Notice (8): Undefined index: CIL_0000JN_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_0000JN_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000JN_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000JN_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000011941' => 'bone morphogenetic protein receptor, type II a (serine/threonine kinase)',
'ENSDARG00000074921' => 'family with sequence similarity 117, member B',
'ENSDARG00000009839' => 'family with sequence similarity 117, member B',
'ENSDARG00000020057' => 'bone morphogenetic protein receptor, type II b (serine/threonine kinase)',
'ENSG00000138439' => 'family with sequence similarity 117, member B',
'ENSG00000204217' => 'bone morphogenetic protein receptor, type II (serine/threonine kinase)',
'ENSG00000223619' => null,
'ENSG00000227454' => 'MT-ND4 pseudogene 30',
'ENSG00000233134' => null,
'ENSG00000233311' => null,
'ENSG00000233888' => null,
'ENSG00000235433' => null,
'ENSG00000236047' => null,
'ENSG00000237542' => null,
'ENSG00000241221' => null,
'ENSG00000270915' => null,
'ENSMUSG00000026018' => 'islet cell autoantigen 1-like',
'ENSMUSG00000041040' => 'family with sequence similarity 117, member B',
'ENSMUSG00000067336' => 'bone morphogenetic protein receptor, type II (serine/threonine kinase)',
'ENSMUSG00000100901' => 'predicted gene, 18829'
),
'gene_name_arr' => array(
'ENSDARG00000011941' => 'bmpr2a',
'ENSDARG00000074921' => 'FAM117B (2 of 2)',
'ENSDARG00000009839' => 'FAM117B (1 of 2)',
'ENSDARG00000020057' => 'bmpr2b',
'ENSG00000138439' => 'FAM117B',
'ENSG00000204217' => 'BMPR2',
'ENSG00000223619' => 'AC009960.1',
'ENSG00000227454' => 'MTND4P30',
'ENSG00000233134' => 'AC009960.7',
'ENSG00000233311' => 'AC009960.3',
'ENSG00000233888' => 'AC009960.2',
'ENSG00000235433' => 'AC009960.4',
'ENSG00000236047' => 'AC073410.1',
'ENSG00000237542' => 'AC009960.5',
'ENSG00000241221' => 'AC009960.6',
'ENSG00000270915' => 'RP11-27M5.1',
'ENSMUSG00000026018' => 'Ica1l',
'ENSMUSG00000041040' => 'Fam117b',
'ENSMUSG00000067336' => 'Bmpr2',
'ENSMUSG00000100901' => 'RP23-27C10.4'
),
'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) 6 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 28 => 'Brain',
(int) 44 => 'Breast',
(int) 55 => 'Colon',
(int) 64 => 'Heart',
(int) 76 => 'Kidney',
(int) 85 => 'Liver',
(int) 100 => 'Lung',
(int) 110 => 'Muscle',
(int) 121 => 'Ovary',
(int) 130 => 'Placenta',
(int) 135 => '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) 38,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000056764' => array(
'start' => '12709568',
'end' => '12763808',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2a-001'
),
'ENSDART00000148145' => array(
'start' => '12736378',
'end' => '12736938',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'bmpr2a-002'
),
'ENSDART00000150955' => array(
'start' => '12737002',
'end' => '12780321',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'bmpr2a-003'
),
'ENSDART00000090065' => array(
'start' => '12768223',
'end' => '12781813',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (2 of 2)-201'
),
'ENSDART00000156341' => array(
'start' => '12765575',
'end' => '12777747',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (2 of 2)-001'
),
'ENSDART00000026644' => array(
'start' => '13454175',
'end' => '13488594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (1 of 2)-201'
),
'ENSDART00000141005' => array(
'start' => '13396651',
'end' => '13489022',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (1 of 2)-001'
),
'ENSDART00000002334' => array(
'start' => '13235992',
'end' => '13387395',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2b-201'
),
'ENSDART00000125961' => array(
'start' => '13235992',
'end' => '13387395',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2b-001'
),
'ENSDART00000137937' => array(
'start' => '13353084',
'end' => '13366095',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'bmpr2b-002'
),
'ENST00000392238' => array(
'start' => '202635188',
'end' => '202769757',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B-001'
),
'ENST00000481658' => array(
'start' => '202635489',
'end' => '202725232',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FAM117B-002'
),
'ENST00000374574' => array(
'start' => '202377434',
'end' => '202567751',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BMPR2-002'
),
'ENST00000374580' => array(
'start' => '202376936',
'end' => '202567751',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BMPR2-001'
),
'ENST00000479069' => array(
'start' => '202464826',
'end' => '202475139',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BMPR2-003'
),
'ENST00000411522' => array(
'start' => '202614214',
'end' => '202614704',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.1-001'
),
'ENST00000450281' => array(
'start' => '202617983',
'end' => '202618881',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'MTND4P30-001'
),
'ENST00000416968' => array(
'start' => '202617284',
'end' => '202617627',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.7-001'
),
'ENST00000430139' => array(
'start' => '202619185',
'end' => '202619896',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC009960.3-001'
),
'ENST00000424336' => array(
'start' => '202614853',
'end' => '202615529',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.2-001'
),
'ENST00000431030' => array(
'start' => '202615769',
'end' => '202616440',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.4-001'
),
'ENST00000435125' => array(
'start' => '202520401',
'end' => '202520989',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC073410.1-001'
),
'ENST00000443775' => array(
'start' => '202616700',
