| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000006362-ENSMUSG00000015016 |
CGP |
10090 |
8:122628739-122817880  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0006AJ_0003 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0006AJ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AJ_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000059503' => 'Uncharacterized protein',
'ENSDARG00000079012' => 'core-binding factor, runt domain, alpha subunit 2; translocated to, 3',
'ENSDARG00000088664' => '5S ribosomal RNA',
'ENSG00000129993' => 'core-binding factor, runt domain, alpha subunit 2; translocated to, 3',
'ENSG00000176715' => 'acyl-CoA synthetase family member 3',
'ENSG00000205018' => null,
'ENSG00000256982' => null,
'ENSG00000259881' => null,
'ENSG00000259989' => null,
'ENSG00000261226' => null,
'ENSG00000261546' => null,
'ENSMUSG00000006362' => 'core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)',
'ENSMUSG00000015016' => 'acyl-CoA synthetase family member 3',
'ENSMUSG00000085917' => 'predicted gene 15899',
'ENSMUSG00000090174' => 'predicted gene 10612'
),
'gene_name_arr' => array(
'ENSDARG00000059503' => 'CR848706.1',
'ENSDARG00000079012' => 'CBFA2T3',
'ENSDARG00000088664' => '5S_rRNA',
'ENSG00000129993' => 'CBFA2T3',
'ENSG00000176715' => 'ACSF3',
'ENSG00000205018' => 'RP11-830F9.6',
'ENSG00000256982' => 'CTD-2555A7.2',
'ENSG00000259881' => 'RP11-830F9.5',
'ENSG00000259989' => 'CTD-2555A7.1',
'ENSG00000261226' => 'RP11-830F9.7',
'ENSG00000261546' => 'CTD-2555A7.3',
'ENSMUSG00000006362' => 'Cbfa2t3',
'ENSMUSG00000015016' => 'Acsf3',
'ENSMUSG00000085917' => 'Gm15899',
'ENSMUSG00000090174' => 'Gm10612'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 21 => 'Brain',
(int) 36 => 'Breast',
(int) 44 => 'Colon',
(int) 54 => 'Heart',
(int) 67 => 'Kidney',
(int) 76 => 'Liver',
(int) 88 => 'Lung',
(int) 99 => 'Muscle',
(int) 113 => 'Ovary',
(int) 127 => 'Placenta',
(int) 137 => '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) 52,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000082780' => array(
'start' => '57215011',
'end' => '57300831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CR848706.1-201'
),
'ENSDART00000021009' => array(
'start' => '56923526',
'end' => '56938884',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-201'
),
'ENSDART00000125848' => array(
'start' => '57050282',
'end' => '57050396',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1697-201'
),
'ENST00000268679' => array(
'start' => '88874858',
'end' => '88977204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-001'
),
'ENST00000327483' => array(
'start' => '88874858',
'end' => '88941198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-002'
),
'ENST00000562719' => array(
'start' => '88892285',
'end' => '88902515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-008'
),
'ENST00000563640' => array(
'start' => '88892399',
'end' => '88977080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-009'
),
'ENST00000563856' => array(
'start' => '88875525',
'end' => '88881157',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBFA2T3-004'
),
'ENST00000563920' => array(
'start' => '88876228',
'end' => '88880036',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBFA2T3-005'
),
'ENST00000564416' => array(
'start' => '88898088',
'end' => '88941200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-011'
),
'ENST00000566868' => array(
'start' => '88879430',
'end' => '88881313',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CBFA2T3-007'
),
'ENST00000569443' => array(
'start' => '88892244',
'end' => '88941844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-010'
),
'ENST00000569464' => array(
'start' => '88881112',
'end' => '88941809',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-006'
),
'ENST00000570046' => array(
'start' => '88901558',
'end' => '88957775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-012'
),
'ENST00000317447' => array(
'start' => '89093809',
'end' => '89155763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-001'
),
'ENST00000378345' => array(
'start' => '89093898',
'end' => '89154588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-002'
),
'ENST00000393145' => array(
'start' => '89147567',
'end' => '89154586',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-020'
),
'ENST00000406948' => array(
'start' => '89093883',
'end' => '89154589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-003'
),
'ENST00000535176' => array(
'start' => '89145950',
'end' => '89151348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-013'
),
'ENST00000537116' => array(
'start' => '89136548',
'end' => '89155846',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-005'
),
'ENST00000537155' => array(
'start' => '89145161',
'end' => '89154584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-016'
),
'ENST00000537290' => array(
'start' => '89093855',
'end' => '89102648',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-009'
),
'ENST00000537895' => array(
'start' => '89088375',
'end' => '89114473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-011'
),
'ENST00000538340' => array(
'start' => '89102613',
'end' => '89122392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-015'
),
'ENST00000540697' => array(
'start' => '89093868',
'end' => '89133262',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-010'
),
'ENST00000541755' => array(
'start' => '89093904',
'end' => '89100767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-023'
),
'ENST00000542688' => array(
'start' => '89098711',
'end' => '89154540',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ACSF3-006'
),
'ENST00000543676' => array(
'start' => '89102696',
'end' => '89122832',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-014'
),
'ENST00000544543' => array(
'start' => '89102352',
'end' => '89145400',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-012'
),
'ENST00000562204' => array(
'start' => '89112201',
'end' => '89146044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-021'
),
'ENST00000562750' => array(
'start' => '89150600',
'end' => '89151222',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-019'
),
'ENST00000614302' => array(
'start' => '89093809',
'end' => '89155846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-201'
),
'ENST00000378347' => array(
'start' => '88939789',
'end' => '88951524',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.6-001'
),
'ENST00000537498' => array(
'start' => '89046172',
'end' => '89052965',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2555A7.2-001'
),
'ENST00000562405' => array(
