis'
)
),
'CIL_0007OA_0003' => array(
'genes_in_region' => array(
'ENSDARG00000032317' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Muscle',
(int) 4 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSG00000167912' => null,
'ENSG00000198846' => 'thymocyte selection-associated high mobility group box',
'ENSG00000201231' => 'RNA, U4 small nuclear 50, pseudogene',
'ENSG00000201763' => 'RNA, 5S ribosomal pseudogene 267',
'ENSG00000206853' => 'Small nucleolar RNA SNORA51',
'ENSG00000253260' => null,
'ENSG00000253413' => null,
'ENSG00000253723' => null,
'ENSG00000253879' => null,
'ENSG00000254048' => null,
'ENSG00000254150' => null,
'ENSG00000254775' => null,
'ENSG00000278428' => null,
'ENSMUSG00000041272' => 'thymocyte selection-associated high mobility group box',
'ENSMUSG00000082024' => 'predicted gene 11794',
'ENSMUSG00000083023' => 'predicted gene 11804',
'ENSMUSG00000085630' => 'predicted gene 11795',
'ENSMUSG00000086052' => 'predicted gene 11802',
'ENSMUSG00000086070' => 'RIKEN cDNA 8430436N08 gene',
'ENSMUSG00000094771' => 'predicted gene, 23860',
'ENSDARG00000032317' => 'thymocyte selection-associated high mobility group box'
)
$gene_name_arr = array(
'ENSG00000167912' => 'RP11-25K19.1',
'ENSG00000198846' => 'TOX',
'ENSG00000201231' => 'RNU4-50P',
'ENSG00000201763' => 'RNA5SP267',
'ENSG00000206853' => 'SNORA51',
'ENSG00000253260' => 'RP11-379I19.1',
'ENSG00000253413' => 'RP11-960H2.2',
'ENSG00000253723' => 'RP11-960H2.1',
'ENSG00000253879' => 'RP11-379I19.3',
'ENSG00000254048' => 'RP11-328K2.1',
'ENSG00000254150' => 'RP11-379I19.2',
'ENSG00000254775' => 'RP11-27P7.1',
'ENSG00000278428' => 'RP11-88H1.1',
'ENSMUSG00000041272' => 'Tox',
'ENSMUSG00000082024' => 'Gm11794',
'ENSMUSG00000083023' => 'Gm11804',
'ENSMUSG00000085630' => 'Gm11795',
'ENSMUSG00000086052' => 'Gm11802',
'ENSMUSG00000086070' => '8430436N08Rik',
'ENSMUSG00000094771' => 'Gm23860',
'ENSDARG00000032317' => 'tox'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0001',
'tax_id' => '9606',
'chromosome' => '8',
'seq_start' => '58807160',
'seq_end' => '60051085',
'region_length' => '1243925',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0002',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '6687841',
'seq_end' => '7986858',
'region_length' => '1299017',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0003',
'tax_id' => '7955',
'chromosome' => '2',
'seq_start' => '21742702',
'seq_end' => '21892182',
'region_length' => '149480',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0004',
'tax_id' => '7955',
'chromosome' => 'Zv9_NA363',
'seq_start' => '10903',
'seq_end' => '11223',
'region_length' => '320',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 13 => 'Brain',
(int) 22 => 'Breast',
(int) 27 => 'Colon',
(int) 32 => 'Heart',
(int) 37 => 'Kidney',
(int) 42 => 'Liver',
(int) 49 => 'Lung',
(int) 52 => 'Muscle',
(int) 59 => 'Ovary',
(int) 65 => 'Placenta',
(int) 71 => '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) 29
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000517898' => array(
'start' => '59119946',
'end' => '59121315',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-002'
),
'ENST00000518993' => array(
'start' => '59119218',
'end' => '59121346',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-001'
),
'ENST00000523683' => array(
'start' => '59119040',
'end' => '59120031',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-003'
),
'ENST00000361421' => array(
'start' => '58805418',
'end' => '59119208',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TOX-001'
),
'ENST00000364361' => array(
'start' => '58814412',
'end' => '58814552',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU4-50P-201'
),
'ENST00000364893' => array(
'start' => '59455885',
'end' => '59456010',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP267-201'
),
'ENST00000384126' => array(
'start' => '59137372',
'end' => '59137502',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORA51.1-205'
),
'ENST00000521456' => array(
'start' => '59561327',
'end' => '59593701',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.1-001'
),
'ENST00000522215' => array(
'start' => '59760047',
'end' => '59760263',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-960H2.2-001'
),
'ENST00000518653' => array(
'start' => '59821124',
'end' => '59821433',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-960H2.1-001'
),
'ENST00000521274' => array(
'start' => '59601404',
'end' => '59613775',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.3-002'
),
'ENST00000522898' => array(
'start' => '59601378',
