| Source ID |
Type |
Tax ID |
Position |
| ENSG00000067225-ENSG00000137817 |
CGP |
9606 |
15:72199029-72272999  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0004GV_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_0004GV_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000003933' => 'pyruvate kinase, muscle, a',
'ENSDARG00000042703' => 'poly (ADP-ribose) polymerase family, member 6a',
'ENSG00000067225' => 'pyruvate kinase, muscle',
'ENSG00000137817' => 'poly (ADP-ribose) polymerase family, member 6',
'ENSG00000273025' => 'CUGBP, Elav-like family member 6'
),
'gene_name_arr' => array(
'ENSDARG00000003933' => 'pkma',
'ENSDARG00000042703' => 'parp6a',
'ENSG00000067225' => 'PKM',
'ENSG00000137817' => 'PARP6',
'ENSG00000273025' => 'CELF6'
),
'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) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 8 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 35 => 'Kidney',
(int) 43 => 'Liver',
(int) 51 => 'Lung',
(int) 56 => 'Muscle',
(int) 67 => 'Ovary',
(int) 72 => 'Placenta',
(int) 74 => '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) 57,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000062651' => array(
'start' => '684361',
'end' => '725539',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-201'
),
'ENSDART00000123153' => array(
'start' => '684361',
'end' => '725539',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-202'
),
'ENSDART00000123667' => array(
'start' => '680253',
'end' => '711615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-203'
),
'ENSDART00000151308' => array(
'start' => '710673',
'end' => '729324',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-002'
),
'ENSDART00000151643' => array(
'start' => '710673',
'end' => '725598',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-001'
),
'ENSDART00000062654' => array(
'start' => '737717',
'end' => '749468',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-001'
),
'ENSDART00000150959' => array(
'start' => '743016',
'end' => '748708',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-003'
),
'ENSDART00000151777' => array(
'start' => '737720',
'end' => '748018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-002'
),
'ENST00000319622' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-201'
),
'ENST00000335181' => array(
'start' => '72199032',
'end' => '72231206',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-004'
),
'ENST00000389093' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-202'
),
'ENST00000449901' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-203'
),
'ENST00000561609' => array(
'start' => '72200508',
'end' => '72228676',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-008'
),
'ENST00000562784' => array(
'start' => '72209506',
'end' => '72217451',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-024'
),
'ENST00000562997' => array(
'start' => '72209751',
'end' => '72222531',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-017'
),
'ENST00000563275' => array(
'start' => '72206675',
'end' => '72208962',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-022'
),
'ENST00000563986' => array(
'start' => '72201867',
'end' => '72206798',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-014'
),
'ENST00000564178' => array(
'start' => '72209733',
'end' => '72219425',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-016'
),
'ENST00000564276' => array(
'start' => '72210060',
'end' => '72231190',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-026'
),
'ENST00000564440' => array(
'start' => '72199029',
'end' => '72204559',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-009'
),
'ENST00000564993' => array(
'start' => '72206259',
'end' => '72207167',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-013'
),
'ENST00000565143' => array(
'start' => '72199036',
'end' => '72202053',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-010'
),
'ENST00000565154' => array(
'start' => '72199590',
'end' => '72231113',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-006'
),
'ENST00000565184' => array(
'start' => '72199032',
'end' => '72231171',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-012'
),
'ENST00000566809' => array(
'start' => '72217409',
'end' => '72231624',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-019'
),
'ENST00000567087' => array(
'start' => '72209783',
'end' => '72231680',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-020'
),
'ENST00000567118' => array(
'start' => '72199105',
'end' => '72231190',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PKM-005'
),
'ENST00000568459' => array(
'start' => '72199629',
'end' => '72229722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-007'
),
'ENST00000568743' => array(
'start' => '72208666',
'end' => '72210026',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-025'
),
'ENST00000568883' => array(
'start' => '72199032',
'end' => '72231822',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-204'
),
'ENST00000569050' => array(
'start' => '72218943',
'end' => '72231819',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-018'
),
'ENST00000569857' => array(
'start' => '72202533',
'end' => '72231225',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PKM-002'
),
'ENST00000570166' => array(
'start' => '72202690',
'end' => '72206854',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-015'
),
'ENST00000260376' => array(