'start' => '88881038',
'end' => '88883919',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-001'
),
'ENST00000562574' => array(
'start' => '88881257',
'end' => '88883715',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-002'
),
'ENST00000565053' => array(
'start' => '88883272',
'end' => '88887136',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-004'
),
'ENST00000569249' => array(
'start' => '88881455',
'end' => '88883926',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-003'
),
'ENST00000562040' => array(
'start' => '88984032',
'end' => '88995369',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2555A7.1-001'
),
'ENST00000561980' => array(
'start' => '88936779',
'end' => '88937756',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-830F9.7-002'
),
'ENST00000564646' => array(
'start' => '88936779',
'end' => '88939651',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-830F9.7-001'
),
'ENST00000562782' => array(
'start' => '89113175',
'end' => '89115279',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2555A7.3-001'
),
'ENSMUST00000006525' => array(
'start' => '122629463',
'end' => '122678072',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-003'
),
'ENSMUST00000064674' => array(
'start' => '122629938',
'end' => '122678175',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-002'
),
'ENSMUST00000127984' => array(
'start' => '122628739',
'end' => '122699109',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-001'
),
'ENSMUST00000134045' => array(
'start' => '122639014',
'end' => '122678694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-005'
),
'ENSMUST00000142535' => array(
'start' => '122639018',
'end' => '122646466',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbfa2t3-007'
),
'ENSMUST00000147374' => array(
'start' => '122643004',
'end' => '122678111',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbfa2t3-006'
),
'ENSMUST00000148630' => array(
'start' => '122650028',
'end' => '122698902',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cbfa2t3-004'
),
'ENSMUST00000015160' => array(
'start' => '122775505',
'end' => '122817880',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Acsf3-201'
),
'ENSMUST00000128586' => array(
'start' => '122683602',
'end' => '122683839',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm15899-001'
),
'ENSMUST00000162198' => array(
'start' => '122697860',
'end' => '122700160',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm10612-001'
)
),
'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_0006AJ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AJ_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0006AJ_0001' => array(
'genes_in_region' => array(
'ENSDARG00000059503' => array(
[maximum depth reached]
),
'ENSDARG00000079012' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Liver',
(int) 7 => 'Muscle'
)
),
'CIL_0006AJ_0002' => array(
'genes_in_region' => array(
'ENSG00000129993' => array(
[maximum depth reached]
),
'ENSG00000205018' => array(
[maximum depth reached]
),
'ENSG00000256982' => array(
[maximum depth reached]
),
'ENSG00000259989' => array(
[maximum depth reached]
),
'ENSG00000261226' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Colon',
(int) 1 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Brain',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Testis',
(int) 10 => 'Liver',
(int) 11 => 'Liver',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Ovary',
(int) 36 => 'Heart',
(int) 37 => 'Placenta',
(int) 38 => 'Adipose',
(int) 39 => 'Colon',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Muscle',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Muscle',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis',
(int) 59 => 'Adipose',
(int) 60 => 'Bladder',
(int) 61 => 'Brain',
(int) 62 => 'Breast',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Liver',
(int) 66 => 'Lung',
(int) 67 => 'Ovary',
(int) 68 => 'Placenta',
(int) 69 => 'Muscle',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Heart',
(int) 76 => 'Brain',
(int) 77 => 'Kidney',
(int) 78 => 'Muscle',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Adipose',
(int) 82 => 'Adrenal',
(int) 83 => 'Brain',
(int) 84 => 'Breast',
(int) 85 => 'Heart',
(int) 86 => 'Kidney',
(int) 87 => 'Lung',
(int) 88 => 'Muscle',
(int) 89 => 'Ovary',
(int) 90 => 'Placenta',
(int) 91 => 'Testis',
(int) 92 => 'Brain',
(int) 93 => 'Bladder',
(int) 94 => 'Ovary',
(int) 95 => 'Adipose',
(int) 96 => 'Adrenal',
(int) 97 => 'Brain',
(int) 98 => 'Breast',
(int) 99 => 'Colon',
(int) 100 => 'Heart',
(int) 101 => 'Kidney',
(int) 102 => 'Liver',
(int) 103 => 'Lung',
(int) 104 => 'Ovary',
(int) 105 => 'Placenta',
(int) 106 => 'Testis',
(int) 107 => 'Adrenal',
(int) 108 => 'Brain',
(int) 109 => 'Colon',
(int) 110 => 'Lung',
(int) 111 => 'Brain',
(int) 112 => 'Muscle',
(int) 113 => 'Colon',
(int) 114 => 'Liver',
(int) 115 => 'Ovary',
(int) 116 => 'Adrenal',
(int) 117 => 'Testis',
(int) 118 => 'Bladder',
(int) 119 => 'Brain',
(int) 120 => 'Breast',
(int) 121 => 'Heart',
(int) 122 => 'Lung',
(int) 123 => 'Muscle',
(int) 124 => 'Ovary',
(int) 125 => 'Placenta',
(int) 126 => 'Testis',
(int) 127 => 'Adipose',
(int) 128 => 'Adrenal',
(int) 129 => 'Brain',
(int) 130 => 'Breast',
(int) 131 => 'Colon',
(int) 132 => 'Heart',
(int) 133 => 'Kidney',
(int) 134 => 'Liver',
(int) 135 => 'Lung',
(int) 136 => 'Ovary',
(int) 137 => 'Placenta',
(int) 138 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000059503' => 'Uncharacterized protein',
'ENSDARG00000079012' => 'core-binding factor, runt domain, alpha subunit 2; translocated to, 3',
'ENSDARG00000088664' => '5S ribosomal RNA',
'ENSG00000129993' => 'core-binding factor, runt domain, alpha subunit 2; translocated to, 3',
'ENSG00000176715' => 'acyl-CoA synthetase family member 3',
'ENSG00000205018' => null,
'ENSG00000256982' => null,
'ENSG00000259881' => null,
'ENSG00000259989' => null,
'ENSG00000261226' => null,
'ENSG00000261546' => null,
'ENSMUSG00000006362' => 'core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)',
'ENSMUSG00000015016' => 'acyl-CoA synthetase family member 3',
'ENSMUSG00000085917' => 'predicted gene 15899',
'ENSMUSG00000090174' => 'predicted gene 10612'
)
$gene_name_arr = array(
'ENSDARG00000059503' => 'CR848706.1',
'ENSDARG00000079012' => 'CBFA2T3',
'ENSDARG00000088664' => '5S_rRNA',
'ENSG00000129993' => 'CBFA2T3',
'ENSG00000176715' => 'ACSF3',
'ENSG00000205018' => 'RP11-830F9.6',
'ENSG00000256982' => 'CTD-2555A7.2',
'ENSG00000259881' => 'RP11-830F9.5',
'ENSG00000259989' => 'CTD-2555A7.1',
'ENSG00000261226' => 'RP11-830F9.7',
'ENSG00000261546' => 'CTD-2555A7.3',
