| Source ID |
Type |
Tax ID |
Position |
| hs376 |
VISTA |
10090 |
18:69199161-69800797  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0008DW_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_0008DW_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000196628' => 'transcription factor 4',
'ENSG00000242320' => 'ribosomal protein L21 pseudogene 126',
'ENSG00000252437' => 'RNA, 5S ribosomal pseudogene 459',
'ENSG00000264571' => 'microRNA 4529',
'ENSG00000267013' => null,
'ENSG00000267028' => null,
'ENSG00000267284' => null,
'ENSG00000267402' => null,
'ENSMUSG00000053477' => 'transcription factor 4',
'ENSMUSG00000064706' => 'predicted gene, 22508',
'ENSMUSG00000088659' => 'predicted gene, 24845',
'ENSMUSG00000098060' => 'predicted pseudogene 4842'
),
'gene_name_arr' => array(
'ENSG00000196628' => 'TCF4',
'ENSG00000242320' => 'RPL21P126',
'ENSG00000252437' => 'RNA5SP459',
'ENSG00000264571' => 'MIR4529',
'ENSG00000267013' => 'CTD-2171N6.1',
'ENSG00000267028' => 'RP11-619L19.1',
'ENSG00000267284' => 'RP11-397A16.1',
'ENSG00000267402' => 'RP11-619L19.2',
'ENSMUSG00000053477' => 'Tcf4',
'ENSMUSG00000064706' => 'Gm22508',
'ENSMUSG00000088659' => 'Gm24845',
'ENSMUSG00000098060' => 'Gm4842'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 19 => 'Brain',
(int) 26 => 'Breast',
(int) 33 => 'Colon',
(int) 40 => 'Heart',
(int) 45 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 68 => 'Muscle',
(int) 74 => 'Ovary',
(int) 86 => 'Placenta',
(int) 95 => '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) 76,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000354452' => array(
'start' => '55222331',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-201'
),
'ENST00000356073' => array(
'start' => '55222334',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-002'
),
'ENST00000398339' => array(
'start' => '55227936',
'end' => '55635954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-004'
),
'ENST00000457482' => array(
'start' => '55227689',
'end' => '55322294',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-015'
),
'ENST00000537578' => array(
'start' => '55227752',
'end' => '55589814',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-003'
),
'ENST00000537856' => array(
'start' => '55227849',
'end' => '55401690',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-013'
),
'ENST00000540999' => array(
'start' => '55227690',
'end' => '55586105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-007'
),
'ENST00000543082' => array(
'start' => '55227689',
'end' => '55510769',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-009'
),
'ENST00000544241' => array(
'start' => '55227855',
'end' => '55403995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-011'
),
'ENST00000561831' => array(
'start' => '55227878',
'end' => '55302626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-016'
),
'ENST00000561992' => array(
'start' => '55227864',
'end' => '55422492',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-010'
),
'ENST00000562030' => array(
'start' => '55350359',
'end' => '55401335',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-014'
),
'ENST00000562543' => array(
'start' => '55350955',
'end' => '55591170',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-040'
),
'ENST00000562607' => array(
'start' => '55275648',
'end' => '55351997',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-035'
),
'ENST00000562638' => array(
'start' => '55275662',
'end' => '55401712',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-043'
),
'ENST00000562680' => array(
'start' => '55227849',
'end' => '55401668',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF4-018'
),
'ENST00000562847' => array(
'start' => '55350967',
'end' => '55585966',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-029'
),
'ENST00000563686' => array(
'start' => '55264596',
'end' => '55464144',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF4-017'
),
'ENST00000563760' => array(
'start' => '55254504',
'end' => '55321805',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-037'
),
'ENST00000563824' => array(
'start' => '55350364',
'end' => '55585437',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-028'
),
'ENST00000563888' => array(
'start' => '55350402',
'end' => '55586119',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-025'
),
'ENST00000564228' => array(
'start' => '55227911',
'end' => '55403714',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-042'
),
'ENST00000564343' => array(
'start' => '55350896',
'end' => '55591279',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-023'
),
'ENST00000564403' => array(
'start' => '55227936',
'end' => '55589803',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-019'
),
'ENST00000564999' => array(
'start' => '55227820',
'end' => '55588610',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-006'
),
'ENST00000565018' => array(
'start' => '55227884',
'end' => '55589520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-001'
),
'ENST00000565124' => array(
'start' => '55585280',
'end' => '55635948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-020'
),
'ENST00000565393' => array(
'start' => '55585317',
'end' => '55631362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-039'
),
'ENST00000565580' => array(
'start' => '55403454',
'end' => '55546934',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-030'
),
'ENST00000565908' => array(
'start' => '55275707',
'end' => '55588160',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-024'
),
'ENST00000566279' => array(
'start' => '55227911',
'end' => '55588617',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-045'
),
'ENST00000566286' => array(
'start' => '55227911',
'end' => '55588535',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-041'
),
'ENST00000566376' => array(
'start' => '55332067',
'end' => '55403506',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-036'
),
'ENST00000566514' => array(
'start' => '55269884',
'end' => '55585769',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-027'
),
'ENST00000566777' => array(
'start' => '55275680',
'end' => '55422355',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-032'
),
'ENST00000567880' => array(
'start' => '55227911',
'end' => '55587116',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-046'
),
'ENST00000568147' => array(
'start' => '55350376',
'end' => '55585968',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-026'
),
'ENST00000568169' => array(
'start' => '55269924',
'end' => '55664787',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-021'
),
'ENST00000568186' => array(
'start' => '55275660',
'end' => '55403706',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-033'
),
'ENST00000568673' => array(