'end' => '59607005',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.3-001'
),
'ENST00000518011' => array(
'start' => '58991720',
'end' => '58992938',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-328K2.1-001'
),
'ENST00000524110' => array(
'start' => '59557528',
'end' => '59557855',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-379I19.2-001'
),
'ENST00000531077' => array(
'start' => '60049587',
'end' => '60074715',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-27P7.1-001'
),
'ENST00000615967' => array(
'start' => '59893856',
'end' => '59893942',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'RP11-88H1.1-001'
),
'ENSMUST00000039987' => array(
'start' => '6686353',
'end' => '6990799',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tox-001'
),
'ENSMUST00000125974' => array(
'start' => '6688046',
'end' => '6689351',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tox-003'
),
'ENSMUST00000147657' => array(
'start' => '6740230',
'end' => '6991557',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tox-002'
),
'ENSMUST00000150082' => array(
'start' => '6820694',
'end' => '6990483',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tox-004'
),
'ENSMUST00000119446' => array(
'start' => '7763264',
'end' => '7763500',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11794-001'
),
'ENSMUST00000121663' => array(
'start' => '7039047',
'end' => '7039514',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11804-001'
),
'ENSMUST00000127180' => array(
'start' => '7759670',
'end' => '7763930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm11795-001'
),
'ENSMUST00000137749' => array(
'start' => '6688169',
'end' => '6704160',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm11802-001'
),
'ENSMUST00000129988' => array(
'start' => '7560688',
'end' => '7573801',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '8430436N08Rik-001'
),
'ENSMUST00000179446' => array(
'start' => '7820916',
'end' => '7821047',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23860-201'
),
'ENSDART00000044371' => array(
'start' => '21779436',
'end' => '21901778',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-001'
),
'ENSDART00000132039' => array(
'start' => '21839268',
'end' => '21867729',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-002'
),
'ENSDART00000134912' => array(
'start' => '21779508',
'end' => '21867594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-003'
)
)
$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_0007OA_0001' => array(
'genes_in_region' => array(
'ENSG00000167912' => array(
[maximum depth reached]
),
'ENSG00000198846' => array(
[maximum depth reached]
),
'ENSG00000253260' => array(
[maximum depth reached]
),
'ENSG00000253413' => array(
[maximum depth reached]
),
'ENSG00000253879' => array(
[maximum depth reached]
),
'ENSG00000254048' => array(
[maximum depth reached]
),
'ENSG00000254775' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Liver',
(int) 2 => 'Ovary',
(int) 3 => 'Adrenal',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Colon',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Testis',
(int) 26 => 'Liver',
(int) 27 => 'Testis',
(int) 28 => 'Adrenal',
(int) 29 => 'Brain',
(int) 30 => 'Breast',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Testis',
(int) 35 => 'Brain',
(int) 36 => 'Ovary',
(int) 37 => 'Testis',
(int) 38 => 'Testis'
)
),
'CIL_0007OA_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000041272' => array(
[maximum depth reached]
),
'ENSMUSG00000082024' => array(
[maximum depth reached]
),
'ENSMUSG00000083023' => array(
[maximum depth reached]
),
'ENSMUSG00000085630' => array(
[maximum depth reached]
),
'ENSMUSG00000086052' => array(
[maximum depth reached]
),
'ENSMUSG00000086070' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Muscle',
(int) 15 => 'Testis',
(int) 16 => 'Muscle',
(int) 17 => 'Brain',
(int) 18 => 'Liver',
(int) 19 => 'Muscle',
(int) 20 => 'Brain',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Breast',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta',
(int) 38 => 'Testis'
)
),
'CIL_0007OA_0003' => array(
'genes_in_region' => array(
'ENSDARG00000032317' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Muscle',
(int) 4 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0004',
'tax_id' => '7955',
'chromosome' => 'Zv9_NA363',
'seq_start' => '10903',
'seq_end' => '11223',
'region_length' => '320',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
)
$gene_el = array(
'ENSDART00000044371' => array(
'Brain' => array(
'average_FPKM' => '16.373',
'stddev_FPKM' => '3.94'
),
'Heart' => array(