'ENSMUSG00000006362' => 'Cbfa2t3',
'ENSMUSG00000015016' => 'Acsf3',
'ENSMUSG00000085917' => 'Gm15899',
'ENSMUSG00000090174' => 'Gm10612'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AJ_0001',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '56923526',
'seq_end' => '57300831',
'region_length' => '377305',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000079012-ENSDARG00000059503'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AJ_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '88874858',
'seq_end' => '89155846',
'region_length' => '280988',
'region_type' => 'CGP',
'el_id' => 'ENSG00000129993-ENSG00000176715'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AJ_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122628739',
'seq_end' => '122817880',
'region_length' => '189141',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006362-ENSMUSG00000015016'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 21 => 'Brain',
(int) 36 => 'Breast',
(int) 44 => 'Colon',
(int) 54 => 'Heart',
(int) 67 => 'Kidney',
(int) 76 => 'Liver',
(int) 88 => 'Lung',
(int) 99 => 'Muscle',
(int) 113 => 'Ovary',
(int) 127 => 'Placenta',
(int) 137 => '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) 52
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000082780' => array(
'start' => '57215011',
'end' => '57300831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CR848706.1-201'
),
'ENSDART00000021009' => array(
'start' => '56923526',
'end' => '56938884',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-201'
),
'ENSDART00000125848' => array(
'start' => '57050282',
'end' => '57050396',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1697-201'
),
'ENST00000268679' => array(
'start' => '88874858',
'end' => '88977204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-001'
),
'ENST00000327483' => array(
'start' => '88874858',
'end' => '88941198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-002'
),
'ENST00000562719' => array(
'start' => '88892285',
'end' => '88902515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-008'
),
'ENST00000563640' => array(
'start' => '88892399',
'end' => '88977080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-009'
),
'ENST00000563856' => array(
'start' => '88875525',
'end' => '88881157',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBFA2T3-004'
),
'ENST00000563920' => array(
'start' => '88876228',
'end' => '88880036',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBFA2T3-005'
),
'ENST00000564416' => array(
'start' => '88898088',
'end' => '88941200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-011'
),
'ENST00000566868' => array(
'start' => '88879430',
'end' => '88881313',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CBFA2T3-007'
),
'ENST00000569443' => array(
'start' => '88892244',
'end' => '88941844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-010'
),
'ENST00000569464' => array(
'start' => '88881112',
'end' => '88941809',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-006'
),
'ENST00000570046' => array(
'start' => '88901558',
'end' => '88957775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-012'
),
'ENST00000317447' => array(
'start' => '89093809',
'end' => '89155763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-001'
),
'ENST00000378345' => array(
'start' => '89093898',
'end' => '89154588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-002'
),
'ENST00000393145' => array(
'start' => '89147567',
'end' => '89154586',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-020'
),
'ENST00000406948' => array(
'start' => '89093883',
'end' => '89154589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-003'
),
'ENST00000535176' => array(
'start' => '89145950',
'end' => '89151348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-013'
),
'ENST00000537116' => array(
'start' => '89136548',
'end' => '89155846',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-005'
),
'ENST00000537155' => array(
'start' => '89145161',
'end' => '89154584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-016'
),
'ENST00000537290' => array(
'start' => '89093855',
'end' => '89102648',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-009'
),
'ENST00000537895' => array(
'start' => '89088375',
'end' => '89114473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-011'
),
'ENST00000538340' => array(
'start' => '89102613',
'end' => '89122392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-015'
),
'ENST00000540697' => array(
'start' => '89093868',
'end' => '89133262',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-010'
),
'ENST00000541755' => array(
'start' => '89093904',
'end' => '89100767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-023'
),
'ENST00000542688' => array(
'start' => '89098711',
'end' => '89154540',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ACSF3-006'
),
'ENST00000543676' => array(
'start' => '89102696',
'end' => '89122832',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-014'
),
'ENST00000544543' => array(
'start' => '89102352',
'end' => '89145400',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-012'
),
'ENST00000562204' => array(
'start' => '89112201',
'end' => '89146044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-021'
),
'ENST00000562750' => array(
'start' => '89150600',
'end' => '89151222',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-019'
),
'ENST00000614302' => array(
'start' => '89093809',
'end' => '89155846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-201'
),
'ENST00000378347' => array(
'start' => '88939789',
'end' => '88951524',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.6-001'
),
'ENST00000537498' => array(
'start' => '89046172',
'end' => '89052965',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2555A7.2-001'
),
'ENST00000562405' => array(
'start' => '88881038',
'end' => '88883919',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-001'
),
'ENST00000562574' => array(
'start' => '88881257',
'end' => '88883715',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-002'
),
'ENST00000565053' => array(
'start' => '88883272',
'end' => '88887136',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-004'
),
'ENST00000569249' => array(
'start' => '88881455',
'end' => '88883926',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-003'
),
'ENST00000562040' => array(
'start' => '88984032',
'end' => '88995369',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2555A7.1-001'
),
'ENST00000561980' => array(
'start' => '88936779',
'end' => '88937756',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-830F9.7-002'