'start' => '55227674',
'end' => '55585908',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-008'
),
'ENST00000568740' => array(
'start' => '55227846',
'end' => '55589798',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-005'
),
'ENST00000569012' => array(
'start' => '55269875',
'end' => '55401551',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-034'
),
'ENST00000569357' => array(
'start' => '55403454',
'end' => '55635892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-022'
),
'ENST00000570146' => array(
'start' => '55259621',
'end' => '55275671',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-038'
),
'ENST00000570177' => array(
'start' => '55227984',
'end' => '55402240',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-012'
),
'ENST00000570287' => array(
'start' => '55227911',
'end' => '55321986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-044'
),
'ENST00000590810' => array(
'start' => '55350357',
'end' => '55401851',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-047'
),
'ENST00000616053' => array(
'start' => '55222331',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-202'
),
'ENST00000470049' => array(
'start' => '55635833',
'end' => '55636310',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL21P126-001'
),
'ENST00000516628' => array(
'start' => '55146546',
'end' => '55146645',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP459-201'
),
'ENST00000578110' => array(
'start' => '55479221',
'end' => '55479298',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR4529-201'
),
'ENST00000589125' => array(
'start' => '55105904',
'end' => '55124306',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2171N6.1-001'
),
'ENST00000592405' => array(
'start' => '55108311',
'end' => '55119598',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2171N6.1-002'
),
'ENST00000587660' => array(
'start' => '55452533',
'end' => '55482940',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-619L19.1-001'
),
'ENST00000587346' => array(
'start' => '55721396',
'end' => '55784944',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-001'
),
'ENST00000589662' => array(
'start' => '55721318',
'end' => '55788761',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-002'
),
'ENST00000592936' => array(
'start' => '55721063',
'end' => '55759122',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-003'
),
'ENST00000586467' => array(
'start' => '55492175',
'end' => '55496392',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-619L19.2-001'
),
'ENSMUST00000066717' => array(
'start' => '69344146',
'end' => '69684343',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-003'
),
'ENSMUST00000078486' => array(
'start' => '69345721',
'end' => '69687967',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-201'
),
'ENSMUST00000114977' => array(
'start' => '69593426',
'end' => '69684526',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-008'
),
'ENSMUST00000114978' => array(
'start' => '69593417',
'end' => '69683252',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-007'
),
'ENSMUST00000114980' => array(
'start' => '69346203',
'end' => '69683248',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-004'
),
'ENSMUST00000114982' => array(
'start' => '69345771',
'end' => '69684526',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-002'
),
'ENSMUST00000114985' => array(
'start' => '69344510',
'end' => '69687925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-001'
),
'ENSMUST00000125154' => array(
'start' => '69521538',
'end' => '69564687',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-009'
),
'ENSMUST00000126946' => array(
'start' => '69521793',
'end' => '69633654',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-010'
),
'ENSMUST00000128706' => array(
'start' => '69344492',
'end' => '69565506',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-005'
),
'ENSMUST00000136019' => array(
'start' => '69682380',
'end' => '69683573',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-013'
),
'ENSMUST00000136151' => array(
'start' => '69563335',
'end' => '69636964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-011'
),
'ENSMUST00000145918' => array(
'start' => '69599536',
'end' => '69651289',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-014'
),
'ENSMUST00000146908' => array(
'start' => '69679699',
'end' => '69684528',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-012'
),
'ENSMUST00000155695' => array(
'start' => '69345771',
'end' => '69487850',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-006'
),
'ENSMUST00000082772' => array(
'start' => '69777936',
'end' => '69778045',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm22508-201'
),
'ENSMUST00000158034' => array(
'start' => '69551963',
'end' => '69552071',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'Gm24845-201'
),
'ENSMUST00000183237' => array(
'start' => '69256288',
'end' => '69257122',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm4842-001'
)
),
'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_0008DW_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008DW_0001' => array(
'genes_in_region' => array(
'ENSG00000196628' => array(
[maximum depth reached]
),
'ENSG00000267013' => array(
[maximum depth reached]
),
'ENSG00000267028' => array(
[maximum depth reached]
),
'ENSG00000267284' => array(
[maximum depth reached]
),
'ENSG00000267402' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Liver',
(int) 5 => 'Muscle',
(int) 6 => 'Ovary',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Bladder',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Bladder',
(int) 22 => 'Muscle',
(int) 23 => 'Lung',
(int) 24 => 'Adipose',
(int) 25 => 'Brain',
(int) 26 => 'Heart',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Lung',
(int) 32 => 'Ovary',
(int) 33 => 'Testis',
(int) 34 => 'Adipose',
(int) 35 => 'Breast',
(int) 36 => 'Lung',
(int) 37 => 'Liver',
(int) 38 => 'Placenta',
(int) 39 => 'Placenta',
(int) 40 => 'Bladder',
(int) 41 => 'Brain',
(int) 42 => 'Breast',
(int) 43 => 'Colon',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Adipose',
(int) 52 => 'Bladder',
(int) 53 => 'Breast',
(int) 54 => 'Ovary',
(int) 55 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000196628' => 'transcription factor 4',
'ENSG00000242320' => 'ribosomal protein L21 pseudogene 126',
'ENSG00000252437' => 'RNA, 5S ribosomal pseudogene 459',
'ENSG00000264571' => 'microRNA 4529',
'ENSG00000267013' => null,
'ENSG00000267028' => null,
'ENSG00000267284' => null,
'ENSG00000267402' => null,
'ENSMUSG00000053477' => 'transcription factor 4',
'ENSMUSG00000064706' => 'predicted gene, 22508',
'ENSMUSG00000088659' => 'predicted gene, 24845',
'ENSMUSG00000098060' => 'predicted pseudogene 4842'
)
$gene_name_arr = array(