'start' => '72241182',
'end' => '72267523',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-201'
),
'ENST00000287196' => array(
'start' => '72241182',
'end' => '72271287',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-202'
),
'ENST00000413097' => array(
'start' => '72241182',
'end' => '72267649',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-004'
),
'ENST00000419739' => array(
'start' => '72242206',
'end' => '72267536',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-010'
),
'ENST00000544520' => array(
'start' => '72241199',
'end' => '72267028',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-005'
),
'ENST00000564610' => array(
'start' => '72241199',
'end' => '72265929',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-009'
),
'ENST00000565443' => array(
'start' => '72241199',
'end' => '72271051',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-006'
),
'ENST00000565999' => array(
'start' => '72260594',
'end' => '72266782',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-016'
),
'ENST00000566831' => array(
'start' => '72241287',
'end' => '72251351',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-015'
),
'ENST00000566844' => array(
'start' => '72266747',
'end' => '72272571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-019'
),
'ENST00000566991' => array(
'start' => '72241218',
'end' => '72245787',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-002'
),
'ENST00000567042' => array(
'start' => '72242620',
'end' => '72254481',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-012'
),
'ENST00000567263' => array(
'start' => '72241275',
'end' => '72257420',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-021'
),
'ENST00000567440' => array(
'start' => '72241223',
'end' => '72271215',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-003'
),
'ENST00000567633' => array(
'start' => '72267632',
'end' => '72272498',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-020'
),
'ENST00000567974' => array(
'start' => '72241199',
'end' => '72265930',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-008'
),
'ENST00000568213' => array(
'start' => '72249128',
'end' => '72250448',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-013'
),
'ENST00000568360' => array(
'start' => '72265429',
'end' => '72272999',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-011'
),
'ENST00000569173' => array(
'start' => '72241181',
'end' => '72260623',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-023'
),
'ENST00000569795' => array(
'start' => '72241181',
'end' => '72272621',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-001'
),
'ENST00000569890' => array(
'start' => '72242674',
'end' => '72257435',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-022'
),
'ENST00000569972' => array(
'start' => '72241197',
'end' => '72250265',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-014'
),
'ENST00000616176' => array(
'start' => '72241182',
'end' => '72267523',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-203'
),
'ENST00000569547' => array(
'start' => '72266746',
'end' => '72319946',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CELF6-001'
)
),
'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_0004GV_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004GV_0001' => array(
'genes_in_region' => array(
'ENSDARG00000003933' => array(
[maximum depth reached]
),
'ENSDARG00000042703' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Muscle',
(int) 15 => 'Brain',
(int) 16 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000003933' => 'pyruvate kinase, muscle, a',
'ENSDARG00000042703' => 'poly (ADP-ribose) polymerase family, member 6a',
'ENSG00000067225' => 'pyruvate kinase, muscle',
'ENSG00000137817' => 'poly (ADP-ribose) polymerase family, member 6',
'ENSG00000273025' => 'CUGBP, Elav-like family member 6'
)
$gene_name_arr = array(
'ENSDARG00000003933' => 'pkma',
'ENSDARG00000042703' => 'parp6a',
'ENSG00000067225' => 'PKM',
'ENSG00000137817' => 'PARP6',
'ENSG00000273025' => 'CELF6'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004GV_0001',
'tax_id' => '7955',
'chromosome' => '18',
'seq_start' => '680253',
'seq_end' => '749468',
'region_length' => '69215',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000003933-ENSDARG00000042703'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004GV_0002',
'tax_id' => '9606',
'chromosome' => '15',
'seq_start' => '72199029',
'seq_end' => '72272999',
'region_length' => '73970',
'region_type' => 'CGP',
'el_id' => 'ENSG00000067225-ENSG00000137817'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 8 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 35 => 'Kidney',
(int) 43 => 'Liver',
(int) 51 => 'Lung',
(int) 56 => 'Muscle',
(int) 67 => 'Ovary',
(int) 72 => 'Placenta',
(int) 74 => '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) 57
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000062651' => array(
'start' => '684361',
'end' => '725539',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-201'
),
'ENSDART00000123153' => array(
'start' => '684361',
'end' => '725539',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-202'
),
'ENSDART00000123667' => array(
'start' => '680253',
'end' => '711615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-203'
),
'ENSDART00000151308' => array(
'start' => '710673',
'end' => '729324',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-002'
),