),
'ENST00000564646' => array(
'start' => '88936779',
'end' => '88939651',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-830F9.7-001'
),
'ENST00000562782' => array(
'start' => '89113175',
'end' => '89115279',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2555A7.3-001'
),
'ENSMUST00000006525' => array(
'start' => '122629463',
'end' => '122678072',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-003'
),
'ENSMUST00000064674' => array(
'start' => '122629938',
'end' => '122678175',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-002'
),
'ENSMUST00000127984' => array(
'start' => '122628739',
'end' => '122699109',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-001'
),
'ENSMUST00000134045' => array(
'start' => '122639014',
'end' => '122678694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-005'
),
'ENSMUST00000142535' => array(
'start' => '122639018',
'end' => '122646466',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbfa2t3-007'
),
'ENSMUST00000147374' => array(
'start' => '122643004',
'end' => '122678111',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbfa2t3-006'
),
'ENSMUST00000148630' => array(
'start' => '122650028',
'end' => '122698902',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cbfa2t3-004'
),
'ENSMUST00000015160' => array(
'start' => '122775505',
'end' => '122817880',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Acsf3-201'
),
'ENSMUST00000128586' => array(
'start' => '122683602',
'end' => '122683839',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm15899-001'
),
'ENSMUST00000162198' => array(
'start' => '122697860',
'end' => '122700160',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm10612-001'
)
)
$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_0006AJ_0001' => array(
'genes_in_region' => array(
'ENSDARG00000059503' => array(
[maximum depth reached]
),
'ENSDARG00000079012' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Liver',
(int) 7 => 'Muscle'
)
),
'CIL_0006AJ_0002' => array(
'genes_in_region' => array(
'ENSG00000129993' => array(
[maximum depth reached]
),
'ENSG00000205018' => array(
[maximum depth reached]
),
'ENSG00000256982' => array(
[maximum depth reached]
),
'ENSG00000259989' => array(
[maximum depth reached]
),
'ENSG00000261226' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Colon',
(int) 1 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Brain',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Testis',
(int) 10 => 'Liver',
(int) 11 => 'Liver',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Ovary',
(int) 36 => 'Heart',
(int) 37 => 'Placenta',
(int) 38 => 'Adipose',
(int) 39 => 'Colon',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Muscle',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Muscle',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis',
(int) 59 => 'Adipose',
(int) 60 => 'Bladder',
(int) 61 => 'Brain',
(int) 62 => 'Breast',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Liver',
(int) 66 => 'Lung',
(int) 67 => 'Ovary',
(int) 68 => 'Placenta',
(int) 69 => 'Muscle',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Heart',
(int) 76 => 'Brain',
(int) 77 => 'Kidney',
(int) 78 => 'Muscle',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Adipose',
(int) 82 => 'Adrenal',
(int) 83 => 'Brain',
(int) 84 => 'Breast',
(int) 85 => 'Heart',
(int) 86 => 'Kidney',
(int) 87 => 'Lung',
(int) 88 => 'Muscle',
(int) 89 => 'Ovary',
(int) 90 => 'Placenta',
(int) 91 => 'Testis',
(int) 92 => 'Brain',
(int) 93 => 'Bladder',
(int) 94 => 'Ovary',
(int) 95 => 'Adipose',
(int) 96 => 'Adrenal',
(int) 97 => 'Brain',
(int) 98 => 'Breast',
(int) 99 => 'Colon',
(int) 100 => 'Heart',
(int) 101 => 'Kidney',
(int) 102 => 'Liver',
(int) 103 => 'Lung',
(int) 104 => 'Ovary',
(int) 105 => 'Placenta',
(int) 106 => 'Testis',
(int) 107 => 'Adrenal',
(int) 108 => 'Brain',
(int) 109 => 'Colon',
(int) 110 => 'Lung',
(int) 111 => 'Brain',
(int) 112 => 'Muscle',
(int) 113 => 'Colon',
(int) 114 => 'Liver',
(int) 115 => 'Ovary',
(int) 116 => 'Adrenal',
(int) 117 => 'Testis',
(int) 118 => 'Bladder',
(int) 119 => 'Brain',
(int) 120 => 'Breast',
(int) 121 => 'Heart',
(int) 122 => 'Lung',
(int) 123 => 'Muscle',
(int) 124 => 'Ovary',
(int) 125 => 'Placenta',
(int) 126 => 'Testis',
(int) 127 => 'Adipose',
(int) 128 => 'Adrenal',
(int) 129 => 'Brain',
(int) 130 => 'Breast',
(int) 131 => 'Colon',
(int) 132 => 'Heart',
(int) 133 => 'Kidney',
(int) 134 => 'Liver',
(int) 135 => 'Lung',
(int) 136 => 'Ovary',
(int) 137 => 'Placenta',
(int) 138 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AJ_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122628739',
'seq_end' => '122817880',
'region_length' => '189141',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006362-ENSMUSG00000015016'
)
)
$gene_el = array(
'ENST00000561980' => array(
'Bladder' => array(
'average_FPKM' => '0.415',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.055',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.217',
'stddev_FPKM' => '0.03'
),
'Muscle' => array(
'average_FPKM' => '1.215',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.166',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '1.119',
'stddev_FPKM' => '0.50'
)
),
'ENST00000564646' => array(
'Adipose' => array(
'average_FPKM' => '0.053',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.122',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.02'
),
'Breast' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.164',
'stddev_FPKM' => '0.12'
),
'Heart' => array(
'average_FPKM' => '0.039',
'stddev_FPKM' => '0.03'
),
'Kidney' => array(
'average_FPKM' => '0.010',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.028',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.011',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.028',
'stddev_FPKM' => '0.01'
),
'Placenta' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.01'
)
)
)
$gene_key = 'ENSG00000261226'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.053',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.122',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.02'
),
'Breast' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.164',
'stddev_FPKM' => '0.12'
),
'Heart' => array(
'average_FPKM' => '0.039',
'stddev_FPKM' => '0.03'
),
'Kidney' => array(
'average_FPKM' => '0.010',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.028',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.011',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.028',
'stddev_FPKM' => '0.01'
),
'Placenta' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.01'
