| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000025317-ENSMUSG00000025316 |
CGP |
10090 |
8:121916126-122029258  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0002SY_0002 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0002SY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000172530' => 'BTG3 associated nuclear protein',
'ENSG00000174990' => 'carbonic anhydrase VA, mitochondrial',
'ENSG00000205037' => null,
'ENSG00000260166' => null,
'ENSG00000260443' => null,
'ENSG00000260603' => null,
'ENSG00000261193' => null,
'ENSG00000270385' => null,
'ENSMUSG00000025316' => 'BTG3 associated nuclear protein',
'ENSMUSG00000025317' => 'carbonic anhydrase 5a, mitochondrial',
'ENSMUSG00000074052' => 'cDNA sequence BC048644',
'ENSMUSG00000091952' => 'predicted gene, 17709',
'ENSMUSG00000097969' => 'predicted gene, 26999',
'ENSMUSG00000098184' => 'predicted gene, 27011',
'ENSMUSG00000099140' => 'microRNA 7237'
),
'gene_name_arr' => array(
'ENSG00000172530' => 'BANP',
'ENSG00000174990' => 'CA5A',
'ENSG00000205037' => 'RP11-863P13.4',
'ENSG00000260166' => 'RP11-863P13.6',
'ENSG00000260443' => 'CTD-3057O21.1',
'ENSG00000260603' => 'GS1-21A4.1',
'ENSG00000261193' => 'RP11-863P13.5',
'ENSG00000270385' => 'GS1-21A4.2',
'ENSMUSG00000025316' => 'Banp',
'ENSMUSG00000025317' => 'Car5a',
'ENSMUSG00000074052' => 'BC048644',
'ENSMUSG00000091952' => 'Gm17709',
'ENSMUSG00000097969' => 'Gm26999',
'ENSMUSG00000098184' => 'Gm27011',
'ENSMUSG00000099140' => 'Mir7237'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 16 => 'Brain',
(int) 25 => 'Breast',
(int) 33 => 'Colon',
(int) 43 => 'Heart',
(int) 51 => 'Kidney',
(int) 60 => 'Liver',
(int) 71 => 'Lung',
(int) 80 => 'Muscle',
(int) 87 => 'Ovary',
(int) 98 => 'Placenta',
(int) 102 => '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) 61,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000286122' => array(
'start' => '87951432',
'end' => '88077317',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-201'
),
'ENST00000355022' => array(
'start' => '87951487',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-003'
),
'ENST00000355163' => array(
'start' => '88071073',
'end' => '88118422',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-202'
),
'ENST00000393207' => array(
'start' => '87970018',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-002'
),
'ENST00000393208' => array(
'start' => '87951434',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-001'
),
'ENST00000412691' => array(
'start' => '87951445',
'end' => '87984251',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-004'
),
'ENST00000423252' => array(
'start' => '87950436',
'end' => '87981049',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-007'
),
'ENST00000436274' => array(
'start' => '87963379',
'end' => '87984182',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-013'
),
'ENST00000436970' => array(
'start' => '87959871',
'end' => '88004301',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-012'
),
'ENST00000439677' => array(
'start' => '87951432',
'end' => '88018455',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-010'
),
'ENST00000454563' => array(
'start' => '87951434',
'end' => '87981102',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-011'
),
'ENST00000456902' => array(
'start' => '87966703',
'end' => '87984254',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-014'
),
'ENST00000459966' => array(
'start' => '87951435',
'end' => '88006183',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-006'
),
'ENST00000466197' => array(
'start' => '87951485',
'end' => '88004391',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-016'
),
'ENST00000466847' => array(
'start' => '88035052',
'end' => '88076835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'BANP-019'
),
'ENST00000472964' => array(
'start' => '87982618',
'end' => '87984259',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-015'
),
'ENST00000474563' => array(
'start' => '87980535',
'end' => '87984227',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-023'
),
'ENST00000479780' => array(
'start' => '87951434',
'end' => '88076661',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-021'
),
'ENST00000481948' => array(
'start' => '88071073',
'end' => '88077318',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-020'
),
'ENST00000485772' => array(
'start' => '87951481',
'end' => '88003931',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-005'
),
'ENST00000488074' => array(
'start' => '87950436',
'end' => '87984234',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-008'
),
'ENST00000497491' => array(
'start' => '88017190',
'end' => '88033219',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-018'
),
'ENST00000526460' => array(
'start' => '87951467',
'end' => '87957069',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-022'
),
'ENST00000538234' => array(
'start' => '87959871',
'end' => '88077315',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-203'
),
'ENST00000565242' => array(
'start' => '88037273',
'end' => '88072130',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'BANP-025'
),
'ENST00000569400' => array(
'start' => '87949244',
'end' => '87984251',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-024'
),
'ENST00000612301' => array(
'start' => '87952247',
'end' => '87952748',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-026'
),
'ENST00000309893' => array(
'start' => '87881546',
'end' => '87936516',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CA5A-001'
),
'ENST00000566402' => array(
'start' => '87888018',
'end' => '87892268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CA5A-003'
),
'ENST00000568801' => array(
'start' => '87925539',
'end' => '87936529',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CA5A-002'
),
'ENST00000378417' => array(
'start' => '88088041',
'end' => '88100959',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.4-001'
),
'ENST00000566351' => array(
'start' => '88099409',
'end' => '88100985',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.4-002'
),
'ENST00000566155' => array(
'start' => '88087387',
'end' => '88087932',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.6-001'
),
'ENST00000565496' => array(
'start' => '87945058',
'end' => '87945202',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-3057O21.1-001'
),
'ENST00000562644' => array(
'start' => '87892938',
'end' => '87893685',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'GS1-21A4.1-001'
),
'ENST00000568267' => array(
'start' => '88079161',
'end' => '88087383',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.5-001'