'ENSDART00000151643' => array(
'start' => '710673',
'end' => '725598',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-001'
),
'ENSDART00000062654' => array(
'start' => '737717',
'end' => '749468',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-001'
),
'ENSDART00000150959' => array(
'start' => '743016',
'end' => '748708',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-003'
),
'ENSDART00000151777' => array(
'start' => '737720',
'end' => '748018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-002'
),
'ENST00000319622' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-201'
),
'ENST00000335181' => array(
'start' => '72199032',
'end' => '72231206',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-004'
),
'ENST00000389093' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-202'
),
'ENST00000449901' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-203'
),
'ENST00000561609' => array(
'start' => '72200508',
'end' => '72228676',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-008'
),
'ENST00000562784' => array(
'start' => '72209506',
'end' => '72217451',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-024'
),
'ENST00000562997' => array(
'start' => '72209751',
'end' => '72222531',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-017'
),
'ENST00000563275' => array(
'start' => '72206675',
'end' => '72208962',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-022'
),
'ENST00000563986' => array(
'start' => '72201867',
'end' => '72206798',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-014'
),
'ENST00000564178' => array(
'start' => '72209733',
'end' => '72219425',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-016'
),
'ENST00000564276' => array(
'start' => '72210060',
'end' => '72231190',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-026'
),
'ENST00000564440' => array(
'start' => '72199029',
'end' => '72204559',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-009'
),
'ENST00000564993' => array(
'start' => '72206259',
'end' => '72207167',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-013'
),
'ENST00000565143' => array(
'start' => '72199036',
'end' => '72202053',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-010'
),
'ENST00000565154' => array(
'start' => '72199590',
'end' => '72231113',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-006'
),
'ENST00000565184' => array(
'start' => '72199032',
'end' => '72231171',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-012'
),
'ENST00000566809' => array(
'start' => '72217409',
'end' => '72231624',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-019'
),
'ENST00000567087' => array(
'start' => '72209783',
'end' => '72231680',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-020'
),
'ENST00000567118' => array(
'start' => '72199105',
'end' => '72231190',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PKM-005'
),
'ENST00000568459' => array(
'start' => '72199629',
'end' => '72229722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-007'
),
'ENST00000568743' => array(
'start' => '72208666',
'end' => '72210026',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-025'
),
'ENST00000568883' => array(
'start' => '72199032',
'end' => '72231822',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-204'
),
'ENST00000569050' => array(
'start' => '72218943',
'end' => '72231819',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-018'
),
'ENST00000569857' => array(
'start' => '72202533',
'end' => '72231225',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PKM-002'
),
'ENST00000570166' => array(
'start' => '72202690',
'end' => '72206854',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-015'
),
'ENST00000260376' => array(
'start' => '72241182',
'end' => '72267523',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-201'
),
'ENST00000287196' => array(
'start' => '72241182',
'end' => '72271287',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-202'
),
'ENST00000413097' => array(
'start' => '72241182',
'end' => '72267649',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-004'
),
'ENST00000419739' => array(
'start' => '72242206',
'end' => '72267536',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-010'
),
'ENST00000544520' => array(
'start' => '72241199',
'end' => '72267028',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-005'
),
'ENST00000564610' => array(
'start' => '72241199',
'end' => '72265929',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-009'
),
'ENST00000565443' => array(
'start' => '72241199',
'end' => '72271051',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-006'
),
'ENST00000565999' => array(
'start' => '72260594',
'end' => '72266782',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-016'
),
'ENST00000566831' => array(
'start' => '72241287',
'end' => '72251351',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-015'
),
'ENST00000566844' => array(
'start' => '72266747',
'end' => '72272571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-019'
),
'ENST00000566991' => array(
'start' => '72241218',
'end' => '72245787',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-002'
),
'ENST00000567042' => array(
'start' => '72242620',
'end' => '72254481',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-012'
),
'ENST00000567263' => array(
'start' => '72241275',
'end' => '72257420',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-021'
),