'end' => '202617212',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.5-001'
),
'ENST00000414607' => array(
'start' => '202617695',
'end' => '202617987',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.6-001'
),
'ENST00000603240' => array(
'start' => '202505012',
'end' => '202505343',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-27M5.1-001'
),
'ENSMUST00000027172' => array(
'start' => '59989068',
'end' => '60043087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-001'
),
'ENSMUST00000185891' => array(
'start' => '59982490',
'end' => '59990927',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ica1l-006'
),
'ENSMUST00000186970' => array(
'start' => '60020791',
'end' => '60043184',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ica1l-003'
),
'ENSMUST00000187364' => array(
'start' => '60015255',
'end' => '60022615',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ica1l-005'
),
'ENSMUST00000189776' => array(
'start' => '59991124',
'end' => '60028229',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-004'
),
'ENSMUST00000191251' => array(
'start' => '59989075',
'end' => '60043122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-002'
),
'ENSMUST00000036540' => array(
'start' => '59913006',
'end' => '59985346',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fam117b-001'
),
'ENSMUST00000151630' => array(
'start' => '59970680',
'end' => '59981515',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Fam117b-002'
),
'ENSMUST00000189790' => array(
'start' => '59979181',
'end' => '59980938',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fam117b-003'
),
'ENSMUST00000087435' => array(
'start' => '59763400',
'end' => '59879014',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Bmpr2-001'
),
'ENSMUST00000186246' => array(
'start' => '59851477',
'end' => '59856195',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Bmpr2-002'
),
'ENSMUST00000190659' => array(
'start' => '59850665',
'end' => '59852351',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Bmpr2-003'
),
'ENSMUST00000188150' => array(
'start' => '59950403',
'end' => '59952464',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP23-27C10.4-001'
)
),
'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_0000JN_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000JN_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000JN_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0000JN_0001' => array(
'genes_in_region' => array(
'ENSDARG00000011941' => array(
[maximum depth reached]
),
'ENSDARG00000074921' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Liver',
(int) 2 => 'Muscle',
(int) 3 => 'Liver',
(int) 4 => 'Brain',
(int) 5 => 'Liver'
)
),
'CIL_0000JN_0003' => array(
'genes_in_region' => array(
'ENSG00000138439' => array(
[maximum depth reached]
),
'ENSG00000204217' => array(
[maximum depth reached]
),
'ENSG00000223619' => array(
[maximum depth reached]
),
'ENSG00000227454' => array(
[maximum depth reached]
),
'ENSG00000233134' => array(
[maximum depth reached]
),
'ENSG00000233311' => array(
[maximum depth reached]
),
'ENSG00000233888' => array(
[maximum depth reached]
),
'ENSG00000235433' => array(
[maximum depth reached]
),
'ENSG00000236047' => array(
[maximum depth reached]
),
'ENSG00000237542' => array(
[maximum depth reached]
),
'ENSG00000241221' => array(
[maximum depth reached]
),
'ENSG00000270915' => 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 => 'Kidney',
(int) 15 => 'Muscle',
(int) 16 => 'Adrenal',
(int) 17 => 'Breast',
(int) 18 => 'Liver',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Adrenal',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Lung',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Testis',
(int) 52 => 'Adrenal',
(int) 53 => 'Adrenal',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Adrenal',
(int) 57 => 'Brain',
(int) 58 => 'Ovary',
(int) 59 => 'Testis',
(int) 60 => 'Adrenal',
(int) 61 => 'Bladder',
(int) 62 => 'Breast',
(int) 63 => 'Lung',
(int) 64 => 'Ovary',
(int) 65 => 'Testis',
(int) 66 => 'Adipose',
(int) 67 => 'Bladder',
(int) 68 => 'Brain',
(int) 69 => 'Breast',
(int) 70 => 'Colon',
(int) 71 => 'Heart',
(int) 72 => 'Kidney',
(int) 73 => 'Liver',
(int) 74 => 'Lung',
(int) 75 => 'Muscle',
(int) 76 => 'Ovary',
(int) 77 => 'Placenta',
(int) 78 => 'Testis',
(int) 79 => 'Adrenal',
(int) 80 => 'Brain',
(int) 81 => 'Liver',
(int) 82 => 'Testis',
(int) 83 => 'Adrenal',
(int) 84 => 'Adrenal',
(int) 85 => 'Brain',
(int) 86 => 'Breast',
(int) 87 => 'Colon',
(int) 88 => 'Lung',
(int) 89 => 'Testis'
)
),
'CIL_0000JN_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000026018' => array(
[maximum depth reached]
),
'ENSMUSG00000041040' => array(
[maximum depth reached]
),
'ENSMUSG00000067336' => array(
[maximum depth reached]
),
'ENSMUSG00000100901' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Testis',
(int) 2 => 'Ovary',
(int) 3 => 'Brain',
(int) 4 => 'Testis',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Testis',
(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 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000011941' => 'bone morphogenetic protein receptor, type II a (serine/threonine kinase)',
'ENSDARG00000074921' => 'family with sequence similarity 117, member B',
'ENSDARG00000009839' => 'family with sequence similarity 117, member B',
'ENSDARG00000020057' => 'bone morphogenetic protein receptor, type II b (serine/threonine kinase)',
'ENSG00000138439' => 'family with sequence similarity 117, member B',
'ENSG00000204217' => 'bone morphogenetic protein receptor, type II (serine/threonine kinase)',
'ENSG00000223619' => null,
'ENSG00000227454' => 'MT-ND4 pseudogene 30',
'ENSG00000233134' => null,