'average_FPKM' => '1.873',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.155',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.602',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000132039' => array(),
'ENSDART00000134912' => array(
'Heart' => array(
'average_FPKM' => '0.617',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000032317'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '0.617',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000134912'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007OA_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OA_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OA_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000167912' => null,
'ENSG00000198846' => 'thymocyte selection-associated high mobility group box',
'ENSG00000201231' => 'RNA, U4 small nuclear 50, pseudogene',
'ENSG00000201763' => 'RNA, 5S ribosomal pseudogene 267',
'ENSG00000206853' => 'Small nucleolar RNA SNORA51',
'ENSG00000253260' => null,
'ENSG00000253413' => null,
'ENSG00000253723' => null,
'ENSG00000253879' => null,
'ENSG00000254048' => null,
'ENSG00000254150' => null,
'ENSG00000254775' => null,
'ENSG00000278428' => null,
'ENSMUSG00000041272' => 'thymocyte selection-associated high mobility group box',
'ENSMUSG00000082024' => 'predicted gene 11794',
'ENSMUSG00000083023' => 'predicted gene 11804',
'ENSMUSG00000085630' => 'predicted gene 11795',
'ENSMUSG00000086052' => 'predicted gene 11802',
'ENSMUSG00000086070' => 'RIKEN cDNA 8430436N08 gene',
'ENSMUSG00000094771' => 'predicted gene, 23860',
'ENSDARG00000032317' => 'thymocyte selection-associated high mobility group box'
),
'gene_name_arr' => array(
'ENSG00000167912' => 'RP11-25K19.1',
'ENSG00000198846' => 'TOX',
'ENSG00000201231' => 'RNU4-50P',
'ENSG00000201763' => 'RNA5SP267',
'ENSG00000206853' => 'SNORA51',
'ENSG00000253260' => 'RP11-379I19.1',
'ENSG00000253413' => 'RP11-960H2.2',
'ENSG00000253723' => 'RP11-960H2.1',
'ENSG00000253879' => 'RP11-379I19.3',
'ENSG00000254048' => 'RP11-328K2.1',
'ENSG00000254150' => 'RP11-379I19.2',
'ENSG00000254775' => 'RP11-27P7.1',
'ENSG00000278428' => 'RP11-88H1.1',
'ENSMUSG00000041272' => 'Tox',
'ENSMUSG00000082024' => 'Gm11794',
'ENSMUSG00000083023' => 'Gm11804',
'ENSMUSG00000085630' => 'Gm11795',
'ENSMUSG00000086052' => 'Gm11802',
'ENSMUSG00000086070' => '8430436N08Rik',
'ENSMUSG00000094771' => 'Gm23860',
'ENSDARG00000032317' => 'tox'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 13 => 'Brain',
(int) 22 => 'Breast',
(int) 27 => 'Colon',
(int) 32 => 'Heart',
(int) 37 => 'Kidney',
(int) 42 => 'Liver',
(int) 49 => 'Lung',
(int) 52 => 'Muscle',
(int) 59 => 'Ovary',
(int) 65 => 'Placenta',
(int) 71 => '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) 29,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000517898' => array(
'start' => '59119946',
'end' => '59121315',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-002'
),
'ENST00000518993' => array(
'start' => '59119218',
'end' => '59121346',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-001'
),
'ENST00000523683' => array(
'start' => '59119040',
'end' => '59120031',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-003'
),
'ENST00000361421' => array(
'start' => '58805418',
'end' => '59119208',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TOX-001'
),
'ENST00000364361' => array(
'start' => '58814412',
'end' => '58814552',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU4-50P-201'
),
'ENST00000364893' => array(
'start' => '59455885',
'end' => '59456010',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP267-201'
),
'ENST00000384126' => array(
'start' => '59137372',
'end' => '59137502',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORA51.1-205'
),
'ENST00000521456' => array(
'start' => '59561327',
'end' => '59593701',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.1-001'
),
'ENST00000522215' => array(
'start' => '59760047',
'end' => '59760263',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-960H2.2-001'
),
'ENST00000518653' => array(
'start' => '59821124',
'end' => '59821433',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-960H2.1-001'
),
'ENST00000521274' => array(
'start' => '59601404',
'end' => '59613775',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.3-002'
),
'ENST00000522898' => array(
'start' => '59601378',
'end' => '59607005',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.3-001'
),
'ENST00000518011' => array(
'start' => '58991720',
'end' => '58992938',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-328K2.1-001'
),