'ENST00000567440' => array(
'start' => '72241223',
'end' => '72271215',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-003'
),
'ENST00000567633' => array(
'start' => '72267632',
'end' => '72272498',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-020'
),
'ENST00000567974' => array(
'start' => '72241199',
'end' => '72265930',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-008'
),
'ENST00000568213' => array(
'start' => '72249128',
'end' => '72250448',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-013'
),
'ENST00000568360' => array(
'start' => '72265429',
'end' => '72272999',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-011'
),
'ENST00000569173' => array(
'start' => '72241181',
'end' => '72260623',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-023'
),
'ENST00000569795' => array(
'start' => '72241181',
'end' => '72272621',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-001'
),
'ENST00000569890' => array(
'start' => '72242674',
'end' => '72257435',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-022'
),
'ENST00000569972' => array(
'start' => '72241197',
'end' => '72250265',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-014'
),
'ENST00000616176' => array(
'start' => '72241182',
'end' => '72267523',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-203'
),
'ENST00000569547' => array(
'start' => '72266746',
'end' => '72319946',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CELF6-001'
)
)
$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_0004GV_0001' => array(
'genes_in_region' => array(
'ENSDARG00000003933' => array(
[maximum depth reached]
),
'ENSDARG00000042703' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Muscle',
(int) 15 => 'Brain',
(int) 16 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004GV_0002',
'tax_id' => '9606',
'chromosome' => '15',
'seq_start' => '72199029',
'seq_end' => '72272999',
'region_length' => '73970',
'region_type' => 'CGP',
'el_id' => 'ENSG00000067225-ENSG00000137817'
)
)
$gene_el = array(
'ENSDART00000062654' => array(
'Brain' => array(
'average_FPKM' => '14.515',
'stddev_FPKM' => '3.05'
),
'Heart' => array(
'average_FPKM' => '1.655',
'stddev_FPKM' => '0.87'
),
'Kidney' => array(
'average_FPKM' => '1.707',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.168',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.723',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000150959' => array(
'Brain' => array(
'average_FPKM' => '9.337',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.712',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000151777' => array()
)
$gene_key = 'ENSDARG00000042703'
$is_first = false
$tran_el = array()
$tran_key = 'ENSDART00000151777'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0004GV_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000003933' => 'pyruvate kinase, muscle, a',
'ENSDARG00000042703' => 'poly (ADP-ribose) polymerase family, member 6a',
'ENSG00000067225' => 'pyruvate kinase, muscle',
'ENSG00000137817' => 'poly (ADP-ribose) polymerase family, member 6',
'ENSG00000273025' => 'CUGBP, Elav-like family member 6'
),
'gene_name_arr' => array(
'ENSDARG00000003933' => 'pkma',
'ENSDARG00000042703' => 'parp6a',
'ENSG00000067225' => 'PKM',
'ENSG00000137817' => 'PARP6',
'ENSG00000273025' => 'CELF6'
),
'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) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 8 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 35 => 'Kidney',
(int) 43 => 'Liver',
(int) 51 => 'Lung',
(int) 56 => 'Muscle',
(int) 67 => 'Ovary',
(int) 72 => 'Placenta',
(int) 74 => '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) 57,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000062651' => array(
'start' => '684361',
'end' => '725539',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-201'
),
'ENSDART00000123153' => array(
'start' => '684361',
'end' => '725539',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-202'
),
'ENSDART00000123667' => array(
'start' => '680253',
'end' => '711615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-203'
),
'ENSDART00000151308' => array(
'start' => '710673',
'end' => '729324',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-002'
),
'ENSDART00000151643' => array(
'start' => '710673',
'end' => '725598',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-001'
),
'ENSDART00000062654' => array(
'start' => '737717',
'end' => '749468',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-001'
),
'ENSDART00000150959' => array(
'start' => '743016',
'end' => '748708',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-003'
),
'ENSDART00000151777' => array(
'start' => '737720',
'end' => '748018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-002'
),
'ENST00000319622' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-201'
),
'ENST00000335181' => array(
'start' => '72199032',
'end' => '72231206',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-004'
),
'ENST00000389093' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-202'
),
'ENST00000449901' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-203'
),
'ENST00000561609' => array(
'start' => '72200508',
'end' => '72228676',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-008'
),
'ENST00000562784' => array(
'start' => '72209506',
'end' => '72217451',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-024'
),
'ENST00000562997' => array(