),
'ENST00000604757' => array(
'start' => '87892955',
'end' => '87893735',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'GS1-21A4.2-001'
),
'ENSMUST00000026354' => array(
'start' => '121950580',
'end' => '122025937',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-003'
),
'ENSMUST00000093078' => array(
'start' => '121950492',
'end' => '122026177',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-002'
),
'ENSMUST00000167711' => array(
'start' => '121991604',
'end' => '122025958',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-004'
),
'ENSMUST00000170857' => array(
'start' => '121950544',
'end' => '122029258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-001'
),
'ENSMUST00000172511' => array(
'start' => '121950605',
'end' => '121991586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-013'
),
'ENSMUST00000172513' => array(
'start' => '121978322',
'end' => '121990002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-011'
),
'ENSMUST00000172628' => array(
'start' => '121949750',
'end' => '121997183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-005'
),
'ENSMUST00000172681' => array(
'start' => '121950575',
'end' => '121997181',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Banp-010'
),
'ENSMUST00000173201' => array(
'start' => '122000847',
'end' => '122007140',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-007'
),
'ENSMUST00000173254' => array(
'start' => '121974496',
'end' => '122025635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-016'
),
'ENSMUST00000173396' => array(
'start' => '121997089',
'end' => '122025607',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-009'
),
'ENSMUST00000173753' => array(
'start' => '121974448',
'end' => '121976487',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-012'
),
'ENSMUST00000173925' => array(
'start' => '122000669',
'end' => '122020643',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Banp-006'
),
'ENSMUST00000174327' => array(
'start' => '121991458',
'end' => '121997238',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-008'
),
'ENSMUST00000174445' => array(
'start' => '121950596',
'end' => '121991560',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Banp-014'
),
'ENSMUST00000174753' => array(
'start' => '121950585',
'end' => '121991569',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-015'
),
'ENSMUST00000057653' => array(
'start' => '121916126',
'end' => '121944904',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Car5a-001'
),
'ENSMUST00000151462' => array(
'start' => '121918054',
'end' => '121927474',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Car5a-002'
),
'ENSMUST00000140928' => array(
'start' => '121907833',
'end' => '121918428',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC048644-001'
),
'ENSMUST00000181944' => array(
'start' => '121907833',
'end' => '121909824',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC048644-002'
),
'ENSMUST00000174536' => array(
'start' => '121972727',
'end' => '121973822',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm17709-001'
),
'ENSMUST00000183009' => array(
'start' => '121919024',
'end' => '121919690',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm26999-001'
),
'ENSMUST00000182352' => array(
'start' => '121949674',
'end' => '121950645',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27011-001'
),
'ENSMUST00000184699' => array(
'start' => '121978024',
'end' => '121978086',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7237-201'
)
),
'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_0002SY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0002SY_0001' => array(
'genes_in_region' => array(
'ENSG00000172530' => array(
[maximum depth reached]
),
'ENSG00000174990' => array(
[maximum depth reached]
),
'ENSG00000205037' => array(
[maximum depth reached]
),
'ENSG00000260166' => array(
[maximum depth reached]
),
'ENSG00000260443' => array(
[maximum depth reached]
),
'ENSG00000260603' => array(
[maximum depth reached]
),
'ENSG00000261193' => array(
[maximum depth reached]
),
'ENSG00000270385' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Adrenal',
(int) 13 => 'Colon',
(int) 14 => 'Lung',
(int) 15 => 'Ovary',
(int) 16 => 'Placenta',
(int) 17 => 'Kidney',
(int) 18 => 'Lung',
(int) 19 => 'Colon',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Bladder',
(int) 23 => 'Lung',
(int) 24 => 'Liver',
(int) 25 => 'Colon',
(int) 26 => 'Muscle',
(int) 27 => 'Liver',
(int) 28 => 'Brain',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Lung',
(int) 32 => 'Ovary',
(int) 33 => 'Testis',
(int) 34 => 'Brain',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Muscle',
(int) 38 => 'Kidney',
(int) 39 => 'Bladder',
(int) 40 => 'Lung',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Adipose',
(int) 44 => 'Adrenal',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Ovary',
(int) 58 => 'Liver',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Bladder',
(int) 64 => 'Brain',
(int) 65 => 'Breast',
(int) 66 => 'Colon',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Lung',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Brain',
(int) 75 => 'Breast',
(int) 76 => 'Liver',
(int) 77 => 'Adrenal',
(int) 78 => 'Breast',
(int) 79 => 'Colon',
(int) 80 => 'Heart',
(int) 81 => 'Liver',
(int) 82 => 'Ovary',
(int) 83 => 'Testis',
(int) 84 => 'Brain',
(int) 85 => 'Testis',
(int) 86 => 'Adrenal',
(int) 87 => 'Brain',
(int) 88 => 'Breast',
(int) 89 => 'Heart',
(int) 90 => 'Kidney',
(int) 91 => 'Muscle',
(int) 92 => 'Testis',
(int) 93 => 'Adrenal',
(int) 94 => 'Brain',
(int) 95 => 'Breast',
(int) 96 => 'Colon',
(int) 97 => 'Heart',
(int) 98 => 'Ovary',
(int) 99 => 'Testis',
(int) 100 => 'Adipose',
(int) 101 => 'Adrenal',
(int) 102 => 'Breast',
(int) 103 => 'Colon',
(int) 104 => 'Heart',
(int) 105 => 'Kidney',
(int) 106 => 'Liver',
(int) 107 => 'Lung',
(int) 108 => 'Muscle',
(int) 109 => 'Ovary',
(int) 110 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000172530' => 'BTG3 associated nuclear protein',
'ENSG00000174990' => 'carbonic anhydrase VA, mitochondrial',
'ENSG00000205037' => null,
'ENSG00000260166' => null,
'ENSG00000260443' => null,
'ENSG00000260603' => null,
'ENSG00000261193' => null,
'ENSG00000270385' => null,
'ENSMUSG00000025316' => 'BTG3 associated nuclear protein',
'ENSMUSG00000025317' => 'carbonic anhydrase 5a, mitochondrial',
'ENSMUSG00000074052' => 'cDNA sequence BC048644',
'ENSMUSG00000091952' => 'predicted gene, 17709',
'ENSMUSG00000097969' => 'predicted gene, 26999',
'ENSMUSG00000098184' => 'predicted gene, 27011',
'ENSMUSG00000099140' => 'microRNA 7237'
)
$gene_name_arr = array(