'ENST00000524110' => array(
'start' => '59557528',
'end' => '59557855',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-379I19.2-001'
),
'ENST00000531077' => array(
'start' => '60049587',
'end' => '60074715',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-27P7.1-001'
),
'ENST00000615967' => array(
'start' => '59893856',
'end' => '59893942',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'RP11-88H1.1-001'
),
'ENSMUST00000039987' => array(
'start' => '6686353',
'end' => '6990799',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tox-001'
),
'ENSMUST00000125974' => array(
'start' => '6688046',
'end' => '6689351',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tox-003'
),
'ENSMUST00000147657' => array(
'start' => '6740230',
'end' => '6991557',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tox-002'
),
'ENSMUST00000150082' => array(
'start' => '6820694',
'end' => '6990483',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tox-004'
),
'ENSMUST00000119446' => array(
'start' => '7763264',
'end' => '7763500',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11794-001'
),
'ENSMUST00000121663' => array(
'start' => '7039047',
'end' => '7039514',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11804-001'
),
'ENSMUST00000127180' => array(
'start' => '7759670',
'end' => '7763930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm11795-001'
),
'ENSMUST00000137749' => array(
'start' => '6688169',
'end' => '6704160',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm11802-001'
),
'ENSMUST00000129988' => array(
'start' => '7560688',
'end' => '7573801',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '8430436N08Rik-001'
),
'ENSMUST00000179446' => array(
'start' => '7820916',
'end' => '7821047',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23860-201'
),
'ENSDART00000044371' => array(
'start' => '21779436',
'end' => '21901778',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-001'
),
'ENSDART00000132039' => array(
'start' => '21839268',
'end' => '21867729',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-002'
),
'ENSDART00000134912' => array(
'start' => '21779508',
'end' => '21867594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-003'
)
),
'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_0007OA_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OA_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OA_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007OA_0001' => array(
'genes_in_region' => array(
'ENSG00000167912' => array(
[maximum depth reached]
),
'ENSG00000198846' => array(
[maximum depth reached]
),
'ENSG00000253260' => array(
[maximum depth reached]
),
'ENSG00000253413' => array(
[maximum depth reached]
),
'ENSG00000253879' => array(
[maximum depth reached]
),
'ENSG00000254048' => array(
[maximum depth reached]
),
'ENSG00000254775' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Liver',
(int) 2 => 'Ovary',
(int) 3 => 'Adrenal',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Colon',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Testis',
(int) 26 => 'Liver',
(int) 27 => 'Testis',
(int) 28 => 'Adrenal',
(int) 29 => 'Brain',
(int) 30 => 'Breast',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Testis',
(int) 35 => 'Brain',
(int) 36 => 'Ovary',
(int) 37 => 'Testis',
(int) 38 => 'Testis'
)
),
'CIL_0007OA_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000041272' => array(
[maximum depth reached]
),
'ENSMUSG00000082024' => array(
[maximum depth reached]
),
'ENSMUSG00000083023' => array(
[maximum depth reached]
),
'ENSMUSG00000085630' => array(
[maximum depth reached]
),
'ENSMUSG00000086052' => array(
[maximum depth reached]
),
'ENSMUSG00000086070' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Muscle',
(int) 15 => 'Testis',
(int) 16 => 'Muscle',
(int) 17 => 'Brain',
(int) 18 => 'Liver',
(int) 19 => 'Muscle',
(int) 20 => 'Brain',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Breast',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta',
(int) 38 => 'Testis'
)
),
'CIL_0007OA_0003' => array(
'genes_in_region' => array(
'ENSDARG00000032317' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Muscle',
(int) 4 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSG00000167912' => null,
'ENSG00000198846' => 'thymocyte selection-associated high mobility group box',
'ENSG00000201231' => 'RNA, U4 small nuclear 50, pseudogene',
'ENSG00000201763' => 'RNA, 5S ribosomal pseudogene 267',
'ENSG00000206853' => 'Small nucleolar RNA SNORA51',
'ENSG00000253260' => null,
'ENSG00000253413' => null,
'ENSG00000253723' => null,