)
)
$tran_key = 'ENST00000564646'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0006AJ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AJ_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000059503' => 'Uncharacterized protein',
'ENSDARG00000079012' => 'core-binding factor, runt domain, alpha subunit 2; translocated to, 3',
'ENSDARG00000088664' => '5S ribosomal RNA',
'ENSG00000129993' => 'core-binding factor, runt domain, alpha subunit 2; translocated to, 3',
'ENSG00000176715' => 'acyl-CoA synthetase family member 3',
'ENSG00000205018' => null,
'ENSG00000256982' => null,
'ENSG00000259881' => null,
'ENSG00000259989' => null,
'ENSG00000261226' => null,
'ENSG00000261546' => null,
'ENSMUSG00000006362' => 'core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)',
'ENSMUSG00000015016' => 'acyl-CoA synthetase family member 3',
'ENSMUSG00000085917' => 'predicted gene 15899',
'ENSMUSG00000090174' => 'predicted gene 10612'
),
'gene_name_arr' => array(
'ENSDARG00000059503' => 'CR848706.1',
'ENSDARG00000079012' => 'CBFA2T3',
'ENSDARG00000088664' => '5S_rRNA',
'ENSG00000129993' => 'CBFA2T3',
'ENSG00000176715' => 'ACSF3',
'ENSG00000205018' => 'RP11-830F9.6',
'ENSG00000256982' => 'CTD-2555A7.2',
'ENSG00000259881' => 'RP11-830F9.5',
'ENSG00000259989' => 'CTD-2555A7.1',
'ENSG00000261226' => 'RP11-830F9.7',
'ENSG00000261546' => 'CTD-2555A7.3',
'ENSMUSG00000006362' => 'Cbfa2t3',
'ENSMUSG00000015016' => 'Acsf3',
'ENSMUSG00000085917' => 'Gm15899',
'ENSMUSG00000090174' => 'Gm10612'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 21 => 'Brain',
(int) 36 => 'Breast',
(int) 44 => 'Colon',
(int) 54 => 'Heart',
(int) 67 => 'Kidney',
(int) 76 => 'Liver',
(int) 88 => 'Lung',
(int) 99 => 'Muscle',
(int) 113 => 'Ovary',
(int) 127 => 'Placenta',
(int) 137 => '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) 52,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000082780' => array(
'start' => '57215011',
'end' => '57300831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CR848706.1-201'
),
'ENSDART00000021009' => array(
'start' => '56923526',
'end' => '56938884',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-201'
),
'ENSDART00000125848' => array(
'start' => '57050282',
'end' => '57050396',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1697-201'
),
'ENST00000268679' => array(
'start' => '88874858',
'end' => '88977204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-001'
),
'ENST00000327483' => array(
'start' => '88874858',
'end' => '88941198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-002'
),
'ENST00000562719' => array(
'start' => '88892285',
'end' => '88902515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-008'
),
'ENST00000563640' => array(
'start' => '88892399',
'end' => '88977080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-009'
),
'ENST00000563856' => array(
'start' => '88875525',
'end' => '88881157',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBFA2T3-004'
),
'ENST00000563920' => array(
'start' => '88876228',
'end' => '88880036',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBFA2T3-005'
),
'ENST00000564416' => array(
'start' => '88898088',
'end' => '88941200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-011'
),
'ENST00000566868' => array(
'start' => '88879430',
'end' => '88881313',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CBFA2T3-007'
),
'ENST00000569443' => array(
'start' => '88892244',
'end' => '88941844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-010'
),
'ENST00000569464' => array(
'start' => '88881112',
'end' => '88941809',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-006'
),
'ENST00000570046' => array(
'start' => '88901558',
'end' => '88957775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-012'
),
'ENST00000317447' => array(
'start' => '89093809',
'end' => '89155763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-001'
),
'ENST00000378345' => array(
'start' => '89093898',
'end' => '89154588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-002'
),
'ENST00000393145' => array(
'start' => '89147567',
'end' => '89154586',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-020'
),
'ENST00000406948' => array(
'start' => '89093883',
'end' => '89154589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-003'
),
'ENST00000535176' => array(
'start' => '89145950',
'end' => '89151348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-013'
),
'ENST00000537116' => array(
'start' => '89136548',
'end' => '89155846',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-005'
),
'ENST00000537155' => array(
'start' => '89145161',
'end' => '89154584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-016'
),
'ENST00000537290' => array(
'start' => '89093855',
'end' => '89102648',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-009'
),
'ENST00000537895' => array(
'start' => '89088375',
'end' => '89114473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-011'
),
'ENST00000538340' => array(
'start' => '89102613',
'end' => '89122392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-015'
),
'ENST00000540697' => array(
'start' => '89093868',
'end' => '89133262',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-010'
),
'ENST00000541755' => array(
'start' => '89093904',
'end' => '89100767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-023'
),
'ENST00000542688' => array(
'start' => '89098711',
'end' => '89154540',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ACSF3-006'
),
'ENST00000543676' => array(
'start' => '89102696',
'end' => '89122832',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-014'
),
'ENST00000544543' => array(
'start' => '89102352',
'end' => '89145400',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-012'
),
'ENST00000562204' => array(
'start' => '89112201',
'end' => '89146044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-021'
),
'ENST00000562750' => array(
'start' => '89150600',
'end' => '89151222',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-019'
),
'ENST00000614302' => array(
'start' => '89093809',
'end' => '89155846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-201'
),
'ENST00000378347' => array(
'start' => '88939789',
'end' => '88951524',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.6-001'
),
'ENST00000537498' => array(
'start' => '89046172',
'end' => '89052965',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2555A7.2-001'
),
'ENST00000562405' => array(
'start' => '88881038',
'end' => '88883919',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-001'
),
'ENST00000562574' => array(