'ENSG00000172530' => 'BANP',
'ENSG00000174990' => 'CA5A',
'ENSG00000205037' => 'RP11-863P13.4',
'ENSG00000260166' => 'RP11-863P13.6',
'ENSG00000260443' => 'CTD-3057O21.1',
'ENSG00000260603' => 'GS1-21A4.1',
'ENSG00000261193' => 'RP11-863P13.5',
'ENSG00000270385' => 'GS1-21A4.2',
'ENSMUSG00000025316' => 'Banp',
'ENSMUSG00000025317' => 'Car5a',
'ENSMUSG00000074052' => 'BC048644',
'ENSMUSG00000091952' => 'Gm17709',
'ENSMUSG00000097969' => 'Gm26999',
'ENSMUSG00000098184' => 'Gm27011',
'ENSMUSG00000099140' => 'Mir7237'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002SY_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '87881546',
'seq_end' => '88118422',
'region_length' => '236876',
'region_type' => 'CGP',
'el_id' => 'ENSG00000174990-ENSG00000172530'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002SY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121916126',
'seq_end' => '122029258',
'region_length' => '113132',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000025317-ENSMUSG00000025316'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 16 => 'Brain',
(int) 25 => 'Breast',
(int) 33 => 'Colon',
(int) 43 => 'Heart',
(int) 51 => 'Kidney',
(int) 60 => 'Liver',
(int) 71 => 'Lung',
(int) 80 => 'Muscle',
(int) 87 => 'Ovary',
(int) 98 => 'Placenta',
(int) 102 => '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) 61
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000286122' => array(
'start' => '87951432',
'end' => '88077317',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-201'
),
'ENST00000355022' => array(
'start' => '87951487',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-003'
),
'ENST00000355163' => array(
'start' => '88071073',
'end' => '88118422',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-202'
),
'ENST00000393207' => array(
'start' => '87970018',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-002'
),
'ENST00000393208' => array(
'start' => '87951434',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-001'
),
'ENST00000412691' => array(
'start' => '87951445',
'end' => '87984251',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-004'
),
'ENST00000423252' => array(
'start' => '87950436',
'end' => '87981049',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-007'
),
'ENST00000436274' => array(
'start' => '87963379',
'end' => '87984182',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-013'
),
'ENST00000436970' => array(
'start' => '87959871',
'end' => '88004301',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-012'
),
'ENST00000439677' => array(
'start' => '87951432',
'end' => '88018455',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-010'
),
'ENST00000454563' => array(
'start' => '87951434',
'end' => '87981102',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-011'
),
'ENST00000456902' => array(
'start' => '87966703',
'end' => '87984254',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-014'
),
'ENST00000459966' => array(
'start' => '87951435',
'end' => '88006183',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-006'
),
'ENST00000466197' => array(
'start' => '87951485',
'end' => '88004391',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-016'
),
'ENST00000466847' => array(
'start' => '88035052',
'end' => '88076835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'BANP-019'
),
'ENST00000472964' => array(
'start' => '87982618',
'end' => '87984259',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-015'
),
'ENST00000474563' => array(
'start' => '87980535',
'end' => '87984227',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-023'
),
'ENST00000479780' => array(
'start' => '87951434',
'end' => '88076661',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-021'
),
'ENST00000481948' => array(
'start' => '88071073',
'end' => '88077318',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-020'
),
'ENST00000485772' => array(
'start' => '87951481',
'end' => '88003931',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-005'
),
'ENST00000488074' => array(
'start' => '87950436',
'end' => '87984234',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-008'
),
'ENST00000497491' => array(
'start' => '88017190',
'end' => '88033219',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-018'
),
'ENST00000526460' => array(
'start' => '87951467',
'end' => '87957069',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-022'
),
'ENST00000538234' => array(
'start' => '87959871',
'end' => '88077315',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-203'
),
'ENST00000565242' => array(
'start' => '88037273',
'end' => '88072130',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'BANP-025'
),
'ENST00000569400' => array(
'start' => '87949244',
'end' => '87984251',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-024'
),
'ENST00000612301' => array(
'start' => '87952247',
'end' => '87952748',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-026'
),
'ENST00000309893' => array(
'start' => '87881546',
'end' => '87936516',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CA5A-001'
),
'ENST00000566402' => array(
'start' => '87888018',
'end' => '87892268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CA5A-003'
),
'ENST00000568801' => array(
'start' => '87925539',
'end' => '87936529',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CA5A-002'
),
'ENST00000378417' => array(
'start' => '88088041',
'end' => '88100959',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.4-001'
),
'ENST00000566351' => array(
'start' => '88099409',
'end' => '88100985',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.4-002'
),
'ENST00000566155' => array(
'start' => '88087387',
'end' => '88087932',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.6-001'
),
'ENST00000565496' => array(
'start' => '87945058',
'end' => '87945202',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-3057O21.1-001'
),
'ENST00000562644' => array(
'start' => '87892938',
'end' => '87893685',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'GS1-21A4.1-001'
),
'ENST00000568267' => array(
'start' => '88079161',
'end' => '88087383',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.5-001'
),
'ENST00000604757' => array(
'start' => '87892955',
'end' => '87893735',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'GS1-21A4.2-001'
),
'ENSMUST00000026354' => array(
'start' => '121950580',
'end' => '122025937',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-003'
),
'ENSMUST00000093078' => array(
'start' => '121950492',
'end' => '122026177',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-002'
),
'ENSMUST00000167711' => array(