'ENSG00000233311' => null,
'ENSG00000233888' => null,
'ENSG00000235433' => null,
'ENSG00000236047' => null,
'ENSG00000237542' => null,
'ENSG00000241221' => null,
'ENSG00000270915' => null,
'ENSMUSG00000026018' => 'islet cell autoantigen 1-like',
'ENSMUSG00000041040' => 'family with sequence similarity 117, member B',
'ENSMUSG00000067336' => 'bone morphogenetic protein receptor, type II (serine/threonine kinase)',
'ENSMUSG00000100901' => 'predicted gene, 18829'
)
$gene_name_arr = array(
'ENSDARG00000011941' => 'bmpr2a',
'ENSDARG00000074921' => 'FAM117B (2 of 2)',
'ENSDARG00000009839' => 'FAM117B (1 of 2)',
'ENSDARG00000020057' => 'bmpr2b',
'ENSG00000138439' => 'FAM117B',
'ENSG00000204217' => 'BMPR2',
'ENSG00000223619' => 'AC009960.1',
'ENSG00000227454' => 'MTND4P30',
'ENSG00000233134' => 'AC009960.7',
'ENSG00000233311' => 'AC009960.3',
'ENSG00000233888' => 'AC009960.2',
'ENSG00000235433' => 'AC009960.4',
'ENSG00000236047' => 'AC073410.1',
'ENSG00000237542' => 'AC009960.5',
'ENSG00000241221' => 'AC009960.6',
'ENSG00000270915' => 'RP11-27M5.1',
'ENSMUSG00000026018' => 'Ica1l',
'ENSMUSG00000041040' => 'Fam117b',
'ENSMUSG00000067336' => 'Bmpr2',
'ENSMUSG00000100901' => 'RP23-27C10.4'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0001',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '12709568',
'seq_end' => '12781813',
'region_length' => '72245',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000011941-ENSDARG00000074921'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0002',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '13235992',
'seq_end' => '13489022',
'region_length' => '253030',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000020057-ENSDARG00000009839'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0003',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '202376936',
'seq_end' => '202769757',
'region_length' => '392821',
'region_type' => 'CGP',
'el_id' => 'ENSG00000204217-ENSG00000138439'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0004',
'tax_id' => '10090',
'chromosome' => '1',
'seq_start' => '59763400',
'seq_end' => '59985346',
'region_length' => '221946',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000067336-ENSMUSG00000041040'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 28 => 'Brain',
(int) 44 => 'Breast',
(int) 55 => 'Colon',
(int) 64 => 'Heart',
(int) 76 => 'Kidney',
(int) 85 => 'Liver',
(int) 100 => 'Lung',
(int) 110 => 'Muscle',
(int) 121 => 'Ovary',
(int) 130 => 'Placenta',
(int) 135 => '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) 38
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000056764' => array(
'start' => '12709568',
'end' => '12763808',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2a-001'
),
'ENSDART00000148145' => array(
'start' => '12736378',
'end' => '12736938',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'bmpr2a-002'
),
'ENSDART00000150955' => array(
'start' => '12737002',
'end' => '12780321',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'bmpr2a-003'
),
'ENSDART00000090065' => array(
'start' => '12768223',
'end' => '12781813',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (2 of 2)-201'
),
'ENSDART00000156341' => array(
'start' => '12765575',
'end' => '12777747',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (2 of 2)-001'
),
'ENSDART00000026644' => array(
'start' => '13454175',
'end' => '13488594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (1 of 2)-201'
),
'ENSDART00000141005' => array(
'start' => '13396651',
'end' => '13489022',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (1 of 2)-001'
),
'ENSDART00000002334' => array(
'start' => '13235992',
'end' => '13387395',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2b-201'
),
'ENSDART00000125961' => array(
'start' => '13235992',
'end' => '13387395',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2b-001'
),
'ENSDART00000137937' => array(
'start' => '13353084',
'end' => '13366095',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'bmpr2b-002'
),
'ENST00000392238' => array(
'start' => '202635188',
'end' => '202769757',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B-001'
),
'ENST00000481658' => array(
'start' => '202635489',
'end' => '202725232',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FAM117B-002'
),
'ENST00000374574' => array(
'start' => '202377434',
'end' => '202567751',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BMPR2-002'
),
'ENST00000374580' => array(
'start' => '202376936',
'end' => '202567751',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BMPR2-001'
),
'ENST00000479069' => array(
'start' => '202464826',
'end' => '202475139',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BMPR2-003'
),
'ENST00000411522' => array(
'start' => '202614214',
'end' => '202614704',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.1-001'
),
'ENST00000450281' => array(
'start' => '202617983',
'end' => '202618881',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'MTND4P30-001'
),
'ENST00000416968' => array(
'start' => '202617284',
'end' => '202617627',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.7-001'
),
'ENST00000430139' => array(
'start' => '202619185',
'end' => '202619896',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC009960.3-001'
),
'ENST00000424336' => array(
'start' => '202614853',
'end' => '202615529',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.2-001'
),
'ENST00000431030' => array(
'start' => '202615769',
'end' => '202616440',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.4-001'
),
'ENST00000435125' => array(
'start' => '202520401',
'end' => '202520989',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC073410.1-001'