'ENSG00000196628' => 'TCF4',
'ENSG00000242320' => 'RPL21P126',
'ENSG00000252437' => 'RNA5SP459',
'ENSG00000264571' => 'MIR4529',
'ENSG00000267013' => 'CTD-2171N6.1',
'ENSG00000267028' => 'RP11-619L19.1',
'ENSG00000267284' => 'RP11-397A16.1',
'ENSG00000267402' => 'RP11-619L19.2',
'ENSMUSG00000053477' => 'Tcf4',
'ENSMUSG00000064706' => 'Gm22508',
'ENSMUSG00000088659' => 'Gm24845',
'ENSMUSG00000098060' => 'Gm4842'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008DW_0001',
'tax_id' => '9606',
'chromosome' => '18',
'seq_start' => '55122394',
'seq_end' => '55723848',
'region_length' => '601454',
'region_type' => 'VISTA',
'el_id' => 'hs376'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008DW_0002',
'tax_id' => '10090',
'chromosome' => '18',
'seq_start' => '69199161',
'seq_end' => '69800797',
'region_length' => '601636',
'region_type' => 'VISTA',
'el_id' => 'hs376'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 19 => 'Brain',
(int) 26 => 'Breast',
(int) 33 => 'Colon',
(int) 40 => 'Heart',
(int) 45 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 68 => 'Muscle',
(int) 74 => 'Ovary',
(int) 86 => 'Placenta',
(int) 95 => '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) 76
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000354452' => array(
'start' => '55222331',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-201'
),
'ENST00000356073' => array(
'start' => '55222334',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-002'
),
'ENST00000398339' => array(
'start' => '55227936',
'end' => '55635954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-004'
),
'ENST00000457482' => array(
'start' => '55227689',
'end' => '55322294',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-015'
),
'ENST00000537578' => array(
'start' => '55227752',
'end' => '55589814',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-003'
),
'ENST00000537856' => array(
'start' => '55227849',
'end' => '55401690',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-013'
),
'ENST00000540999' => array(
'start' => '55227690',
'end' => '55586105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-007'
),
'ENST00000543082' => array(
'start' => '55227689',
'end' => '55510769',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-009'
),
'ENST00000544241' => array(
'start' => '55227855',
'end' => '55403995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-011'
),
'ENST00000561831' => array(
'start' => '55227878',
'end' => '55302626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-016'
),
'ENST00000561992' => array(
'start' => '55227864',
'end' => '55422492',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-010'
),
'ENST00000562030' => array(
'start' => '55350359',
'end' => '55401335',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-014'
),
'ENST00000562543' => array(
'start' => '55350955',
'end' => '55591170',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-040'
),
'ENST00000562607' => array(
'start' => '55275648',
'end' => '55351997',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-035'
),
'ENST00000562638' => array(
'start' => '55275662',
'end' => '55401712',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-043'
),
'ENST00000562680' => array(
'start' => '55227849',
'end' => '55401668',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF4-018'
),
'ENST00000562847' => array(
'start' => '55350967',
'end' => '55585966',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-029'
),
'ENST00000563686' => array(
'start' => '55264596',
'end' => '55464144',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF4-017'
),
'ENST00000563760' => array(
'start' => '55254504',
'end' => '55321805',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-037'
),
'ENST00000563824' => array(
'start' => '55350364',
'end' => '55585437',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-028'
),
'ENST00000563888' => array(
'start' => '55350402',
'end' => '55586119',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-025'
),
'ENST00000564228' => array(
'start' => '55227911',
'end' => '55403714',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-042'
),
'ENST00000564343' => array(
'start' => '55350896',
'end' => '55591279',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-023'
),
'ENST00000564403' => array(
'start' => '55227936',
'end' => '55589803',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-019'
),
'ENST00000564999' => array(
'start' => '55227820',
'end' => '55588610',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-006'
),
'ENST00000565018' => array(
'start' => '55227884',
'end' => '55589520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-001'
),
'ENST00000565124' => array(
'start' => '55585280',
'end' => '55635948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-020'
),
'ENST00000565393' => array(
'start' => '55585317',
'end' => '55631362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-039'
),
'ENST00000565580' => array(
'start' => '55403454',
'end' => '55546934',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-030'
),
'ENST00000565908' => array(
'start' => '55275707',
'end' => '55588160',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-024'
),
'ENST00000566279' => array(
'start' => '55227911',
'end' => '55588617',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-045'
),
'ENST00000566286' => array(
'start' => '55227911',
'end' => '55588535',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-041'
),
'ENST00000566376' => array(
'start' => '55332067',
'end' => '55403506',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-036'
),
'ENST00000566514' => array(
'start' => '55269884',
'end' => '55585769',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-027'
),
'ENST00000566777' => array(
'start' => '55275680',
'end' => '55422355',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-032'
),
'ENST00000567880' => array(
'start' => '55227911',
'end' => '55587116',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-046'
),
'ENST00000568147' => array(
'start' => '55350376',
'end' => '55585968',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-026'
),
'ENST00000568169' => array(
'start' => '55269924',
'end' => '55664787',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-021'
),
'ENST00000568186' => array(
'start' => '55275660',
'end' => '55403706',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-033'
),
'ENST00000568673' => array(
'start' => '55227674',
'end' => '55585908',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-008'
),
'ENST00000568740' => array(
'start' => '55227846',
'end' => '55589798',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-005'
),
'ENST00000569012' => array(
'start' => '55269875',
'end' => '55401551',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-034'