'start' => '121991604',
'end' => '122025958',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-004'
),
'ENSMUST00000170857' => array(
'start' => '121950544',
'end' => '122029258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-001'
),
'ENSMUST00000172511' => array(
'start' => '121950605',
'end' => '121991586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-013'
),
'ENSMUST00000172513' => array(
'start' => '121978322',
'end' => '121990002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-011'
),
'ENSMUST00000172628' => array(
'start' => '121949750',
'end' => '121997183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-005'
),
'ENSMUST00000172681' => array(
'start' => '121950575',
'end' => '121997181',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Banp-010'
),
'ENSMUST00000173201' => array(
'start' => '122000847',
'end' => '122007140',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-007'
),
'ENSMUST00000173254' => array(
'start' => '121974496',
'end' => '122025635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-016'
),
'ENSMUST00000173396' => array(
'start' => '121997089',
'end' => '122025607',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-009'
),
'ENSMUST00000173753' => array(
'start' => '121974448',
'end' => '121976487',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-012'
),
'ENSMUST00000173925' => array(
'start' => '122000669',
'end' => '122020643',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Banp-006'
),
'ENSMUST00000174327' => array(
'start' => '121991458',
'end' => '121997238',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-008'
),
'ENSMUST00000174445' => array(
'start' => '121950596',
'end' => '121991560',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Banp-014'
),
'ENSMUST00000174753' => array(
'start' => '121950585',
'end' => '121991569',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-015'
),
'ENSMUST00000057653' => array(
'start' => '121916126',
'end' => '121944904',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Car5a-001'
),
'ENSMUST00000151462' => array(
'start' => '121918054',
'end' => '121927474',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Car5a-002'
),
'ENSMUST00000140928' => array(
'start' => '121907833',
'end' => '121918428',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC048644-001'
),
'ENSMUST00000181944' => array(
'start' => '121907833',
'end' => '121909824',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC048644-002'
),
'ENSMUST00000174536' => array(
'start' => '121972727',
'end' => '121973822',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm17709-001'
),
'ENSMUST00000183009' => array(
'start' => '121919024',
'end' => '121919690',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm26999-001'
),
'ENSMUST00000182352' => array(
'start' => '121949674',
'end' => '121950645',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27011-001'
),
'ENSMUST00000184699' => array(
'start' => '121978024',
'end' => '121978086',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7237-201'
)
)
$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_0002SY_0001' => array(
'genes_in_region' => array(
'ENSG00000172530' => array(
[maximum depth reached]
),
'ENSG00000174990' => array(
[maximum depth reached]
),
'ENSG00000205037' => array(
[maximum depth reached]
),
'ENSG00000260166' => array(
[maximum depth reached]
),
'ENSG00000260443' => array(
[maximum depth reached]
),
'ENSG00000260603' => array(
[maximum depth reached]
),
'ENSG00000261193' => array(
[maximum depth reached]
),
'ENSG00000270385' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Adrenal',
(int) 13 => 'Colon',
(int) 14 => 'Lung',
(int) 15 => 'Ovary',
(int) 16 => 'Placenta',
(int) 17 => 'Kidney',
(int) 18 => 'Lung',
(int) 19 => 'Colon',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Bladder',
(int) 23 => 'Lung',
(int) 24 => 'Liver',
(int) 25 => 'Colon',
(int) 26 => 'Muscle',
(int) 27 => 'Liver',
(int) 28 => 'Brain',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Lung',
(int) 32 => 'Ovary',
(int) 33 => 'Testis',
(int) 34 => 'Brain',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Muscle',
(int) 38 => 'Kidney',
(int) 39 => 'Bladder',
(int) 40 => 'Lung',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Adipose',
(int) 44 => 'Adrenal',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Ovary',
(int) 58 => 'Liver',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Bladder',
(int) 64 => 'Brain',
(int) 65 => 'Breast',
(int) 66 => 'Colon',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Lung',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Brain',
(int) 75 => 'Breast',
(int) 76 => 'Liver',
(int) 77 => 'Adrenal',
(int) 78 => 'Breast',
(int) 79 => 'Colon',
(int) 80 => 'Heart',
(int) 81 => 'Liver',
(int) 82 => 'Ovary',
(int) 83 => 'Testis',
(int) 84 => 'Brain',
(int) 85 => 'Testis',
(int) 86 => 'Adrenal',
(int) 87 => 'Brain',
(int) 88 => 'Breast',
(int) 89 => 'Heart',
(int) 90 => 'Kidney',
(int) 91 => 'Muscle',
(int) 92 => 'Testis',
(int) 93 => 'Adrenal',
(int) 94 => 'Brain',
(int) 95 => 'Breast',
(int) 96 => 'Colon',
(int) 97 => 'Heart',
(int) 98 => 'Ovary',
(int) 99 => 'Testis',
(int) 100 => 'Adipose',
(int) 101 => 'Adrenal',
(int) 102 => 'Breast',
(int) 103 => 'Colon',
(int) 104 => 'Heart',
(int) 105 => 'Kidney',
(int) 106 => 'Liver',
(int) 107 => 'Lung',
(int) 108 => 'Muscle',
(int) 109 => 'Ovary',
(int) 110 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0002SY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121916126',
'seq_end' => '122029258',
'region_length' => '113132',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000025317-ENSMUSG00000025316'
)
)
$gene_el = array(
'ENST00000604757' => array(
'Adipose' => array(
'average_FPKM' => '0.089',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.240',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.045',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.101',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.618',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.084',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.064',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000270385'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.089',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.240',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.045',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.101',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.618',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.084',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.064',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000604757'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0002SY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000172530' => 'BTG3 associated nuclear protein',