),
'ENST00000443775' => array(
'start' => '202616700',
'end' => '202617212',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.5-001'
),
'ENST00000414607' => array(
'start' => '202617695',
'end' => '202617987',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.6-001'
),
'ENST00000603240' => array(
'start' => '202505012',
'end' => '202505343',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-27M5.1-001'
),
'ENSMUST00000027172' => array(
'start' => '59989068',
'end' => '60043087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-001'
),
'ENSMUST00000185891' => array(
'start' => '59982490',
'end' => '59990927',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ica1l-006'
),
'ENSMUST00000186970' => array(
'start' => '60020791',
'end' => '60043184',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ica1l-003'
),
'ENSMUST00000187364' => array(
'start' => '60015255',
'end' => '60022615',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ica1l-005'
),
'ENSMUST00000189776' => array(
'start' => '59991124',
'end' => '60028229',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-004'
),
'ENSMUST00000191251' => array(
'start' => '59989075',
'end' => '60043122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-002'
),
'ENSMUST00000036540' => array(
'start' => '59913006',
'end' => '59985346',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fam117b-001'
),
'ENSMUST00000151630' => array(
'start' => '59970680',
'end' => '59981515',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Fam117b-002'
),
'ENSMUST00000189790' => array(
'start' => '59979181',
'end' => '59980938',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fam117b-003'
),
'ENSMUST00000087435' => array(
'start' => '59763400',
'end' => '59879014',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Bmpr2-001'
),
'ENSMUST00000186246' => array(
'start' => '59851477',
'end' => '59856195',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Bmpr2-002'
),
'ENSMUST00000190659' => array(
'start' => '59850665',
'end' => '59852351',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Bmpr2-003'
),
'ENSMUST00000188150' => array(
'start' => '59950403',
'end' => '59952464',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP23-27C10.4-001'
)
)
$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_0000JN_0001' => array(
'genes_in_region' => array(
'ENSDARG00000011941' => array(
[maximum depth reached]
),
'ENSDARG00000074921' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Liver',
(int) 2 => 'Muscle',
(int) 3 => 'Liver',
(int) 4 => 'Brain',
(int) 5 => 'Liver'
)
),
'CIL_0000JN_0003' => array(
'genes_in_region' => array(
'ENSG00000138439' => array(
[maximum depth reached]
),
'ENSG00000204217' => array(
[maximum depth reached]
),
'ENSG00000223619' => array(
[maximum depth reached]
),
'ENSG00000227454' => array(
[maximum depth reached]
),
'ENSG00000233134' => array(
[maximum depth reached]
),
'ENSG00000233311' => array(
[maximum depth reached]
),
'ENSG00000233888' => array(
[maximum depth reached]
),
'ENSG00000235433' => array(
[maximum depth reached]
),
'ENSG00000236047' => array(
[maximum depth reached]
),
'ENSG00000237542' => array(
[maximum depth reached]
),
'ENSG00000241221' => array(
[maximum depth reached]
),
'ENSG00000270915' => 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 => 'Kidney',
(int) 15 => 'Muscle',
(int) 16 => 'Adrenal',
(int) 17 => 'Breast',
(int) 18 => 'Liver',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Adrenal',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Lung',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Testis',
(int) 52 => 'Adrenal',
(int) 53 => 'Adrenal',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Adrenal',
(int) 57 => 'Brain',
(int) 58 => 'Ovary',
(int) 59 => 'Testis',
(int) 60 => 'Adrenal',
(int) 61 => 'Bladder',
(int) 62 => 'Breast',
(int) 63 => 'Lung',
(int) 64 => 'Ovary',
(int) 65 => 'Testis',
(int) 66 => 'Adipose',
(int) 67 => 'Bladder',
(int) 68 => 'Brain',
(int) 69 => 'Breast',
(int) 70 => 'Colon',
(int) 71 => 'Heart',
(int) 72 => 'Kidney',
(int) 73 => 'Liver',
(int) 74 => 'Lung',
(int) 75 => 'Muscle',
(int) 76 => 'Ovary',
(int) 77 => 'Placenta',
(int) 78 => 'Testis',
(int) 79 => 'Adrenal',
(int) 80 => 'Brain',
(int) 81 => 'Liver',
(int) 82 => 'Testis',
(int) 83 => 'Adrenal',
(int) 84 => 'Adrenal',
(int) 85 => 'Brain',
(int) 86 => 'Breast',
(int) 87 => 'Colon',
(int) 88 => 'Lung',
(int) 89 => 'Testis'
)
),
'CIL_0000JN_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000026018' => array(
[maximum depth reached]
),
'ENSMUSG00000041040' => array(
[maximum depth reached]
),
'ENSMUSG00000067336' => array(
[maximum depth reached]
),
'ENSMUSG00000100901' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Testis',
(int) 2 => 'Ovary',
(int) 3 => 'Brain',
(int) 4 => 'Testis',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Testis',
(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 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0002',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '13235992',
'seq_end' => '13489022',
'region_length' => '253030',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000020057-ENSDARG00000009839'
)
)
$gene_el = array(
'ENSDART00000090065' => array(
'Brain' => array(
'average_FPKM' => '19.468',
'stddev_FPKM' => '7.89'
),
'Liver' => array(
'average_FPKM' => '0.057',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000156341' => array()
)
$gene_key = 'ENSDARG00000074921'
$is_first = false
$tran_el = array()