),
'ENST00000569357' => array(
'start' => '55403454',
'end' => '55635892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-022'
),
'ENST00000570146' => array(
'start' => '55259621',
'end' => '55275671',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-038'
),
'ENST00000570177' => array(
'start' => '55227984',
'end' => '55402240',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-012'
),
'ENST00000570287' => array(
'start' => '55227911',
'end' => '55321986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-044'
),
'ENST00000590810' => array(
'start' => '55350357',
'end' => '55401851',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-047'
),
'ENST00000616053' => array(
'start' => '55222331',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-202'
),
'ENST00000470049' => array(
'start' => '55635833',
'end' => '55636310',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL21P126-001'
),
'ENST00000516628' => array(
'start' => '55146546',
'end' => '55146645',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP459-201'
),
'ENST00000578110' => array(
'start' => '55479221',
'end' => '55479298',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR4529-201'
),
'ENST00000589125' => array(
'start' => '55105904',
'end' => '55124306',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2171N6.1-001'
),
'ENST00000592405' => array(
'start' => '55108311',
'end' => '55119598',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2171N6.1-002'
),
'ENST00000587660' => array(
'start' => '55452533',
'end' => '55482940',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-619L19.1-001'
),
'ENST00000587346' => array(
'start' => '55721396',
'end' => '55784944',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-001'
),
'ENST00000589662' => array(
'start' => '55721318',
'end' => '55788761',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-002'
),
'ENST00000592936' => array(
'start' => '55721063',
'end' => '55759122',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-003'
),
'ENST00000586467' => array(
'start' => '55492175',
'end' => '55496392',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-619L19.2-001'
),
'ENSMUST00000066717' => array(
'start' => '69344146',
'end' => '69684343',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-003'
),
'ENSMUST00000078486' => array(
'start' => '69345721',
'end' => '69687967',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-201'
),
'ENSMUST00000114977' => array(
'start' => '69593426',
'end' => '69684526',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-008'
),
'ENSMUST00000114978' => array(
'start' => '69593417',
'end' => '69683252',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-007'
),
'ENSMUST00000114980' => array(
'start' => '69346203',
'end' => '69683248',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-004'
),
'ENSMUST00000114982' => array(
'start' => '69345771',
'end' => '69684526',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-002'
),
'ENSMUST00000114985' => array(
'start' => '69344510',
'end' => '69687925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-001'
),
'ENSMUST00000125154' => array(
'start' => '69521538',
'end' => '69564687',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-009'
),
'ENSMUST00000126946' => array(
'start' => '69521793',
'end' => '69633654',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-010'
),
'ENSMUST00000128706' => array(
'start' => '69344492',
'end' => '69565506',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-005'
),
'ENSMUST00000136019' => array(
'start' => '69682380',
'end' => '69683573',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-013'
),
'ENSMUST00000136151' => array(
'start' => '69563335',
'end' => '69636964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-011'
),
'ENSMUST00000145918' => array(
'start' => '69599536',
'end' => '69651289',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-014'
),
'ENSMUST00000146908' => array(
'start' => '69679699',
'end' => '69684528',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-012'
),
'ENSMUST00000155695' => array(
'start' => '69345771',
'end' => '69487850',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-006'
),
'ENSMUST00000082772' => array(
'start' => '69777936',
'end' => '69778045',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm22508-201'
),
'ENSMUST00000158034' => array(
'start' => '69551963',
'end' => '69552071',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'Gm24845-201'
),
'ENSMUST00000183237' => array(
'start' => '69256288',
'end' => '69257122',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm4842-001'
)
)
$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_0008DW_0001' => array(
'genes_in_region' => array(
'ENSG00000196628' => array(
[maximum depth reached]
),
'ENSG00000267013' => array(
[maximum depth reached]
),
'ENSG00000267028' => array(
[maximum depth reached]
),
'ENSG00000267284' => array(
[maximum depth reached]
),
'ENSG00000267402' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Liver',
(int) 5 => 'Muscle',
(int) 6 => 'Ovary',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Bladder',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Bladder',
(int) 22 => 'Muscle',
(int) 23 => 'Lung',
(int) 24 => 'Adipose',
(int) 25 => 'Brain',
(int) 26 => 'Heart',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Lung',
(int) 32 => 'Ovary',
(int) 33 => 'Testis',
(int) 34 => 'Adipose',
(int) 35 => 'Breast',
(int) 36 => 'Lung',
(int) 37 => 'Liver',
(int) 38 => 'Placenta',
(int) 39 => 'Placenta',
(int) 40 => 'Bladder',
(int) 41 => 'Brain',
(int) 42 => 'Breast',
(int) 43 => 'Colon',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Adipose',
(int) 52 => 'Bladder',
(int) 53 => 'Breast',
(int) 54 => 'Ovary',
(int) 55 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008DW_0002',
'tax_id' => '10090',
'chromosome' => '18',
'seq_start' => '69199161',
'seq_end' => '69800797',
'region_length' => '601636',
'region_type' => 'VISTA',
'el_id' => 'hs376'
)
)
$gene_el = array(
'ENST00000586467' => array(
'Adipose' => array(
'average_FPKM' => '0.101',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.503',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.113',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.406',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.069',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000267402'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.101',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.503',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.113',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.406',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.069',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000586467'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0008DW_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000196628' => 'transcription factor 4',