'ENSG00000174990' => 'carbonic anhydrase VA, mitochondrial',
'ENSG00000205037' => null,
'ENSG00000260166' => null,
'ENSG00000260443' => null,
'ENSG00000260603' => null,
'ENSG00000261193' => null,
'ENSG00000270385' => null,
'ENSMUSG00000025316' => 'BTG3 associated nuclear protein',
'ENSMUSG00000025317' => 'carbonic anhydrase 5a, mitochondrial',
'ENSMUSG00000074052' => 'cDNA sequence BC048644',
'ENSMUSG00000091952' => 'predicted gene, 17709',
'ENSMUSG00000097969' => 'predicted gene, 26999',
'ENSMUSG00000098184' => 'predicted gene, 27011',
'ENSMUSG00000099140' => 'microRNA 7237'
),
'gene_name_arr' => array(
'ENSG00000172530' => 'BANP',
'ENSG00000174990' => 'CA5A',
'ENSG00000205037' => 'RP11-863P13.4',
'ENSG00000260166' => 'RP11-863P13.6',
'ENSG00000260443' => 'CTD-3057O21.1',
'ENSG00000260603' => 'GS1-21A4.1',
'ENSG00000261193' => 'RP11-863P13.5',
'ENSG00000270385' => 'GS1-21A4.2',
'ENSMUSG00000025316' => 'Banp',
'ENSMUSG00000025317' => 'Car5a',
'ENSMUSG00000074052' => 'BC048644',
'ENSMUSG00000091952' => 'Gm17709',
'ENSMUSG00000097969' => 'Gm26999',
'ENSMUSG00000098184' => 'Gm27011',
'ENSMUSG00000099140' => 'Mir7237'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 16 => 'Brain',
(int) 25 => 'Breast',
(int) 33 => 'Colon',
(int) 43 => 'Heart',
(int) 51 => 'Kidney',
(int) 60 => 'Liver',
(int) 71 => 'Lung',
(int) 80 => 'Muscle',
(int) 87 => 'Ovary',
(int) 98 => 'Placenta',
(int) 102 => '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) 61,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000286122' => array(
'start' => '87951432',
'end' => '88077317',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-201'
),
'ENST00000355022' => array(
'start' => '87951487',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-003'
),
'ENST00000355163' => array(
'start' => '88071073',
'end' => '88118422',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-202'
),
'ENST00000393207' => array(
'start' => '87970018',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-002'
),
'ENST00000393208' => array(
'start' => '87951434',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-001'
),
'ENST00000412691' => array(
'start' => '87951445',
'end' => '87984251',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-004'
),
'ENST00000423252' => array(
'start' => '87950436',
'end' => '87981049',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-007'
),
'ENST00000436274' => array(
'start' => '87963379',
'end' => '87984182',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-013'
),
'ENST00000436970' => array(
'start' => '87959871',
'end' => '88004301',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-012'
),
'ENST00000439677' => array(
'start' => '87951432',
'end' => '88018455',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-010'
),
'ENST00000454563' => array(
'start' => '87951434',
'end' => '87981102',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-011'
),
'ENST00000456902' => array(
'start' => '87966703',
'end' => '87984254',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-014'
),
'ENST00000459966' => array(
'start' => '87951435',
'end' => '88006183',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-006'
),
'ENST00000466197' => array(
'start' => '87951485',
'end' => '88004391',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-016'
),
'ENST00000466847' => array(
'start' => '88035052',
'end' => '88076835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'BANP-019'
),
'ENST00000472964' => array(
'start' => '87982618',
'end' => '87984259',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-015'
),
'ENST00000474563' => array(
'start' => '87980535',
'end' => '87984227',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-023'
),
'ENST00000479780' => array(
'start' => '87951434',
'end' => '88076661',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-021'
),
'ENST00000481948' => array(
'start' => '88071073',
'end' => '88077318',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-020'
),
'ENST00000485772' => array(
'start' => '87951481',
'end' => '88003931',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-005'
),
'ENST00000488074' => array(
'start' => '87950436',
'end' => '87984234',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-008'
),
'ENST00000497491' => array(
'start' => '88017190',
'end' => '88033219',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-018'
),
'ENST00000526460' => array(
'start' => '87951467',
'end' => '87957069',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-022'
),
'ENST00000538234' => array(
'start' => '87959871',
'end' => '88077315',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-203'
),
'ENST00000565242' => array(
'start' => '88037273',
'end' => '88072130',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'BANP-025'
),
'ENST00000569400' => array(
'start' => '87949244',
'end' => '87984251',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-024'
),
'ENST00000612301' => array(
'start' => '87952247',
'end' => '87952748',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-026'
),
'ENST00000309893' => array(
'start' => '87881546',
'end' => '87936516',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CA5A-001'
),
'ENST00000566402' => array(
'start' => '87888018',
'end' => '87892268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CA5A-003'
),
'ENST00000568801' => array(
'start' => '87925539',
'end' => '87936529',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CA5A-002'
),
'ENST00000378417' => array(
'start' => '88088041',
'end' => '88100959',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.4-001'
),
'ENST00000566351' => array(
'start' => '88099409',
'end' => '88100985',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.4-002'
),
'ENST00000566155' => array(
'start' => '88087387',
'end' => '88087932',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.6-001'
),
'ENST00000565496' => array(
'start' => '87945058',
'end' => '87945202',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-3057O21.1-001'
),
'ENST00000562644' => array(
'start' => '87892938',
'end' => '87893685',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'GS1-21A4.1-001'
),
'ENST00000568267' => array(
'start' => '88079161',
'end' => '88087383',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.5-001'
),
'ENST00000604757' => array(
'start' => '87892955',
'end' => '87893735',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'GS1-21A4.2-001'