$tran_key = 'ENSDART00000156341'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0000JN_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000JN_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000JN_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000011941' => 'bone morphogenetic protein receptor, type II a (serine/threonine kinase)',
'ENSDARG00000074921' => 'family with sequence similarity 117, member B',
'ENSDARG00000009839' => 'family with sequence similarity 117, member B',
'ENSDARG00000020057' => 'bone morphogenetic protein receptor, type II b (serine/threonine kinase)',
'ENSG00000138439' => 'family with sequence similarity 117, member B',
'ENSG00000204217' => 'bone morphogenetic protein receptor, type II (serine/threonine kinase)',
'ENSG00000223619' => null,
'ENSG00000227454' => 'MT-ND4 pseudogene 30',
'ENSG00000233134' => null,
'ENSG00000233311' => null,
'ENSG00000233888' => null,
'ENSG00000235433' => null,
'ENSG00000236047' => null,
'ENSG00000237542' => null,
'ENSG00000241221' => null,
'ENSG00000270915' => null,
'ENSMUSG00000026018' => 'islet cell autoantigen 1-like',
'ENSMUSG00000041040' => 'family with sequence similarity 117, member B',
'ENSMUSG00000067336' => 'bone morphogenetic protein receptor, type II (serine/threonine kinase)',
'ENSMUSG00000100901' => 'predicted gene, 18829'
),
'gene_name_arr' => array(
'ENSDARG00000011941' => 'bmpr2a',
'ENSDARG00000074921' => 'FAM117B (2 of 2)',
'ENSDARG00000009839' => 'FAM117B (1 of 2)',
'ENSDARG00000020057' => 'bmpr2b',
'ENSG00000138439' => 'FAM117B',
'ENSG00000204217' => 'BMPR2',
'ENSG00000223619' => 'AC009960.1',
'ENSG00000227454' => 'MTND4P30',
'ENSG00000233134' => 'AC009960.7',
'ENSG00000233311' => 'AC009960.3',
'ENSG00000233888' => 'AC009960.2',
'ENSG00000235433' => 'AC009960.4',
'ENSG00000236047' => 'AC073410.1',
'ENSG00000237542' => 'AC009960.5',
'ENSG00000241221' => 'AC009960.6',
'ENSG00000270915' => 'RP11-27M5.1',
'ENSMUSG00000026018' => 'Ica1l',
'ENSMUSG00000041040' => 'Fam117b',
'ENSMUSG00000067336' => 'Bmpr2',
'ENSMUSG00000100901' => 'RP23-27C10.4'
),
'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) 6 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 28 => 'Brain',
(int) 44 => 'Breast',
(int) 55 => 'Colon',
(int) 64 => 'Heart',
(int) 76 => 'Kidney',
(int) 85 => 'Liver',
(int) 100 => 'Lung',
(int) 110 => 'Muscle',
(int) 121 => 'Ovary',
(int) 130 => 'Placenta',
(int) 135 => '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) 38,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000056764' => array(
'start' => '12709568',
'end' => '12763808',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2a-001'
),
'ENSDART00000148145' => array(
'start' => '12736378',
'end' => '12736938',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'bmpr2a-002'
),
'ENSDART00000150955' => array(
'start' => '12737002',
'end' => '12780321',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'bmpr2a-003'
),
'ENSDART00000090065' => array(
'start' => '12768223',
'end' => '12781813',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (2 of 2)-201'
),
'ENSDART00000156341' => array(
'start' => '12765575',
'end' => '12777747',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (2 of 2)-001'
),
'ENSDART00000026644' => array(
'start' => '13454175',
'end' => '13488594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (1 of 2)-201'
),
'ENSDART00000141005' => array(
'start' => '13396651',
'end' => '13489022',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (1 of 2)-001'
),
'ENSDART00000002334' => array(
'start' => '13235992',
'end' => '13387395',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2b-201'
),
'ENSDART00000125961' => array(
'start' => '13235992',
'end' => '13387395',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2b-001'
),
'ENSDART00000137937' => array(
'start' => '13353084',
'end' => '13366095',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'bmpr2b-002'
),
'ENST00000392238' => array(
'start' => '202635188',
'end' => '202769757',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B-001'
),
'ENST00000481658' => array(
'start' => '202635489',
'end' => '202725232',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FAM117B-002'
),
'ENST00000374574' => array(
'start' => '202377434',
'end' => '202567751',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BMPR2-002'
),
'ENST00000374580' => array(
'start' => '202376936',
'end' => '202567751',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BMPR2-001'
),
'ENST00000479069' => array(
'start' => '202464826',
'end' => '202475139',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BMPR2-003'
),
'ENST00000411522' => array(
'start' => '202614214',
'end' => '202614704',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.1-001'
),
'ENST00000450281' => array(
'start' => '202617983',
'end' => '202618881',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'MTND4P30-001'
),
'ENST00000416968' => array(
'start' => '202617284',
'end' => '202617627',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.7-001'
),
'ENST00000430139' => array(
'start' => '202619185',
'end' => '202619896',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC009960.3-001'
),
'ENST00000424336' => array(
'start' => '202614853',
'end' => '202615529',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.2-001'
),
'ENST00000431030' => array(
'start' => '202615769',
'end' => '202616440',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.4-001'
),
'ENST00000435125' => array(
'start' => '202520401',
'end' => '202520989',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC073410.1-001'
),
'ENST00000443775' => array(
'start' => '202616700',
'end' => '202617212',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.5-001'
),
'ENST00000414607' => array(
'start' => '202617695',