'ENSG00000242320' => 'ribosomal protein L21 pseudogene 126',
'ENSG00000252437' => 'RNA, 5S ribosomal pseudogene 459',
'ENSG00000264571' => 'microRNA 4529',
'ENSG00000267013' => null,
'ENSG00000267028' => null,
'ENSG00000267284' => null,
'ENSG00000267402' => null,
'ENSMUSG00000053477' => 'transcription factor 4',
'ENSMUSG00000064706' => 'predicted gene, 22508',
'ENSMUSG00000088659' => 'predicted gene, 24845',
'ENSMUSG00000098060' => 'predicted pseudogene 4842'
),
'gene_name_arr' => array(
'ENSG00000196628' => 'TCF4',
'ENSG00000242320' => 'RPL21P126',
'ENSG00000252437' => 'RNA5SP459',
'ENSG00000264571' => 'MIR4529',
'ENSG00000267013' => 'CTD-2171N6.1',
'ENSG00000267028' => 'RP11-619L19.1',
'ENSG00000267284' => 'RP11-397A16.1',
'ENSG00000267402' => 'RP11-619L19.2',
'ENSMUSG00000053477' => 'Tcf4',
'ENSMUSG00000064706' => 'Gm22508',
'ENSMUSG00000088659' => 'Gm24845',
'ENSMUSG00000098060' => 'Gm4842'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 19 => 'Brain',
(int) 26 => 'Breast',
(int) 33 => 'Colon',
(int) 40 => 'Heart',
(int) 45 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 68 => 'Muscle',
(int) 74 => 'Ovary',
(int) 86 => 'Placenta',
(int) 95 => '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) 76,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000354452' => array(
'start' => '55222331',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-201'
),
'ENST00000356073' => array(
'start' => '55222334',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-002'
),
'ENST00000398339' => array(
'start' => '55227936',
'end' => '55635954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-004'
),
'ENST00000457482' => array(
'start' => '55227689',
'end' => '55322294',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-015'
),
'ENST00000537578' => array(
'start' => '55227752',
'end' => '55589814',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-003'
),
'ENST00000537856' => array(
'start' => '55227849',
'end' => '55401690',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-013'
),
'ENST00000540999' => array(
'start' => '55227690',
'end' => '55586105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-007'
),
'ENST00000543082' => array(
'start' => '55227689',
'end' => '55510769',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-009'
),
'ENST00000544241' => array(
'start' => '55227855',
'end' => '55403995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-011'
),
'ENST00000561831' => array(
'start' => '55227878',
'end' => '55302626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-016'
),
'ENST00000561992' => array(
'start' => '55227864',
'end' => '55422492',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-010'
),
'ENST00000562030' => array(
'start' => '55350359',
'end' => '55401335',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-014'
),
'ENST00000562543' => array(
'start' => '55350955',
'end' => '55591170',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-040'
),
'ENST00000562607' => array(
'start' => '55275648',
'end' => '55351997',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-035'
),
'ENST00000562638' => array(
'start' => '55275662',
'end' => '55401712',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-043'
),
'ENST00000562680' => array(
'start' => '55227849',
'end' => '55401668',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF4-018'
),
'ENST00000562847' => array(
'start' => '55350967',
'end' => '55585966',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-029'
),
'ENST00000563686' => array(
'start' => '55264596',
'end' => '55464144',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF4-017'
),
'ENST00000563760' => array(
'start' => '55254504',
'end' => '55321805',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-037'
),
'ENST00000563824' => array(
'start' => '55350364',
'end' => '55585437',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-028'
),
'ENST00000563888' => array(
'start' => '55350402',
'end' => '55586119',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-025'
),
'ENST00000564228' => array(
'start' => '55227911',
'end' => '55403714',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-042'
),
'ENST00000564343' => array(
'start' => '55350896',
'end' => '55591279',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-023'
),
'ENST00000564403' => array(
'start' => '55227936',
'end' => '55589803',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-019'
),
'ENST00000564999' => array(
'start' => '55227820',
'end' => '55588610',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-006'
),
'ENST00000565018' => array(
'start' => '55227884',
'end' => '55589520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-001'
),
'ENST00000565124' => array(
'start' => '55585280',
'end' => '55635948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-020'
),
'ENST00000565393' => array(
'start' => '55585317',
'end' => '55631362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-039'
),
'ENST00000565580' => array(
'start' => '55403454',
'end' => '55546934',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-030'
),
'ENST00000565908' => array(
'start' => '55275707',
'end' => '55588160',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-024'
),
'ENST00000566279' => array(
'start' => '55227911',
'end' => '55588617',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-045'
),
'ENST00000566286' => array(
'start' => '55227911',
'end' => '55588535',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-041'
),
'ENST00000566376' => array(
'start' => '55332067',
'end' => '55403506',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-036'
),
'ENST00000566514' => array(
'start' => '55269884',
'end' => '55585769',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-027'
),
'ENST00000566777' => array(
'start' => '55275680',
'end' => '55422355',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-032'
),
'ENST00000567880' => array(
'start' => '55227911',
'end' => '55587116',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-046'
),
'ENST00000568147' => array(
'start' => '55350376',
'end' => '55585968',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-026'
),
'ENST00000568169' => array(
'start' => '55269924',
'end' => '55664787',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-021'
),
'ENST00000568186' => array(
'start' => '55275660',
'end' => '55403706',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-033'
),
'ENST00000568673' => array(
'start' => '55227674',
'end' => '55585908',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-008'
),
'ENST00000568740' => array(