'start' => '72209751',
'end' => '72222531',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-017'
),
'ENST00000563275' => array(
'start' => '72206675',
'end' => '72208962',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-022'
),
'ENST00000563986' => array(
'start' => '72201867',
'end' => '72206798',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-014'
),
'ENST00000564178' => array(
'start' => '72209733',
'end' => '72219425',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-016'
),
'ENST00000564276' => array(
'start' => '72210060',
'end' => '72231190',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-026'
),
'ENST00000564440' => array(
'start' => '72199029',
'end' => '72204559',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-009'
),
'ENST00000564993' => array(
'start' => '72206259',
'end' => '72207167',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-013'
),
'ENST00000565143' => array(
'start' => '72199036',
'end' => '72202053',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-010'
),
'ENST00000565154' => array(
'start' => '72199590',
'end' => '72231113',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-006'
),
'ENST00000565184' => array(
'start' => '72199032',
'end' => '72231171',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-012'
),
'ENST00000566809' => array(
'start' => '72217409',
'end' => '72231624',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-019'
),
'ENST00000567087' => array(
'start' => '72209783',
'end' => '72231680',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-020'
),
'ENST00000567118' => array(
'start' => '72199105',
'end' => '72231190',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PKM-005'
),
'ENST00000568459' => array(
'start' => '72199629',
'end' => '72229722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-007'
),
'ENST00000568743' => array(
'start' => '72208666',
'end' => '72210026',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-025'
),
'ENST00000568883' => array(
'start' => '72199032',
'end' => '72231822',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-204'
),
'ENST00000569050' => array(
'start' => '72218943',
'end' => '72231819',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-018'
),
'ENST00000569857' => array(
'start' => '72202533',
'end' => '72231225',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PKM-002'
),
'ENST00000570166' => array(
'start' => '72202690',
'end' => '72206854',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-015'
),
'ENST00000260376' => array(
'start' => '72241182',
'end' => '72267523',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-201'
),
'ENST00000287196' => array(
'start' => '72241182',
'end' => '72271287',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-202'
),
'ENST00000413097' => array(
'start' => '72241182',
'end' => '72267649',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-004'
),
'ENST00000419739' => array(
'start' => '72242206',
'end' => '72267536',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-010'
),
'ENST00000544520' => array(
'start' => '72241199',
'end' => '72267028',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-005'
),
'ENST00000564610' => array(
'start' => '72241199',
'end' => '72265929',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-009'
),
'ENST00000565443' => array(
'start' => '72241199',
'end' => '72271051',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-006'
),
'ENST00000565999' => array(
'start' => '72260594',
'end' => '72266782',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-016'
),
'ENST00000566831' => array(
'start' => '72241287',
'end' => '72251351',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-015'
),
'ENST00000566844' => array(
'start' => '72266747',
'end' => '72272571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-019'
),
'ENST00000566991' => array(
'start' => '72241218',
'end' => '72245787',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-002'
),
'ENST00000567042' => array(
'start' => '72242620',
'end' => '72254481',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-012'
),
'ENST00000567263' => array(
'start' => '72241275',
'end' => '72257420',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-021'
),
'ENST00000567440' => array(
'start' => '72241223',
'end' => '72271215',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-003'
),
'ENST00000567633' => array(
'start' => '72267632',
'end' => '72272498',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-020'
),
'ENST00000567974' => array(
'start' => '72241199',
'end' => '72265930',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-008'
),
'ENST00000568213' => array(
'start' => '72249128',
'end' => '72250448',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-013'
),
'ENST00000568360' => array(
'start' => '72265429',
'end' => '72272999',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-011'
),
'ENST00000569173' => array(
'start' => '72241181',
'end' => '72260623',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-023'
),
'ENST00000569795' => array(
'start' => '72241181',
'end' => '72272621',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-001'
),
'ENST00000569890' => array(
'start' => '72242674',
'end' => '72257435',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-022'
),
'ENST00000569972' => array(
'start' => '72241197',
'end' => '72250265',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-014'