'end' => '202617987',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.6-001'
),
'ENST00000603240' => array(
'start' => '202505012',
'end' => '202505343',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-27M5.1-001'
),
'ENSMUST00000027172' => array(
'start' => '59989068',
'end' => '60043087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-001'
),
'ENSMUST00000185891' => array(
'start' => '59982490',
'end' => '59990927',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ica1l-006'
),
'ENSMUST00000186970' => array(
'start' => '60020791',
'end' => '60043184',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ica1l-003'
),
'ENSMUST00000187364' => array(
'start' => '60015255',
'end' => '60022615',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ica1l-005'
),
'ENSMUST00000189776' => array(
'start' => '59991124',
'end' => '60028229',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-004'
),
'ENSMUST00000191251' => array(
'start' => '59989075',
'end' => '60043122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-002'
),
'ENSMUST00000036540' => array(
'start' => '59913006',
'end' => '59985346',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fam117b-001'
),
'ENSMUST00000151630' => array(
'start' => '59970680',
'end' => '59981515',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Fam117b-002'
),
'ENSMUST00000189790' => array(
'start' => '59979181',
'end' => '59980938',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fam117b-003'
),
'ENSMUST00000087435' => array(
'start' => '59763400',
'end' => '59879014',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Bmpr2-001'
),
'ENSMUST00000186246' => array(
'start' => '59851477',
'end' => '59856195',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Bmpr2-002'
),
'ENSMUST00000190659' => array(
'start' => '59850665',
'end' => '59852351',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Bmpr2-003'
),
'ENSMUST00000188150' => array(
'start' => '59950403',
'end' => '59952464',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP23-27C10.4-001'
)
),
'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_0000JN_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000JN_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000JN_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0000JN_0001' => array(
'genes_in_region' => array(
'ENSDARG00000011941' => array(
[maximum depth reached]
),
'ENSDARG00000074921' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Liver',
(int) 2 => 'Muscle',
(int) 3 => 'Liver',
(int) 4 => 'Brain',
(int) 5 => 'Liver'
)
),
'CIL_0000JN_0003' => array(
'genes_in_region' => array(
'ENSG00000138439' => array(
[maximum depth reached]
),
'ENSG00000204217' => array(
[maximum depth reached]
),
'ENSG00000223619' => array(
[maximum depth reached]
),
'ENSG00000227454' => array(
[maximum depth reached]
),
'ENSG00000233134' => array(
[maximum depth reached]
),
'ENSG00000233311' => array(
[maximum depth reached]
),
'ENSG00000233888' => array(
[maximum depth reached]
),
'ENSG00000235433' => array(
[maximum depth reached]
),
'ENSG00000236047' => array(
[maximum depth reached]
),
'ENSG00000237542' => array(
[maximum depth reached]
),
'ENSG00000241221' => array(
[maximum depth reached]
),
'ENSG00000270915' => 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 => 'Kidney',
(int) 15 => 'Muscle',
(int) 16 => 'Adrenal',
(int) 17 => 'Breast',
(int) 18 => 'Liver',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Adrenal',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Lung',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Testis',
(int) 52 => 'Adrenal',
(int) 53 => 'Adrenal',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Adrenal',
(int) 57 => 'Brain',
(int) 58 => 'Ovary',
(int) 59 => 'Testis',
(int) 60 => 'Adrenal',
(int) 61 => 'Bladder',
(int) 62 => 'Breast',
(int) 63 => 'Lung',
(int) 64 => 'Ovary',
(int) 65 => 'Testis',
(int) 66 => 'Adipose',
(int) 67 => 'Bladder',
(int) 68 => 'Brain',
(int) 69 => 'Breast',
(int) 70 => 'Colon',
(int) 71 => 'Heart',
(int) 72 => 'Kidney',
(int) 73 => 'Liver',
(int) 74 => 'Lung',
(int) 75 => 'Muscle',
(int) 76 => 'Ovary',
(int) 77 => 'Placenta',
(int) 78 => 'Testis',
(int) 79 => 'Adrenal',
(int) 80 => 'Brain',
(int) 81 => 'Liver',
(int) 82 => 'Testis',
(int) 83 => 'Adrenal',
(int) 84 => 'Adrenal',
(int) 85 => 'Brain',
(int) 86 => 'Breast',
(int) 87 => 'Colon',
(int) 88 => 'Lung',
(int) 89 => 'Testis'
)
),
'CIL_0000JN_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000026018' => array(
[maximum depth reached]
),
'ENSMUSG00000041040' => array(
[maximum depth reached]
),
'ENSMUSG00000067336' => array(
[maximum depth reached]
),
'ENSMUSG00000100901' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Testis',
(int) 2 => 'Ovary',
(int) 3 => 'Brain',
(int) 4 => 'Testis',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Testis',
(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 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000011941' => 'bone morphogenetic protein receptor, type II a (serine/threonine kinase)',
'ENSDARG00000074921' => 'family with sequence similarity 117, member B',
'ENSDARG00000009839' => 'family with sequence similarity 117, member B',
'ENSDARG00000020057' => 'bone morphogenetic protein receptor, type II b (serine/threonine kinase)',
'ENSG00000138439' => 'family with sequence similarity 117, member B',
'ENSG00000204217' => 'bone morphogenetic protein receptor, type II (serine/threonine kinase)',
'ENSG00000223619' => null,
'ENSG00000227454' => 'MT-ND4 pseudogene 30',
'ENSG00000233134' => null,
'ENSG00000233311' => null,
'ENSG00000233888' => null,
'ENSG00000235433' => null,
'ENSG00000236047' => null,
'ENSG00000237542' => null,