),
'ENSMUST00000026354' => array(
'start' => '121950580',
'end' => '122025937',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-003'
),
'ENSMUST00000093078' => array(
'start' => '121950492',
'end' => '122026177',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-002'
),
'ENSMUST00000167711' => array(
'start' => '121991604',
'end' => '122025958',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-004'
),
'ENSMUST00000170857' => array(
'start' => '121950544',
'end' => '122029258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-001'
),
'ENSMUST00000172511' => array(
'start' => '121950605',
'end' => '121991586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-013'
),
'ENSMUST00000172513' => array(
'start' => '121978322',
'end' => '121990002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-011'
),
'ENSMUST00000172628' => array(
'start' => '121949750',
'end' => '121997183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-005'
),
'ENSMUST00000172681' => array(
'start' => '121950575',
'end' => '121997181',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Banp-010'
),
'ENSMUST00000173201' => array(
'start' => '122000847',
'end' => '122007140',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-007'
),
'ENSMUST00000173254' => array(
'start' => '121974496',
'end' => '122025635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-016'
),
'ENSMUST00000173396' => array(
'start' => '121997089',
'end' => '122025607',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-009'
),
'ENSMUST00000173753' => array(
'start' => '121974448',
'end' => '121976487',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-012'
),
'ENSMUST00000173925' => array(
'start' => '122000669',
'end' => '122020643',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Banp-006'
),
'ENSMUST00000174327' => array(
'start' => '121991458',
'end' => '121997238',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-008'
),
'ENSMUST00000174445' => array(
'start' => '121950596',
'end' => '121991560',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Banp-014'
),
'ENSMUST00000174753' => array(
'start' => '121950585',
'end' => '121991569',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-015'
),
'ENSMUST00000057653' => array(
'start' => '121916126',
'end' => '121944904',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Car5a-001'
),
'ENSMUST00000151462' => array(
'start' => '121918054',
'end' => '121927474',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Car5a-002'
),
'ENSMUST00000140928' => array(
'start' => '121907833',
'end' => '121918428',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC048644-001'
),
'ENSMUST00000181944' => array(
'start' => '121907833',
'end' => '121909824',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC048644-002'
),
'ENSMUST00000174536' => array(
'start' => '121972727',
'end' => '121973822',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm17709-001'
),
'ENSMUST00000183009' => array(
'start' => '121919024',
'end' => '121919690',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm26999-001'
),
'ENSMUST00000182352' => array(
'start' => '121949674',
'end' => '121950645',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27011-001'
),
'ENSMUST00000184699' => array(
'start' => '121978024',
'end' => '121978086',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7237-201'
)
),
'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_0002SY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0002SY_0001' => array(
'genes_in_region' => array(
'ENSG00000172530' => array(
[maximum depth reached]
),
'ENSG00000174990' => array(
[maximum depth reached]
),
'ENSG00000205037' => array(
[maximum depth reached]
),
'ENSG00000260166' => array(
[maximum depth reached]
),
'ENSG00000260443' => array(
[maximum depth reached]
),
'ENSG00000260603' => array(
[maximum depth reached]
),
'ENSG00000261193' => array(
[maximum depth reached]
),
'ENSG00000270385' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Adrenal',
(int) 13 => 'Colon',
(int) 14 => 'Lung',
(int) 15 => 'Ovary',
(int) 16 => 'Placenta',
(int) 17 => 'Kidney',
(int) 18 => 'Lung',
(int) 19 => 'Colon',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Bladder',
(int) 23 => 'Lung',
(int) 24 => 'Liver',
(int) 25 => 'Colon',
(int) 26 => 'Muscle',
(int) 27 => 'Liver',
(int) 28 => 'Brain',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Lung',
(int) 32 => 'Ovary',
(int) 33 => 'Testis',
(int) 34 => 'Brain',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Muscle',
(int) 38 => 'Kidney',
(int) 39 => 'Bladder',
(int) 40 => 'Lung',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Adipose',
(int) 44 => 'Adrenal',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Ovary',
(int) 58 => 'Liver',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Bladder',
(int) 64 => 'Brain',
(int) 65 => 'Breast',
(int) 66 => 'Colon',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Lung',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Brain',
(int) 75 => 'Breast',
(int) 76 => 'Liver',
(int) 77 => 'Adrenal',
(int) 78 => 'Breast',
(int) 79 => 'Colon',
(int) 80 => 'Heart',
(int) 81 => 'Liver',
(int) 82 => 'Ovary',
(int) 83 => 'Testis',
(int) 84 => 'Brain',
(int) 85 => 'Testis',
(int) 86 => 'Adrenal',
(int) 87 => 'Brain',
(int) 88 => 'Breast',
(int) 89 => 'Heart',
(int) 90 => 'Kidney',
(int) 91 => 'Muscle',
(int) 92 => 'Testis',
(int) 93 => 'Adrenal',
(int) 94 => 'Brain',
(int) 95 => 'Breast',
(int) 96 => 'Colon',
(int) 97 => 'Heart',
(int) 98 => 'Ovary',
(int) 99 => 'Testis',
(int) 100 => 'Adipose',
(int) 101 => 'Adrenal',
(int) 102 => 'Breast',
(int) 103 => 'Colon',
(int) 104 => 'Heart',
(int) 105 => 'Kidney',
(int) 106 => 'Liver',
(int) 107 => 'Lung',
(int) 108 => 'Muscle',
(int) 109 => 'Ovary',
(int) 110 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000172530' => 'BTG3 associated nuclear protein',
'ENSG00000174990' => 'carbonic anhydrase VA, mitochondrial',
'ENSG00000205037' => null,
'ENSG00000260166' => null,
'ENSG00000260443' => null,
'ENSG00000260603' => null,
'ENSG00000261193' => null,
'ENSG00000270385' => null,
'ENSMUSG00000025316' => 'BTG3 associated nuclear protein',
'ENSMUSG00000025317' => 'carbonic anhydrase 5a, mitochondrial',
'ENSMUSG00000074052' => 'cDNA sequence BC048644',
'ENSMUSG00000091952' => 'predicted gene, 17709',
'ENSMUSG00000097969' => 'predicted gene, 26999',
'ENSMUSG00000098184' => 'predicted gene, 27011',
'ENSMUSG00000099140' => 'microRNA 7237'
)
$gene_name_arr = array(
'ENSG00000172530' => 'BANP',
'ENSG00000174990' => 'CA5A',
'ENSG00000205037' => 'RP11-863P13.4',
'ENSG00000260166' => 'RP11-863P13.6',