),
'ENST00000616176' => array(
'start' => '72241182',
'end' => '72267523',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-203'
),
'ENST00000569547' => array(
'start' => '72266746',
'end' => '72319946',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CELF6-001'
)
),
'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_0004GV_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004GV_0001' => array(
'genes_in_region' => array(
'ENSDARG00000003933' => array(
[maximum depth reached]
),
'ENSDARG00000042703' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Muscle',
(int) 15 => 'Brain',
(int) 16 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000003933' => 'pyruvate kinase, muscle, a',
'ENSDARG00000042703' => 'poly (ADP-ribose) polymerase family, member 6a',
'ENSG00000067225' => 'pyruvate kinase, muscle',
'ENSG00000137817' => 'poly (ADP-ribose) polymerase family, member 6',
'ENSG00000273025' => 'CUGBP, Elav-like family member 6'
)
$gene_name_arr = array(
'ENSDARG00000003933' => 'pkma',
'ENSDARG00000042703' => 'parp6a',
'ENSG00000067225' => 'PKM',
'ENSG00000137817' => 'PARP6',
'ENSG00000273025' => 'CELF6'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004GV_0001',
'tax_id' => '7955',
'chromosome' => '18',
'seq_start' => '680253',
'seq_end' => '749468',
'region_length' => '69215',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000003933-ENSDARG00000042703'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004GV_0002',
'tax_id' => '9606',
'chromosome' => '15',
'seq_start' => '72199029',
'seq_end' => '72272999',
'region_length' => '73970',
'region_type' => 'CGP',
'el_id' => 'ENSG00000067225-ENSG00000137817'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 8 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 35 => 'Kidney',
(int) 43 => 'Liver',
(int) 51 => 'Lung',
(int) 56 => 'Muscle',
(int) 67 => 'Ovary',
(int) 72 => 'Placenta',
(int) 74 => '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) 57
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000062651' => array(
'start' => '684361',
'end' => '725539',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-201'
),
'ENSDART00000123153' => array(
'start' => '684361',
'end' => '725539',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-202'
),
'ENSDART00000123667' => array(
'start' => '680253',
'end' => '711615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-203'
),
'ENSDART00000151308' => array(
'start' => '710673',
'end' => '729324',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-002'
),
'ENSDART00000151643' => array(
'start' => '710673',
'end' => '725598',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pkma-001'
),
'ENSDART00000062654' => array(
'start' => '737717',
'end' => '749468',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-001'
),
'ENSDART00000150959' => array(
'start' => '743016',
'end' => '748708',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-003'
),
'ENSDART00000151777' => array(
'start' => '737720',
'end' => '748018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'parp6a-002'
),
'ENST00000319622' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-201'
),
'ENST00000335181' => array(
'start' => '72199032',
'end' => '72231206',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-004'
),
'ENST00000389093' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-202'
),
'ENST00000449901' => array(
'start' => '72199029',
'end' => '72231386',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-203'
),
'ENST00000561609' => array(
'start' => '72200508',
'end' => '72228676',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-008'
),
'ENST00000562784' => array(
'start' => '72209506',
'end' => '72217451',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-024'
),
'ENST00000562997' => array(
'start' => '72209751',
'end' => '72222531',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-017'
),
'ENST00000563275' => array(
'start' => '72206675',
'end' => '72208962',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-022'
),
'ENST00000563986' => array(
'start' => '72201867',
'end' => '72206798',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-014'
),
'ENST00000564178' => array(
'start' => '72209733',
'end' => '72219425',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-016'
),
'ENST00000564276' => array(
'start' => '72210060',
'end' => '72231190',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-026'
),
'ENST00000564440' => array(
'start' => '72199029',
'end' => '72204559',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-009'
),
'ENST00000564993' => array(
'start' => '72206259',
'end' => '72207167',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-013'
),
'ENST00000565143' => array(
'start' => '72199036',
'end' => '72202053',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-010'
),
'ENST00000565154' => array(
'start' => '72199590',
'end' => '72231113',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-006'
),
'ENST00000565184' => array(
'start' => '72199032',
'end' => '72231171',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-012'
),
'ENST00000566809' => array(
'start' => '72217409',
'end' => '72231624',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-019'
),
'ENST00000567087' => array(
'start' => '72209783',
'end' => '72231680',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-020'
),
'ENST00000567118' => array(
'start' => '72199105',