'ENSG00000241221' => null,
'ENSG00000270915' => null,
'ENSMUSG00000026018' => 'islet cell autoantigen 1-like',
'ENSMUSG00000041040' => 'family with sequence similarity 117, member B',
'ENSMUSG00000067336' => 'bone morphogenetic protein receptor, type II (serine/threonine kinase)',
'ENSMUSG00000100901' => 'predicted gene, 18829'
)
$gene_name_arr = array(
'ENSDARG00000011941' => 'bmpr2a',
'ENSDARG00000074921' => 'FAM117B (2 of 2)',
'ENSDARG00000009839' => 'FAM117B (1 of 2)',
'ENSDARG00000020057' => 'bmpr2b',
'ENSG00000138439' => 'FAM117B',
'ENSG00000204217' => 'BMPR2',
'ENSG00000223619' => 'AC009960.1',
'ENSG00000227454' => 'MTND4P30',
'ENSG00000233134' => 'AC009960.7',
'ENSG00000233311' => 'AC009960.3',
'ENSG00000233888' => 'AC009960.2',
'ENSG00000235433' => 'AC009960.4',
'ENSG00000236047' => 'AC073410.1',
'ENSG00000237542' => 'AC009960.5',
'ENSG00000241221' => 'AC009960.6',
'ENSG00000270915' => 'RP11-27M5.1',
'ENSMUSG00000026018' => 'Ica1l',
'ENSMUSG00000041040' => 'Fam117b',
'ENSMUSG00000067336' => 'Bmpr2',
'ENSMUSG00000100901' => 'RP23-27C10.4'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0001',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '12709568',
'seq_end' => '12781813',
'region_length' => '72245',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000011941-ENSDARG00000074921'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0002',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '13235992',
'seq_end' => '13489022',
'region_length' => '253030',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000020057-ENSDARG00000009839'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0003',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '202376936',
'seq_end' => '202769757',
'region_length' => '392821',
'region_type' => 'CGP',
'el_id' => 'ENSG00000204217-ENSG00000138439'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0004',
'tax_id' => '10090',
'chromosome' => '1',
'seq_start' => '59763400',
'seq_end' => '59985346',
'region_length' => '221946',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000067336-ENSMUSG00000041040'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 28 => 'Brain',
(int) 44 => 'Breast',
(int) 55 => 'Colon',
(int) 64 => 'Heart',
(int) 76 => 'Kidney',
(int) 85 => 'Liver',
(int) 100 => 'Lung',
(int) 110 => 'Muscle',
(int) 121 => 'Ovary',
(int) 130 => 'Placenta',
(int) 135 => '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) 38
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000056764' => array(
'start' => '12709568',
'end' => '12763808',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2a-001'
),
'ENSDART00000148145' => array(
'start' => '12736378',
'end' => '12736938',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'bmpr2a-002'
),
'ENSDART00000150955' => array(
'start' => '12737002',
'end' => '12780321',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'bmpr2a-003'
),
'ENSDART00000090065' => array(
'start' => '12768223',
'end' => '12781813',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (2 of 2)-201'
),
'ENSDART00000156341' => array(
'start' => '12765575',
'end' => '12777747',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (2 of 2)-001'
),
'ENSDART00000026644' => array(
'start' => '13454175',
'end' => '13488594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (1 of 2)-201'
),
'ENSDART00000141005' => array(
'start' => '13396651',
'end' => '13489022',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B (1 of 2)-001'
),
'ENSDART00000002334' => array(
'start' => '13235992',
'end' => '13387395',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2b-201'
),
'ENSDART00000125961' => array(
'start' => '13235992',
'end' => '13387395',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'bmpr2b-001'
),
'ENSDART00000137937' => array(
'start' => '13353084',
'end' => '13366095',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'bmpr2b-002'
),
'ENST00000392238' => array(
'start' => '202635188',
'end' => '202769757',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FAM117B-001'
),
'ENST00000481658' => array(
'start' => '202635489',
'end' => '202725232',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FAM117B-002'
),
'ENST00000374574' => array(
'start' => '202377434',
'end' => '202567751',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BMPR2-002'
),
'ENST00000374580' => array(
'start' => '202376936',
'end' => '202567751',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BMPR2-001'
),
'ENST00000479069' => array(
'start' => '202464826',
'end' => '202475139',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BMPR2-003'
),
'ENST00000411522' => array(
'start' => '202614214',
'end' => '202614704',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.1-001'
),
'ENST00000450281' => array(
'start' => '202617983',
'end' => '202618881',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'MTND4P30-001'
),
'ENST00000416968' => array(
'start' => '202617284',
'end' => '202617627',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.7-001'
),
'ENST00000430139' => array(
'start' => '202619185',
'end' => '202619896',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC009960.3-001'
),
'ENST00000424336' => array(
'start' => '202614853',
'end' => '202615529',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.2-001'
),
'ENST00000431030' => array(
'start' => '202615769',
'end' => '202616440',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.4-001'
),
'ENST00000435125' => array(
'start' => '202520401',
'end' => '202520989',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC073410.1-001'
),
'ENST00000443775' => array(
'start' => '202616700',
'end' => '202617212',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.5-001'