'start' => '88881257',
'end' => '88883715',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-002'
),
'ENST00000565053' => array(
'start' => '88883272',
'end' => '88887136',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-004'
),
'ENST00000569249' => array(
'start' => '88881455',
'end' => '88883926',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-003'
),
'ENST00000562040' => array(
'start' => '88984032',
'end' => '88995369',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2555A7.1-001'
),
'ENST00000561980' => array(
'start' => '88936779',
'end' => '88937756',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-830F9.7-002'
),
'ENST00000564646' => array(
'start' => '88936779',
'end' => '88939651',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-830F9.7-001'
),
'ENST00000562782' => array(
'start' => '89113175',
'end' => '89115279',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2555A7.3-001'
),
'ENSMUST00000006525' => array(
'start' => '122629463',
'end' => '122678072',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-003'
),
'ENSMUST00000064674' => array(
'start' => '122629938',
'end' => '122678175',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-002'
),
'ENSMUST00000127984' => array(
'start' => '122628739',
'end' => '122699109',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-001'
),
'ENSMUST00000134045' => array(
'start' => '122639014',
'end' => '122678694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-005'
),
'ENSMUST00000142535' => array(
'start' => '122639018',
'end' => '122646466',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbfa2t3-007'
),
'ENSMUST00000147374' => array(
'start' => '122643004',
'end' => '122678111',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbfa2t3-006'
),
'ENSMUST00000148630' => array(
'start' => '122650028',
'end' => '122698902',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cbfa2t3-004'
),
'ENSMUST00000015160' => array(
'start' => '122775505',
'end' => '122817880',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Acsf3-201'
),
'ENSMUST00000128586' => array(
'start' => '122683602',
'end' => '122683839',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm15899-001'
),
'ENSMUST00000162198' => array(
'start' => '122697860',
'end' => '122700160',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm10612-001'
)
),
'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_0006AJ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AJ_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0006AJ_0001' => array(
'genes_in_region' => array(
'ENSDARG00000059503' => array(
[maximum depth reached]
),
'ENSDARG00000079012' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Liver',
(int) 7 => 'Muscle'
)
),
'CIL_0006AJ_0002' => array(
'genes_in_region' => array(
'ENSG00000129993' => array(
[maximum depth reached]
),
'ENSG00000205018' => array(
[maximum depth reached]
),
'ENSG00000256982' => array(
[maximum depth reached]
),
'ENSG00000259989' => array(
[maximum depth reached]
),
'ENSG00000261226' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Colon',
(int) 1 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Brain',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Testis',
(int) 10 => 'Liver',
(int) 11 => 'Liver',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Ovary',
(int) 36 => 'Heart',
(int) 37 => 'Placenta',
(int) 38 => 'Adipose',
(int) 39 => 'Colon',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Muscle',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Muscle',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis',
(int) 59 => 'Adipose',
(int) 60 => 'Bladder',
(int) 61 => 'Brain',
(int) 62 => 'Breast',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Liver',
(int) 66 => 'Lung',
(int) 67 => 'Ovary',
(int) 68 => 'Placenta',
(int) 69 => 'Muscle',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Heart',
(int) 76 => 'Brain',
(int) 77 => 'Kidney',
(int) 78 => 'Muscle',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Adipose',
(int) 82 => 'Adrenal',
(int) 83 => 'Brain',
(int) 84 => 'Breast',
(int) 85 => 'Heart',
(int) 86 => 'Kidney',
(int) 87 => 'Lung',
(int) 88 => 'Muscle',
(int) 89 => 'Ovary',
(int) 90 => 'Placenta',
(int) 91 => 'Testis',
(int) 92 => 'Brain',
(int) 93 => 'Bladder',
(int) 94 => 'Ovary',
(int) 95 => 'Adipose',
(int) 96 => 'Adrenal',
(int) 97 => 'Brain',
(int) 98 => 'Breast',
(int) 99 => 'Colon',
(int) 100 => 'Heart',
(int) 101 => 'Kidney',
(int) 102 => 'Liver',
(int) 103 => 'Lung',
(int) 104 => 'Ovary',
(int) 105 => 'Placenta',
(int) 106 => 'Testis',
(int) 107 => 'Adrenal',
(int) 108 => 'Brain',
(int) 109 => 'Colon',
(int) 110 => 'Lung',
(int) 111 => 'Brain',
(int) 112 => 'Muscle',
(int) 113 => 'Colon',
(int) 114 => 'Liver',
(int) 115 => 'Ovary',
(int) 116 => 'Adrenal',
(int) 117 => 'Testis',
(int) 118 => 'Bladder',
(int) 119 => 'Brain',
(int) 120 => 'Breast',
(int) 121 => 'Heart',
(int) 122 => 'Lung',
(int) 123 => 'Muscle',
(int) 124 => 'Ovary',
(int) 125 => 'Placenta',
(int) 126 => 'Testis',
(int) 127 => 'Adipose',
(int) 128 => 'Adrenal',
(int) 129 => 'Brain',
(int) 130 => 'Breast',
(int) 131 => 'Colon',
(int) 132 => 'Heart',
(int) 133 => 'Kidney',
(int) 134 => 'Liver',
(int) 135 => 'Lung',
(int) 136 => 'Ovary',
(int) 137 => 'Placenta',
(int) 138 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000059503' => 'Uncharacterized protein',
'ENSDARG00000079012' => 'core-binding factor, runt domain, alpha subunit 2; translocated to, 3',
'ENSDARG00000088664' => '5S ribosomal RNA',
'ENSG00000129993' => 'core-binding factor, runt domain, alpha subunit 2; translocated to, 3',
'ENSG00000176715' => 'acyl-CoA synthetase family member 3',
'ENSG00000205018' => null,
'ENSG00000256982' => null,
'ENSG00000259881' => null,
'ENSG00000259989' => null,
'ENSG00000261226' => null,
'ENSG00000261546' => null,
'ENSMUSG00000006362' => 'core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)',
'ENSMUSG00000015016' => 'acyl-CoA synthetase family member 3',
'ENSMUSG00000085917' => 'predicted gene 15899',
'ENSMUSG00000090174' => 'predicted gene 10612'
)
$gene_name_arr = array(
'ENSDARG00000059503' => 'CR848706.1',
'ENSDARG00000079012' => 'CBFA2T3',
'ENSDARG00000088664' => '5S_rRNA',
'ENSG00000129993' => 'CBFA2T3',
'ENSG00000176715' => 'ACSF3',
'ENSG00000205018' => 'RP11-830F9.6',
'ENSG00000256982' => 'CTD-2555A7.2',
'ENSG00000259881' => 'RP11-830F9.5',
'ENSG00000259989' => 'CTD-2555A7.1',
'ENSG00000261226' => 'RP11-830F9.7',
'ENSG00000261546' => 'CTD-2555A7.3',
'ENSMUSG00000006362' => 'Cbfa2t3',
'ENSMUSG00000015016' => 'Acsf3',
'ENSMUSG00000085917' => 'Gm15899',