'ENSG00000260443' => 'CTD-3057O21.1',
'ENSG00000260603' => 'GS1-21A4.1',
'ENSG00000261193' => 'RP11-863P13.5',
'ENSG00000270385' => 'GS1-21A4.2',
'ENSMUSG00000025316' => 'Banp',
'ENSMUSG00000025317' => 'Car5a',
'ENSMUSG00000074052' => 'BC048644',
'ENSMUSG00000091952' => 'Gm17709',
'ENSMUSG00000097969' => 'Gm26999',
'ENSMUSG00000098184' => 'Gm27011',
'ENSMUSG00000099140' => 'Mir7237'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002SY_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '87881546',
'seq_end' => '88118422',
'region_length' => '236876',
'region_type' => 'CGP',
'el_id' => 'ENSG00000174990-ENSG00000172530'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002SY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121916126',
'seq_end' => '122029258',
'region_length' => '113132',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000025317-ENSMUSG00000025316'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 16 => 'Brain',
(int) 25 => 'Breast',
(int) 33 => 'Colon',
(int) 43 => 'Heart',
(int) 51 => 'Kidney',
(int) 60 => 'Liver',
(int) 71 => 'Lung',
(int) 80 => 'Muscle',
(int) 87 => 'Ovary',
(int) 98 => 'Placenta',
(int) 102 => '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) 61
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000286122' => array(
'start' => '87951432',
'end' => '88077317',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-201'
),
'ENST00000355022' => array(
'start' => '87951487',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-003'
),
'ENST00000355163' => array(
'start' => '88071073',
'end' => '88118422',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-202'
),
'ENST00000393207' => array(
'start' => '87970018',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-002'
),
'ENST00000393208' => array(
'start' => '87951434',
'end' => '88077318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-001'
),
'ENST00000412691' => array(
'start' => '87951445',
'end' => '87984251',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-004'
),
'ENST00000423252' => array(
'start' => '87950436',
'end' => '87981049',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-007'
),
'ENST00000436274' => array(
'start' => '87963379',
'end' => '87984182',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-013'
),
'ENST00000436970' => array(
'start' => '87959871',
'end' => '88004301',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-012'
),
'ENST00000439677' => array(
'start' => '87951432',
'end' => '88018455',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-010'
),
'ENST00000454563' => array(
'start' => '87951434',
'end' => '87981102',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-011'
),
'ENST00000456902' => array(
'start' => '87966703',
'end' => '87984254',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-014'
),
'ENST00000459966' => array(
'start' => '87951435',
'end' => '88006183',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-006'
),
'ENST00000466197' => array(
'start' => '87951485',
'end' => '88004391',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-016'
),
'ENST00000466847' => array(
'start' => '88035052',
'end' => '88076835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'BANP-019'
),
'ENST00000472964' => array(
'start' => '87982618',
'end' => '87984259',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-015'
),
'ENST00000474563' => array(
'start' => '87980535',
'end' => '87984227',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-023'
),
'ENST00000479780' => array(
'start' => '87951434',
'end' => '88076661',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-021'
),
'ENST00000481948' => array(
'start' => '88071073',
'end' => '88077318',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-020'
),
'ENST00000485772' => array(
'start' => '87951481',
'end' => '88003931',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'BANP-005'
),
'ENST00000488074' => array(
'start' => '87950436',
'end' => '87984234',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-008'
),
'ENST00000497491' => array(
'start' => '88017190',
'end' => '88033219',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-018'
),
'ENST00000526460' => array(
'start' => '87951467',
'end' => '87957069',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-022'
),
'ENST00000538234' => array(
'start' => '87959871',
'end' => '88077315',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BANP-203'
),
'ENST00000565242' => array(
'start' => '88037273',
'end' => '88072130',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'BANP-025'
),
'ENST00000569400' => array(
'start' => '87949244',
'end' => '87984251',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-024'
),
'ENST00000612301' => array(
'start' => '87952247',
'end' => '87952748',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BANP-026'
),
'ENST00000309893' => array(
'start' => '87881546',
'end' => '87936516',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CA5A-001'
),
'ENST00000566402' => array(
'start' => '87888018',
'end' => '87892268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CA5A-003'
),
'ENST00000568801' => array(
'start' => '87925539',
'end' => '87936529',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CA5A-002'
),
'ENST00000378417' => array(
'start' => '88088041',
'end' => '88100959',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.4-001'
),
'ENST00000566351' => array(
'start' => '88099409',
'end' => '88100985',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.4-002'
),
'ENST00000566155' => array(
'start' => '88087387',
'end' => '88087932',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.6-001'
),
'ENST00000565496' => array(
'start' => '87945058',
'end' => '87945202',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-3057O21.1-001'
),
'ENST00000562644' => array(
'start' => '87892938',
'end' => '87893685',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'GS1-21A4.1-001'
),
'ENST00000568267' => array(
'start' => '88079161',
'end' => '88087383',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-863P13.5-001'
),
'ENST00000604757' => array(
'start' => '87892955',
'end' => '87893735',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'GS1-21A4.2-001'
),
'ENSMUST00000026354' => array(
'start' => '121950580',
'end' => '122025937',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-003'
),
'ENSMUST00000093078' => array(
'start' => '121950492',
'end' => '122026177',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-002'
),
'ENSMUST00000167711' => array(
'start' => '121991604',
'end' => '122025958',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-004'