),
'ENST00000414607' => array(
'start' => '202617695',
'end' => '202617987',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'AC009960.6-001'
),
'ENST00000603240' => array(
'start' => '202505012',
'end' => '202505343',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-27M5.1-001'
),
'ENSMUST00000027172' => array(
'start' => '59989068',
'end' => '60043087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-001'
),
'ENSMUST00000185891' => array(
'start' => '59982490',
'end' => '59990927',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ica1l-006'
),
'ENSMUST00000186970' => array(
'start' => '60020791',
'end' => '60043184',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ica1l-003'
),
'ENSMUST00000187364' => array(
'start' => '60015255',
'end' => '60022615',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ica1l-005'
),
'ENSMUST00000189776' => array(
'start' => '59991124',
'end' => '60028229',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-004'
),
'ENSMUST00000191251' => array(
'start' => '59989075',
'end' => '60043122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ica1l-002'
),
'ENSMUST00000036540' => array(
'start' => '59913006',
'end' => '59985346',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fam117b-001'
),
'ENSMUST00000151630' => array(
'start' => '59970680',
'end' => '59981515',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Fam117b-002'
),
'ENSMUST00000189790' => array(
'start' => '59979181',
'end' => '59980938',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fam117b-003'
),
'ENSMUST00000087435' => array(
'start' => '59763400',
'end' => '59879014',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Bmpr2-001'
),
'ENSMUST00000186246' => array(
'start' => '59851477',
'end' => '59856195',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Bmpr2-002'
),
'ENSMUST00000190659' => array(
'start' => '59850665',
'end' => '59852351',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Bmpr2-003'
),
'ENSMUST00000188150' => array(
'start' => '59950403',
'end' => '59952464',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP23-27C10.4-001'
)
)
$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_0000JN_0001' => array(
'genes_in_region' => array(
'ENSDARG00000011941' => array(
[maximum depth reached]
),
'ENSDARG00000074921' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Liver',
(int) 2 => 'Muscle',
(int) 3 => 'Liver',
(int) 4 => 'Brain',
(int) 5 => 'Liver'
)
),
'CIL_0000JN_0003' => array(
'genes_in_region' => array(
'ENSG00000138439' => array(
[maximum depth reached]
),
'ENSG00000204217' => array(
[maximum depth reached]
),
'ENSG00000223619' => array(
[maximum depth reached]
),
'ENSG00000227454' => array(
[maximum depth reached]
),
'ENSG00000233134' => array(
[maximum depth reached]
),
'ENSG00000233311' => array(
[maximum depth reached]
),
'ENSG00000233888' => array(
[maximum depth reached]
),
'ENSG00000235433' => array(
[maximum depth reached]
),
'ENSG00000236047' => array(
[maximum depth reached]
),
'ENSG00000237542' => array(
[maximum depth reached]
),
'ENSG00000241221' => array(
[maximum depth reached]
),
'ENSG00000270915' => 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 => 'Kidney',
(int) 15 => 'Muscle',
(int) 16 => 'Adrenal',
(int) 17 => 'Breast',
(int) 18 => 'Liver',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Adrenal',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Lung',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Testis',
(int) 52 => 'Adrenal',
(int) 53 => 'Adrenal',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Adrenal',
(int) 57 => 'Brain',
(int) 58 => 'Ovary',
(int) 59 => 'Testis',
(int) 60 => 'Adrenal',
(int) 61 => 'Bladder',
(int) 62 => 'Breast',
(int) 63 => 'Lung',
(int) 64 => 'Ovary',
(int) 65 => 'Testis',
(int) 66 => 'Adipose',
(int) 67 => 'Bladder',
(int) 68 => 'Brain',
(int) 69 => 'Breast',
(int) 70 => 'Colon',
(int) 71 => 'Heart',
(int) 72 => 'Kidney',
(int) 73 => 'Liver',
(int) 74 => 'Lung',
(int) 75 => 'Muscle',
(int) 76 => 'Ovary',
(int) 77 => 'Placenta',
(int) 78 => 'Testis',
(int) 79 => 'Adrenal',
(int) 80 => 'Brain',
(int) 81 => 'Liver',
(int) 82 => 'Testis',
(int) 83 => 'Adrenal',
(int) 84 => 'Adrenal',
(int) 85 => 'Brain',
(int) 86 => 'Breast',
(int) 87 => 'Colon',
(int) 88 => 'Lung',
(int) 89 => 'Testis'
)
),
'CIL_0000JN_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000026018' => array(
[maximum depth reached]
),
'ENSMUSG00000041040' => array(
[maximum depth reached]
),
'ENSMUSG00000067336' => array(
[maximum depth reached]
),
'ENSMUSG00000100901' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Testis',
(int) 2 => 'Ovary',
(int) 3 => 'Brain',
(int) 4 => 'Testis',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Testis',
(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 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0000JN_0002',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '13235992',
'seq_end' => '13489022',
'region_length' => '253030',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000020057-ENSDARG00000009839'
)
)
$gene_el = array(
'ENSDART00000090065' => array(
'Brain' => array(
'average_FPKM' => '19.468',
'stddev_FPKM' => '7.89'
),
'Liver' => array(
'average_FPKM' => '0.057',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000156341' => array()
)
$gene_key = 'ENSDARG00000074921'
$is_first = false
$tran_el = array()
$tran_key = 'ENSDART00000156341'
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
| Source ID |
Type |
Tax ID |
Position |
| ENSDARG00000020057-ENSDARG00000009839 |
CGP |
7955 |
9:13235992-13489022  |
| Gene | Transcript | Position | Biotype |
|---|
(bmpr2a)