'start' => '55227846',
'end' => '55589798',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-005'
),
'ENST00000569012' => array(
'start' => '55269875',
'end' => '55401551',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-034'
),
'ENST00000569357' => array(
'start' => '55403454',
'end' => '55635892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-022'
),
'ENST00000570146' => array(
'start' => '55259621',
'end' => '55275671',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-038'
),
'ENST00000570177' => array(
'start' => '55227984',
'end' => '55402240',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-012'
),
'ENST00000570287' => array(
'start' => '55227911',
'end' => '55321986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-044'
),
'ENST00000590810' => array(
'start' => '55350357',
'end' => '55401851',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-047'
),
'ENST00000616053' => array(
'start' => '55222331',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-202'
),
'ENST00000470049' => array(
'start' => '55635833',
'end' => '55636310',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL21P126-001'
),
'ENST00000516628' => array(
'start' => '55146546',
'end' => '55146645',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP459-201'
),
'ENST00000578110' => array(
'start' => '55479221',
'end' => '55479298',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR4529-201'
),
'ENST00000589125' => array(
'start' => '55105904',
'end' => '55124306',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2171N6.1-001'
),
'ENST00000592405' => array(
'start' => '55108311',
'end' => '55119598',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2171N6.1-002'
),
'ENST00000587660' => array(
'start' => '55452533',
'end' => '55482940',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-619L19.1-001'
),
'ENST00000587346' => array(
'start' => '55721396',
'end' => '55784944',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-001'
),
'ENST00000589662' => array(
'start' => '55721318',
'end' => '55788761',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-002'
),
'ENST00000592936' => array(
'start' => '55721063',
'end' => '55759122',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-003'
),
'ENST00000586467' => array(
'start' => '55492175',
'end' => '55496392',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-619L19.2-001'
),
'ENSMUST00000066717' => array(
'start' => '69344146',
'end' => '69684343',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-003'
),
'ENSMUST00000078486' => array(
'start' => '69345721',
'end' => '69687967',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-201'
),
'ENSMUST00000114977' => array(
'start' => '69593426',
'end' => '69684526',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-008'
),
'ENSMUST00000114978' => array(
'start' => '69593417',
'end' => '69683252',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-007'
),
'ENSMUST00000114980' => array(
'start' => '69346203',
'end' => '69683248',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-004'
),
'ENSMUST00000114982' => array(
'start' => '69345771',
'end' => '69684526',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-002'
),
'ENSMUST00000114985' => array(
'start' => '69344510',
'end' => '69687925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-001'
),
'ENSMUST00000125154' => array(
'start' => '69521538',
'end' => '69564687',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-009'
),
'ENSMUST00000126946' => array(
'start' => '69521793',
'end' => '69633654',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-010'
),
'ENSMUST00000128706' => array(
'start' => '69344492',
'end' => '69565506',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-005'
),
'ENSMUST00000136019' => array(
'start' => '69682380',
'end' => '69683573',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-013'
),
'ENSMUST00000136151' => array(
'start' => '69563335',
'end' => '69636964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-011'
),
'ENSMUST00000145918' => array(
'start' => '69599536',
'end' => '69651289',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-014'
),
'ENSMUST00000146908' => array(
'start' => '69679699',
'end' => '69684528',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-012'
),
'ENSMUST00000155695' => array(
'start' => '69345771',
'end' => '69487850',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-006'
),
'ENSMUST00000082772' => array(
'start' => '69777936',
'end' => '69778045',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm22508-201'
),
'ENSMUST00000158034' => array(
'start' => '69551963',
'end' => '69552071',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'Gm24845-201'
),
'ENSMUST00000183237' => array(
'start' => '69256288',
'end' => '69257122',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm4842-001'
)
),
'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_0008DW_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008DW_0001' => array(
'genes_in_region' => array(
'ENSG00000196628' => array(
[maximum depth reached]
),
'ENSG00000267013' => array(
[maximum depth reached]
),
'ENSG00000267028' => array(
[maximum depth reached]
),
'ENSG00000267284' => array(
[maximum depth reached]
),
'ENSG00000267402' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Liver',
(int) 5 => 'Muscle',
(int) 6 => 'Ovary',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Bladder',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Bladder',
(int) 22 => 'Muscle',
(int) 23 => 'Lung',
(int) 24 => 'Adipose',
(int) 25 => 'Brain',
(int) 26 => 'Heart',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Lung',
(int) 32 => 'Ovary',
(int) 33 => 'Testis',
(int) 34 => 'Adipose',
(int) 35 => 'Breast',
(int) 36 => 'Lung',
(int) 37 => 'Liver',
(int) 38 => 'Placenta',
(int) 39 => 'Placenta',
(int) 40 => 'Bladder',
(int) 41 => 'Brain',
(int) 42 => 'Breast',
(int) 43 => 'Colon',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Adipose',
(int) 52 => 'Bladder',
(int) 53 => 'Breast',
(int) 54 => 'Ovary',
(int) 55 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000196628' => 'transcription factor 4',
'ENSG00000242320' => 'ribosomal protein L21 pseudogene 126',
'ENSG00000252437' => 'RNA, 5S ribosomal pseudogene 459',
'ENSG00000264571' => 'microRNA 4529',
'ENSG00000267013' => null,
'ENSG00000267028' => null,
'ENSG00000267284' => null,
'ENSG00000267402' => null,
'ENSMUSG00000053477' => 'transcription factor 4',
'ENSMUSG00000064706' => 'predicted gene, 22508',
'ENSMUSG00000088659' => 'predicted gene, 24845',
'ENSMUSG00000098060' => 'predicted pseudogene 4842'
)
$gene_name_arr = array(
'ENSG00000196628' => 'TCF4',
'ENSG00000242320' => 'RPL21P126',
'ENSG00000252437' => 'RNA5SP459',
'ENSG00000264571' => 'MIR4529',