'ENSMUSG00000090174' => 'Gm10612'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AJ_0001',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '56923526',
'seq_end' => '57300831',
'region_length' => '377305',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000079012-ENSDARG00000059503'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AJ_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '88874858',
'seq_end' => '89155846',
'region_length' => '280988',
'region_type' => 'CGP',
'el_id' => 'ENSG00000129993-ENSG00000176715'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AJ_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122628739',
'seq_end' => '122817880',
'region_length' => '189141',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006362-ENSMUSG00000015016'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 21 => 'Brain',
(int) 36 => 'Breast',
(int) 44 => 'Colon',
(int) 54 => 'Heart',
(int) 67 => 'Kidney',
(int) 76 => 'Liver',
(int) 88 => 'Lung',
(int) 99 => 'Muscle',
(int) 113 => 'Ovary',
(int) 127 => 'Placenta',
(int) 137 => '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) 52
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000082780' => array(
'start' => '57215011',
'end' => '57300831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CR848706.1-201'
),
'ENSDART00000021009' => array(
'start' => '56923526',
'end' => '56938884',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-201'
),
'ENSDART00000125848' => array(
'start' => '57050282',
'end' => '57050396',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1697-201'
),
'ENST00000268679' => array(
'start' => '88874858',
'end' => '88977204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-001'
),
'ENST00000327483' => array(
'start' => '88874858',
'end' => '88941198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-002'
),
'ENST00000562719' => array(
'start' => '88892285',
'end' => '88902515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-008'
),
'ENST00000563640' => array(
'start' => '88892399',
'end' => '88977080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-009'
),
'ENST00000563856' => array(
'start' => '88875525',
'end' => '88881157',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBFA2T3-004'
),
'ENST00000563920' => array(
'start' => '88876228',
'end' => '88880036',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBFA2T3-005'
),
'ENST00000564416' => array(
'start' => '88898088',
'end' => '88941200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-011'
),
'ENST00000566868' => array(
'start' => '88879430',
'end' => '88881313',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CBFA2T3-007'
),
'ENST00000569443' => array(
'start' => '88892244',
'end' => '88941844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-010'
),
'ENST00000569464' => array(
'start' => '88881112',
'end' => '88941809',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-006'
),
'ENST00000570046' => array(
'start' => '88901558',
'end' => '88957775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBFA2T3-012'
),
'ENST00000317447' => array(
'start' => '89093809',
'end' => '89155763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-001'
),
'ENST00000378345' => array(
'start' => '89093898',
'end' => '89154588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-002'
),
'ENST00000393145' => array(
'start' => '89147567',
'end' => '89154586',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-020'
),
'ENST00000406948' => array(
'start' => '89093883',
'end' => '89154589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-003'
),
'ENST00000535176' => array(
'start' => '89145950',
'end' => '89151348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-013'
),
'ENST00000537116' => array(
'start' => '89136548',
'end' => '89155846',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-005'
),
'ENST00000537155' => array(
'start' => '89145161',
'end' => '89154584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-016'
),
'ENST00000537290' => array(
'start' => '89093855',
'end' => '89102648',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-009'
),
'ENST00000537895' => array(
'start' => '89088375',
'end' => '89114473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-011'
),
'ENST00000538340' => array(
'start' => '89102613',
'end' => '89122392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-015'
),
'ENST00000540697' => array(
'start' => '89093868',
'end' => '89133262',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-010'
),
'ENST00000541755' => array(
'start' => '89093904',
'end' => '89100767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-023'
),
'ENST00000542688' => array(
'start' => '89098711',
'end' => '89154540',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ACSF3-006'
),
'ENST00000543676' => array(
'start' => '89102696',
'end' => '89122832',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-014'
),
'ENST00000544543' => array(
'start' => '89102352',
'end' => '89145400',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-012'
),
'ENST00000562204' => array(
'start' => '89112201',
'end' => '89146044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-021'
),
'ENST00000562750' => array(
'start' => '89150600',
'end' => '89151222',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-019'
),
'ENST00000614302' => array(
'start' => '89093809',
'end' => '89155846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-201'
),
'ENST00000378347' => array(
'start' => '88939789',
'end' => '88951524',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.6-001'
),
'ENST00000537498' => array(
'start' => '89046172',
'end' => '89052965',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2555A7.2-001'
),
'ENST00000562405' => array(
'start' => '88881038',
'end' => '88883919',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-001'
),
'ENST00000562574' => array(
'start' => '88881257',
'end' => '88883715',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-002'
),
'ENST00000565053' => array(
'start' => '88883272',
'end' => '88887136',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-004'
),
'ENST00000569249' => array(
'start' => '88881455',
'end' => '88883926',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-830F9.5-003'
),
'ENST00000562040' => array(
'start' => '88984032',
'end' => '88995369',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2555A7.1-001'
),
'ENST00000561980' => array(
'start' => '88936779',
'end' => '88937756',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-830F9.7-002'
),
'ENST00000564646' => array(
'start' => '88936779',