'end' => '72231190',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PKM-005'
),
'ENST00000568459' => array(
'start' => '72199629',
'end' => '72229722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-007'
),
'ENST00000568743' => array(
'start' => '72208666',
'end' => '72210026',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-025'
),
'ENST00000568883' => array(
'start' => '72199032',
'end' => '72231822',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-204'
),
'ENST00000569050' => array(
'start' => '72218943',
'end' => '72231819',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PKM-018'
),
'ENST00000569857' => array(
'start' => '72202533',
'end' => '72231225',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PKM-002'
),
'ENST00000570166' => array(
'start' => '72202690',
'end' => '72206854',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PKM-015'
),
'ENST00000260376' => array(
'start' => '72241182',
'end' => '72267523',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-201'
),
'ENST00000287196' => array(
'start' => '72241182',
'end' => '72271287',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-202'
),
'ENST00000413097' => array(
'start' => '72241182',
'end' => '72267649',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-004'
),
'ENST00000419739' => array(
'start' => '72242206',
'end' => '72267536',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-010'
),
'ENST00000544520' => array(
'start' => '72241199',
'end' => '72267028',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-005'
),
'ENST00000564610' => array(
'start' => '72241199',
'end' => '72265929',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-009'
),
'ENST00000565443' => array(
'start' => '72241199',
'end' => '72271051',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-006'
),
'ENST00000565999' => array(
'start' => '72260594',
'end' => '72266782',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-016'
),
'ENST00000566831' => array(
'start' => '72241287',
'end' => '72251351',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-015'
),
'ENST00000566844' => array(
'start' => '72266747',
'end' => '72272571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-019'
),
'ENST00000566991' => array(
'start' => '72241218',
'end' => '72245787',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-002'
),
'ENST00000567042' => array(
'start' => '72242620',
'end' => '72254481',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-012'
),
'ENST00000567263' => array(
'start' => '72241275',
'end' => '72257420',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-021'
),
'ENST00000567440' => array(
'start' => '72241223',
'end' => '72271215',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-003'
),
'ENST00000567633' => array(
'start' => '72267632',
'end' => '72272498',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PARP6-020'
),
'ENST00000567974' => array(
'start' => '72241199',
'end' => '72265930',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-008'
),
'ENST00000568213' => array(
'start' => '72249128',
'end' => '72250448',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-013'
),
'ENST00000568360' => array(
'start' => '72265429',
'end' => '72272999',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-011'
),
'ENST00000569173' => array(
'start' => '72241181',
'end' => '72260623',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-023'
),
'ENST00000569795' => array(
'start' => '72241181',
'end' => '72272621',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-001'
),
'ENST00000569890' => array(
'start' => '72242674',
'end' => '72257435',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PARP6-022'
),
'ENST00000569972' => array(
'start' => '72241197',
'end' => '72250265',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PARP6-014'
),
'ENST00000616176' => array(
'start' => '72241182',
'end' => '72267523',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PARP6-203'
),
'ENST00000569547' => array(
'start' => '72266746',
'end' => '72319946',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CELF6-001'
)
)
$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_0004GV_0001' => array(
'genes_in_region' => array(
'ENSDARG00000003933' => array(
[maximum depth reached]
),
'ENSDARG00000042703' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Muscle',
(int) 15 => 'Brain',
(int) 16 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004GV_0002',
'tax_id' => '9606',
'chromosome' => '15',
'seq_start' => '72199029',
'seq_end' => '72272999',
'region_length' => '73970',
'region_type' => 'CGP',
'el_id' => 'ENSG00000067225-ENSG00000137817'
)
)
$gene_el = array(
'ENSDART00000062654' => array(
'Brain' => array(
'average_FPKM' => '14.515',
'stddev_FPKM' => '3.05'
),
'Heart' => array(
'average_FPKM' => '1.655',
'stddev_FPKM' => '0.87'
),
'Kidney' => array(
'average_FPKM' => '1.707',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.168',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.723',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000150959' => array(
'Brain' => array(
'average_FPKM' => '9.337',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.712',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000151777' => array()
)
$gene_key = 'ENSDARG00000042703'
$is_first = false
$tran_el = array()
$tran_key = 'ENSDART00000151777'
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
(pkma)