'ENSG00000267013' => 'CTD-2171N6.1',
'ENSG00000267028' => 'RP11-619L19.1',
'ENSG00000267284' => 'RP11-397A16.1',
'ENSG00000267402' => 'RP11-619L19.2',
'ENSMUSG00000053477' => 'Tcf4',
'ENSMUSG00000064706' => 'Gm22508',
'ENSMUSG00000088659' => 'Gm24845',
'ENSMUSG00000098060' => 'Gm4842'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008DW_0001',
'tax_id' => '9606',
'chromosome' => '18',
'seq_start' => '55122394',
'seq_end' => '55723848',
'region_length' => '601454',
'region_type' => 'VISTA',
'el_id' => 'hs376'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008DW_0002',
'tax_id' => '10090',
'chromosome' => '18',
'seq_start' => '69199161',
'seq_end' => '69800797',
'region_length' => '601636',
'region_type' => 'VISTA',
'el_id' => 'hs376'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 19 => 'Brain',
(int) 26 => 'Breast',
(int) 33 => 'Colon',
(int) 40 => 'Heart',
(int) 45 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 68 => 'Muscle',
(int) 74 => 'Ovary',
(int) 86 => 'Placenta',
(int) 95 => '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) 76
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000354452' => array(
'start' => '55222331',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-201'
),
'ENST00000356073' => array(
'start' => '55222334',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-002'
),
'ENST00000398339' => array(
'start' => '55227936',
'end' => '55635954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-004'
),
'ENST00000457482' => array(
'start' => '55227689',
'end' => '55322294',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-015'
),
'ENST00000537578' => array(
'start' => '55227752',
'end' => '55589814',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-003'
),
'ENST00000537856' => array(
'start' => '55227849',
'end' => '55401690',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-013'
),
'ENST00000540999' => array(
'start' => '55227690',
'end' => '55586105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-007'
),
'ENST00000543082' => array(
'start' => '55227689',
'end' => '55510769',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-009'
),
'ENST00000544241' => array(
'start' => '55227855',
'end' => '55403995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-011'
),
'ENST00000561831' => array(
'start' => '55227878',
'end' => '55302626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-016'
),
'ENST00000561992' => array(
'start' => '55227864',
'end' => '55422492',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-010'
),
'ENST00000562030' => array(
'start' => '55350359',
'end' => '55401335',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-014'
),
'ENST00000562543' => array(
'start' => '55350955',
'end' => '55591170',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-040'
),
'ENST00000562607' => array(
'start' => '55275648',
'end' => '55351997',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-035'
),
'ENST00000562638' => array(
'start' => '55275662',
'end' => '55401712',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-043'
),
'ENST00000562680' => array(
'start' => '55227849',
'end' => '55401668',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF4-018'
),
'ENST00000562847' => array(
'start' => '55350967',
'end' => '55585966',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-029'
),
'ENST00000563686' => array(
'start' => '55264596',
'end' => '55464144',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF4-017'
),
'ENST00000563760' => array(
'start' => '55254504',
'end' => '55321805',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-037'
),
'ENST00000563824' => array(
'start' => '55350364',
'end' => '55585437',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-028'
),
'ENST00000563888' => array(
'start' => '55350402',
'end' => '55586119',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-025'
),
'ENST00000564228' => array(
'start' => '55227911',
'end' => '55403714',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-042'
),
'ENST00000564343' => array(
'start' => '55350896',
'end' => '55591279',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-023'
),
'ENST00000564403' => array(
'start' => '55227936',
'end' => '55589803',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-019'
),
'ENST00000564999' => array(
'start' => '55227820',
'end' => '55588610',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-006'
),
'ENST00000565018' => array(
'start' => '55227884',
'end' => '55589520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-001'
),
'ENST00000565124' => array(
'start' => '55585280',
'end' => '55635948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-020'
),
'ENST00000565393' => array(
'start' => '55585317',
'end' => '55631362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-039'
),
'ENST00000565580' => array(
'start' => '55403454',
'end' => '55546934',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-030'
),
'ENST00000565908' => array(
'start' => '55275707',
'end' => '55588160',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-024'
),
'ENST00000566279' => array(
'start' => '55227911',
'end' => '55588617',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-045'
),
'ENST00000566286' => array(
'start' => '55227911',
'end' => '55588535',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-041'
),
'ENST00000566376' => array(
'start' => '55332067',
'end' => '55403506',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF4-036'
),
'ENST00000566514' => array(
'start' => '55269884',
'end' => '55585769',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-027'
),
'ENST00000566777' => array(
'start' => '55275680',
'end' => '55422355',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-032'
),
'ENST00000567880' => array(
'start' => '55227911',
'end' => '55587116',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-046'
),
'ENST00000568147' => array(
'start' => '55350376',
'end' => '55585968',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-026'
),
'ENST00000568169' => array(
'start' => '55269924',
'end' => '55664787',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-021'
),
'ENST00000568186' => array(
'start' => '55275660',
'end' => '55403706',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-033'
),
'ENST00000568673' => array(
'start' => '55227674',
'end' => '55585908',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-008'
),
'ENST00000568740' => array(
'start' => '55227846',
'end' => '55589798',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-005'
),
'ENST00000569012' => array(
'start' => '55269875',
'end' => '55401551',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-034'
),
'ENST00000569357' => array(
'start' => '55403454',