'end' => '88939651',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-830F9.7-001'
),
'ENST00000562782' => array(
'start' => '89113175',
'end' => '89115279',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2555A7.3-001'
),
'ENSMUST00000006525' => array(
'start' => '122629463',
'end' => '122678072',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-003'
),
'ENSMUST00000064674' => array(
'start' => '122629938',
'end' => '122678175',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-002'
),
'ENSMUST00000127984' => array(
'start' => '122628739',
'end' => '122699109',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-001'
),
'ENSMUST00000134045' => array(
'start' => '122639014',
'end' => '122678694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbfa2t3-005'
),
'ENSMUST00000142535' => array(
'start' => '122639018',
'end' => '122646466',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbfa2t3-007'
),
'ENSMUST00000147374' => array(
'start' => '122643004',
'end' => '122678111',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbfa2t3-006'
),
'ENSMUST00000148630' => array(
'start' => '122650028',
'end' => '122698902',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cbfa2t3-004'
),
'ENSMUST00000015160' => array(
'start' => '122775505',
'end' => '122817880',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Acsf3-201'
),
'ENSMUST00000128586' => array(
'start' => '122683602',
'end' => '122683839',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm15899-001'
),
'ENSMUST00000162198' => array(
'start' => '122697860',
'end' => '122700160',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm10612-001'
)
)
$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_0006AJ_0001' => array(
'genes_in_region' => array(
'ENSDARG00000059503' => array(
[maximum depth reached]
),
'ENSDARG00000079012' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Liver',
(int) 7 => 'Muscle'
)
),
'CIL_0006AJ_0002' => array(
'genes_in_region' => array(
'ENSG00000129993' => array(
[maximum depth reached]
),
'ENSG00000205018' => array(
[maximum depth reached]
),
'ENSG00000256982' => array(
[maximum depth reached]
),
'ENSG00000259989' => array(
[maximum depth reached]
),
'ENSG00000261226' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Colon',
(int) 1 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Brain',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Testis',
(int) 10 => 'Liver',
(int) 11 => 'Liver',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Ovary',
(int) 36 => 'Heart',
(int) 37 => 'Placenta',
(int) 38 => 'Adipose',
(int) 39 => 'Colon',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Muscle',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Muscle',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis',
(int) 59 => 'Adipose',
(int) 60 => 'Bladder',
(int) 61 => 'Brain',
(int) 62 => 'Breast',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Liver',
(int) 66 => 'Lung',
(int) 67 => 'Ovary',
(int) 68 => 'Placenta',
(int) 69 => 'Muscle',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Heart',
(int) 76 => 'Brain',
(int) 77 => 'Kidney',
(int) 78 => 'Muscle',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Adipose',
(int) 82 => 'Adrenal',
(int) 83 => 'Brain',
(int) 84 => 'Breast',
(int) 85 => 'Heart',
(int) 86 => 'Kidney',
(int) 87 => 'Lung',
(int) 88 => 'Muscle',
(int) 89 => 'Ovary',
(int) 90 => 'Placenta',
(int) 91 => 'Testis',
(int) 92 => 'Brain',
(int) 93 => 'Bladder',
(int) 94 => 'Ovary',
(int) 95 => 'Adipose',
(int) 96 => 'Adrenal',
(int) 97 => 'Brain',
(int) 98 => 'Breast',
(int) 99 => 'Colon',
(int) 100 => 'Heart',
(int) 101 => 'Kidney',
(int) 102 => 'Liver',
(int) 103 => 'Lung',
(int) 104 => 'Ovary',
(int) 105 => 'Placenta',
(int) 106 => 'Testis',
(int) 107 => 'Adrenal',
(int) 108 => 'Brain',
(int) 109 => 'Colon',
(int) 110 => 'Lung',
(int) 111 => 'Brain',
(int) 112 => 'Muscle',
(int) 113 => 'Colon',
(int) 114 => 'Liver',
(int) 115 => 'Ovary',
(int) 116 => 'Adrenal',
(int) 117 => 'Testis',
(int) 118 => 'Bladder',
(int) 119 => 'Brain',
(int) 120 => 'Breast',
(int) 121 => 'Heart',
(int) 122 => 'Lung',
(int) 123 => 'Muscle',
(int) 124 => 'Ovary',
(int) 125 => 'Placenta',
(int) 126 => 'Testis',
(int) 127 => 'Adipose',
(int) 128 => 'Adrenal',
(int) 129 => 'Brain',
(int) 130 => 'Breast',
(int) 131 => 'Colon',
(int) 132 => 'Heart',
(int) 133 => 'Kidney',
(int) 134 => 'Liver',
(int) 135 => 'Lung',
(int) 136 => 'Ovary',
(int) 137 => 'Placenta',
(int) 138 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AJ_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122628739',
'seq_end' => '122817880',
'region_length' => '189141',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006362-ENSMUSG00000015016'
)
)
$gene_el = array(
'ENST00000561980' => array(
'Bladder' => array(
'average_FPKM' => '0.415',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.055',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.217',
'stddev_FPKM' => '0.03'
),
'Muscle' => array(
'average_FPKM' => '1.215',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.166',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '1.119',
'stddev_FPKM' => '0.50'
)
),
'ENST00000564646' => array(
'Adipose' => array(
'average_FPKM' => '0.053',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.122',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.02'
),
'Breast' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.164',
'stddev_FPKM' => '0.12'
),
'Heart' => array(
'average_FPKM' => '0.039',
'stddev_FPKM' => '0.03'
),
'Kidney' => array(
'average_FPKM' => '0.010',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.028',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.011',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.028',
'stddev_FPKM' => '0.01'
),
'Placenta' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.01'
)
)
)
$gene_key = 'ENSG00000261226'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.053',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.122',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.02'
),
'Breast' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.164',
'stddev_FPKM' => '0.12'
),
'Heart' => array(
'average_FPKM' => '0.039',
'stddev_FPKM' => '0.03'
),
'Kidney' => array(
'average_FPKM' => '0.010',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.028',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.011',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.028',
'stddev_FPKM' => '0.01'
),
'Placenta' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.01'
)
)
$tran_key = 'ENST00000564646'
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
(CR848706.1)