'ENSG00000253879' => null,
'ENSG00000254048' => null,
'ENSG00000254150' => null,
'ENSG00000254775' => null,
'ENSG00000278428' => null,
'ENSMUSG00000041272' => 'thymocyte selection-associated high mobility group box',
'ENSMUSG00000082024' => 'predicted gene 11794',
'ENSMUSG00000083023' => 'predicted gene 11804',
'ENSMUSG00000085630' => 'predicted gene 11795',
'ENSMUSG00000086052' => 'predicted gene 11802',
'ENSMUSG00000086070' => 'RIKEN cDNA 8430436N08 gene',
'ENSMUSG00000094771' => 'predicted gene, 23860',
'ENSDARG00000032317' => 'thymocyte selection-associated high mobility group box'
)
$gene_name_arr = array(
'ENSG00000167912' => 'RP11-25K19.1',
'ENSG00000198846' => 'TOX',
'ENSG00000201231' => 'RNU4-50P',
'ENSG00000201763' => 'RNA5SP267',
'ENSG00000206853' => 'SNORA51',
'ENSG00000253260' => 'RP11-379I19.1',
'ENSG00000253413' => 'RP11-960H2.2',
'ENSG00000253723' => 'RP11-960H2.1',
'ENSG00000253879' => 'RP11-379I19.3',
'ENSG00000254048' => 'RP11-328K2.1',
'ENSG00000254150' => 'RP11-379I19.2',
'ENSG00000254775' => 'RP11-27P7.1',
'ENSG00000278428' => 'RP11-88H1.1',
'ENSMUSG00000041272' => 'Tox',
'ENSMUSG00000082024' => 'Gm11794',
'ENSMUSG00000083023' => 'Gm11804',
'ENSMUSG00000085630' => 'Gm11795',
'ENSMUSG00000086052' => 'Gm11802',
'ENSMUSG00000086070' => '8430436N08Rik',
'ENSMUSG00000094771' => 'Gm23860',
'ENSDARG00000032317' => 'tox'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0001',
'tax_id' => '9606',
'chromosome' => '8',
'seq_start' => '58807160',
'seq_end' => '60051085',
'region_length' => '1243925',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0002',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '6687841',
'seq_end' => '7986858',
'region_length' => '1299017',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0003',
'tax_id' => '7955',
'chromosome' => '2',
'seq_start' => '21742702',
'seq_end' => '21892182',
'region_length' => '149480',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0004',
'tax_id' => '7955',
'chromosome' => 'Zv9_NA363',
'seq_start' => '10903',
'seq_end' => '11223',
'region_length' => '320',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 13 => 'Brain',
(int) 22 => 'Breast',
(int) 27 => 'Colon',
(int) 32 => 'Heart',
(int) 37 => 'Kidney',
(int) 42 => 'Liver',
(int) 49 => 'Lung',
(int) 52 => 'Muscle',
(int) 59 => 'Ovary',
(int) 65 => 'Placenta',
(int) 71 => '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) 29
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000517898' => array(
'start' => '59119946',
'end' => '59121315',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-002'
),
'ENST00000518993' => array(
'start' => '59119218',
'end' => '59121346',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-001'
),
'ENST00000523683' => array(
'start' => '59119040',
'end' => '59120031',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-25K19.1-003'
),
'ENST00000361421' => array(
'start' => '58805418',
'end' => '59119208',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TOX-001'
),
'ENST00000364361' => array(
'start' => '58814412',
'end' => '58814552',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU4-50P-201'
),
'ENST00000364893' => array(
'start' => '59455885',
'end' => '59456010',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP267-201'
),
'ENST00000384126' => array(
'start' => '59137372',
'end' => '59137502',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORA51.1-205'
),
'ENST00000521456' => array(
'start' => '59561327',
'end' => '59593701',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.1-001'
),
'ENST00000522215' => array(
'start' => '59760047',
'end' => '59760263',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-960H2.2-001'
),
'ENST00000518653' => array(
'start' => '59821124',
'end' => '59821433',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-960H2.1-001'
),
'ENST00000521274' => array(
'start' => '59601404',
'end' => '59613775',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.3-002'
),
'ENST00000522898' => array(
'start' => '59601378',
'end' => '59607005',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-379I19.3-001'
),
'ENST00000518011' => array(
'start' => '58991720',
'end' => '58992938',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-328K2.1-001'
),
'ENST00000524110' => array(
'start' => '59557528',
'end' => '59557855',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-379I19.2-001'
),
'ENST00000531077' => array(
'start' => '60049587',
'end' => '60074715',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-27P7.1-001'
),
'ENST00000615967' => array(
'start' => '59893856',