'end' => '55635892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-022'
),
'ENST00000570146' => array(
'start' => '55259621',
'end' => '55275671',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-038'
),
'ENST00000570177' => array(
'start' => '55227984',
'end' => '55402240',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-012'
),
'ENST00000570287' => array(
'start' => '55227911',
'end' => '55321986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-044'
),
'ENST00000590810' => array(
'start' => '55350357',
'end' => '55401851',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-047'
),
'ENST00000616053' => array(
'start' => '55222331',
'end' => '55588629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF4-202'
),
'ENST00000470049' => array(
'start' => '55635833',
'end' => '55636310',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL21P126-001'
),
'ENST00000516628' => array(
'start' => '55146546',
'end' => '55146645',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP459-201'
),
'ENST00000578110' => array(
'start' => '55479221',
'end' => '55479298',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR4529-201'
),
'ENST00000589125' => array(
'start' => '55105904',
'end' => '55124306',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2171N6.1-001'
),
'ENST00000592405' => array(
'start' => '55108311',
'end' => '55119598',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2171N6.1-002'
),
'ENST00000587660' => array(
'start' => '55452533',
'end' => '55482940',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-619L19.1-001'
),
'ENST00000587346' => array(
'start' => '55721396',
'end' => '55784944',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-001'
),
'ENST00000589662' => array(
'start' => '55721318',
'end' => '55788761',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-002'
),
'ENST00000592936' => array(
'start' => '55721063',
'end' => '55759122',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-397A16.1-003'
),
'ENST00000586467' => array(
'start' => '55492175',
'end' => '55496392',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-619L19.2-001'
),
'ENSMUST00000066717' => array(
'start' => '69344146',
'end' => '69684343',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-003'
),
'ENSMUST00000078486' => array(
'start' => '69345721',
'end' => '69687967',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-201'
),
'ENSMUST00000114977' => array(
'start' => '69593426',
'end' => '69684526',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-008'
),
'ENSMUST00000114978' => array(
'start' => '69593417',
'end' => '69683252',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-007'
),
'ENSMUST00000114980' => array(
'start' => '69346203',
'end' => '69683248',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-004'
),
'ENSMUST00000114982' => array(
'start' => '69345771',
'end' => '69684526',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-002'
),
'ENSMUST00000114985' => array(
'start' => '69344510',
'end' => '69687925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf4-001'
),
'ENSMUST00000125154' => array(
'start' => '69521538',
'end' => '69564687',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-009'
),
'ENSMUST00000126946' => array(
'start' => '69521793',
'end' => '69633654',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-010'
),
'ENSMUST00000128706' => array(
'start' => '69344492',
'end' => '69565506',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-005'
),
'ENSMUST00000136019' => array(
'start' => '69682380',
'end' => '69683573',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-013'
),
'ENSMUST00000136151' => array(
'start' => '69563335',
'end' => '69636964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-011'
),
'ENSMUST00000145918' => array(
'start' => '69599536',
'end' => '69651289',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-014'
),
'ENSMUST00000146908' => array(
'start' => '69679699',
'end' => '69684528',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Tcf4-012'
),
'ENSMUST00000155695' => array(
'start' => '69345771',
'end' => '69487850',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Tcf4-006'
),
'ENSMUST00000082772' => array(
'start' => '69777936',
'end' => '69778045',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm22508-201'
),
'ENSMUST00000158034' => array(
'start' => '69551963',
'end' => '69552071',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'Gm24845-201'
),
'ENSMUST00000183237' => array(
'start' => '69256288',
'end' => '69257122',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm4842-001'
)
)
$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_0008DW_0001' => array(
'genes_in_region' => array(
'ENSG00000196628' => array(
[maximum depth reached]
),
'ENSG00000267013' => array(
[maximum depth reached]
),
'ENSG00000267028' => array(
[maximum depth reached]
),
'ENSG00000267284' => array(
[maximum depth reached]
),
'ENSG00000267402' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Liver',
(int) 5 => 'Muscle',
(int) 6 => 'Ovary',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Bladder',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Bladder',
(int) 22 => 'Muscle',
(int) 23 => 'Lung',
(int) 24 => 'Adipose',
(int) 25 => 'Brain',
(int) 26 => 'Heart',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Lung',
(int) 32 => 'Ovary',
(int) 33 => 'Testis',
(int) 34 => 'Adipose',
(int) 35 => 'Breast',
(int) 36 => 'Lung',
(int) 37 => 'Liver',
(int) 38 => 'Placenta',
(int) 39 => 'Placenta',
(int) 40 => 'Bladder',
(int) 41 => 'Brain',
(int) 42 => 'Breast',
(int) 43 => 'Colon',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Adipose',
(int) 52 => 'Bladder',
(int) 53 => 'Breast',
(int) 54 => 'Ovary',
(int) 55 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008DW_0002',
'tax_id' => '10090',
'chromosome' => '18',
'seq_start' => '69199161',
'seq_end' => '69800797',
'region_length' => '601636',
'region_type' => 'VISTA',
'el_id' => 'hs376'
)
)
$gene_el = array(
'ENST00000586467' => array(
'Adipose' => array(
'average_FPKM' => '0.101',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.503',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.113',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.406',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.069',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000267402'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.101',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.503',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.113',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.406',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.069',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000586467'
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
(TCF4)