),
'ENSMUST00000170857' => array(
'start' => '121950544',
'end' => '122029258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-001'
),
'ENSMUST00000172511' => array(
'start' => '121950605',
'end' => '121991586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-013'
),
'ENSMUST00000172513' => array(
'start' => '121978322',
'end' => '121990002',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-011'
),
'ENSMUST00000172628' => array(
'start' => '121949750',
'end' => '121997183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-005'
),
'ENSMUST00000172681' => array(
'start' => '121950575',
'end' => '121997181',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Banp-010'
),
'ENSMUST00000173201' => array(
'start' => '122000847',
'end' => '122007140',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-007'
),
'ENSMUST00000173254' => array(
'start' => '121974496',
'end' => '122025635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-016'
),
'ENSMUST00000173396' => array(
'start' => '121997089',
'end' => '122025607',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-009'
),
'ENSMUST00000173753' => array(
'start' => '121974448',
'end' => '121976487',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-012'
),
'ENSMUST00000173925' => array(
'start' => '122000669',
'end' => '122020643',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Banp-006'
),
'ENSMUST00000174327' => array(
'start' => '121991458',
'end' => '121997238',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Banp-008'
),
'ENSMUST00000174445' => array(
'start' => '121950596',
'end' => '121991560',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Banp-014'
),
'ENSMUST00000174753' => array(
'start' => '121950585',
'end' => '121991569',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Banp-015'
),
'ENSMUST00000057653' => array(
'start' => '121916126',
'end' => '121944904',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Car5a-001'
),
'ENSMUST00000151462' => array(
'start' => '121918054',
'end' => '121927474',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Car5a-002'
),
'ENSMUST00000140928' => array(
'start' => '121907833',
'end' => '121918428',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC048644-001'
),
'ENSMUST00000181944' => array(
'start' => '121907833',
'end' => '121909824',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC048644-002'
),
'ENSMUST00000174536' => array(
'start' => '121972727',
'end' => '121973822',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm17709-001'
),
'ENSMUST00000183009' => array(
'start' => '121919024',
'end' => '121919690',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm26999-001'
),
'ENSMUST00000182352' => array(
'start' => '121949674',
'end' => '121950645',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27011-001'
),
'ENSMUST00000184699' => array(
'start' => '121978024',
'end' => '121978086',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7237-201'
)
)
$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_0002SY_0001' => array(
'genes_in_region' => array(
'ENSG00000172530' => array(
[maximum depth reached]
),
'ENSG00000174990' => array(
[maximum depth reached]
),
'ENSG00000205037' => array(
[maximum depth reached]
),
'ENSG00000260166' => array(
[maximum depth reached]
),
'ENSG00000260443' => array(
[maximum depth reached]
),
'ENSG00000260603' => array(
[maximum depth reached]
),
'ENSG00000261193' => array(
[maximum depth reached]
),
'ENSG00000270385' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Adrenal',
(int) 13 => 'Colon',
(int) 14 => 'Lung',
(int) 15 => 'Ovary',
(int) 16 => 'Placenta',
(int) 17 => 'Kidney',
(int) 18 => 'Lung',
(int) 19 => 'Colon',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Bladder',
(int) 23 => 'Lung',
(int) 24 => 'Liver',
(int) 25 => 'Colon',
(int) 26 => 'Muscle',
(int) 27 => 'Liver',
(int) 28 => 'Brain',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Lung',
(int) 32 => 'Ovary',
(int) 33 => 'Testis',
(int) 34 => 'Brain',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Muscle',
(int) 38 => 'Kidney',
(int) 39 => 'Bladder',
(int) 40 => 'Lung',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Adipose',
(int) 44 => 'Adrenal',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Ovary',
(int) 58 => 'Liver',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Bladder',
(int) 64 => 'Brain',
(int) 65 => 'Breast',
(int) 66 => 'Colon',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Lung',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Brain',
(int) 75 => 'Breast',
(int) 76 => 'Liver',
(int) 77 => 'Adrenal',
(int) 78 => 'Breast',
(int) 79 => 'Colon',
(int) 80 => 'Heart',
(int) 81 => 'Liver',
(int) 82 => 'Ovary',
(int) 83 => 'Testis',
(int) 84 => 'Brain',
(int) 85 => 'Testis',
(int) 86 => 'Adrenal',
(int) 87 => 'Brain',
(int) 88 => 'Breast',
(int) 89 => 'Heart',
(int) 90 => 'Kidney',
(int) 91 => 'Muscle',
(int) 92 => 'Testis',
(int) 93 => 'Adrenal',
(int) 94 => 'Brain',
(int) 95 => 'Breast',
(int) 96 => 'Colon',
(int) 97 => 'Heart',
(int) 98 => 'Ovary',
(int) 99 => 'Testis',
(int) 100 => 'Adipose',
(int) 101 => 'Adrenal',
(int) 102 => 'Breast',
(int) 103 => 'Colon',
(int) 104 => 'Heart',
(int) 105 => 'Kidney',
(int) 106 => 'Liver',
(int) 107 => 'Lung',
(int) 108 => 'Muscle',
(int) 109 => 'Ovary',
(int) 110 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0002SY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121916126',
'seq_end' => '122029258',
'region_length' => '113132',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000025317-ENSMUSG00000025316'
)
)
$gene_el = array(
'ENST00000604757' => array(
'Adipose' => array(
'average_FPKM' => '0.089',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.240',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.045',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.101',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.618',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.084',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.064',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000270385'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.089',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.240',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.045',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.101',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.618',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.084',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.064',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000604757'
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
(BANP)