'end' => '59893942',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'RP11-88H1.1-001'
),
'ENSMUST00000039987' => array(
'start' => '6686353',
'end' => '6990799',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tox-001'
),
'ENSMUST00000125974' => array(
'start' => '6688046',
'end' => '6689351',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tox-003'
),
'ENSMUST00000147657' => array(
'start' => '6740230',
'end' => '6991557',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tox-002'
),
'ENSMUST00000150082' => array(
'start' => '6820694',
'end' => '6990483',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tox-004'
),
'ENSMUST00000119446' => array(
'start' => '7763264',
'end' => '7763500',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11794-001'
),
'ENSMUST00000121663' => array(
'start' => '7039047',
'end' => '7039514',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11804-001'
),
'ENSMUST00000127180' => array(
'start' => '7759670',
'end' => '7763930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm11795-001'
),
'ENSMUST00000137749' => array(
'start' => '6688169',
'end' => '6704160',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm11802-001'
),
'ENSMUST00000129988' => array(
'start' => '7560688',
'end' => '7573801',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '8430436N08Rik-001'
),
'ENSMUST00000179446' => array(
'start' => '7820916',
'end' => '7821047',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23860-201'
),
'ENSDART00000044371' => array(
'start' => '21779436',
'end' => '21901778',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-001'
),
'ENSDART00000132039' => array(
'start' => '21839268',
'end' => '21867729',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-002'
),
'ENSDART00000134912' => array(
'start' => '21779508',
'end' => '21867594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tox-003'
)
)
$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_0007OA_0001' => array(
'genes_in_region' => array(
'ENSG00000167912' => array(
[maximum depth reached]
),
'ENSG00000198846' => array(
[maximum depth reached]
),
'ENSG00000253260' => array(
[maximum depth reached]
),
'ENSG00000253413' => array(
[maximum depth reached]
),
'ENSG00000253879' => array(
[maximum depth reached]
),
'ENSG00000254048' => array(
[maximum depth reached]
),
'ENSG00000254775' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Liver',
(int) 2 => 'Ovary',
(int) 3 => 'Adrenal',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Colon',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Testis',
(int) 26 => 'Liver',
(int) 27 => 'Testis',
(int) 28 => 'Adrenal',
(int) 29 => 'Brain',
(int) 30 => 'Breast',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Testis',
(int) 35 => 'Brain',
(int) 36 => 'Ovary',
(int) 37 => 'Testis',
(int) 38 => 'Testis'
)
),
'CIL_0007OA_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000041272' => array(
[maximum depth reached]
),
'ENSMUSG00000082024' => array(
[maximum depth reached]
),
'ENSMUSG00000083023' => array(
[maximum depth reached]
),
'ENSMUSG00000085630' => array(
[maximum depth reached]
),
'ENSMUSG00000086052' => array(
[maximum depth reached]
),
'ENSMUSG00000086070' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Muscle',
(int) 15 => 'Testis',
(int) 16 => 'Muscle',
(int) 17 => 'Brain',
(int) 18 => 'Liver',
(int) 19 => 'Muscle',
(int) 20 => 'Brain',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Breast',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta',
(int) 38 => 'Testis'
)
),
'CIL_0007OA_0003' => array(
'genes_in_region' => array(
'ENSDARG00000032317' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Muscle',
(int) 4 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OA_0004',
'tax_id' => '7955',
'chromosome' => 'Zv9_NA363',
'seq_start' => '10903',
'seq_end' => '11223',
'region_length' => '320',
'region_type' => 'UCNEbase',
'el_id' => 'TOX'
)
)
$gene_el = array(
'ENSDART00000044371' => array(
'Brain' => array(
'average_FPKM' => '16.373',
'stddev_FPKM' => '3.94'
),
'Heart' => array(
'average_FPKM' => '1.873',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.155',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.602',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000132039' => array(),
'ENSDART00000134912' => array(
'Heart' => array(
'average_FPKM' => '0.617',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000032317'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '0.617',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000134912'
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
(RP11-25K19.1)