| Source ID |
Type |
Tax ID |
Position |
| PTPRD |
UCNEbase |
7955 |
7:76959895-76964764  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007LL_0004 [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_0007LL_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000153707' => 'protein tyrosine phosphatase, receptor type, D',
'ENSMUSG00000028399' => 'protein tyrosine phosphatase, receptor type, D',
'ENSMUSG00000081844' => 'predicted gene 11241',
'ENSMUSG00000084253' => 'predicted gene 11256'
),
'gene_name_arr' => array(
'ENSG00000153707' => 'PTPRD',
'ENSMUSG00000028399' => 'Ptprd',
'ENSMUSG00000081844' => 'Gm11241',
'ENSMUSG00000084253' => 'Gm11256'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 19 => 'Breast',
(int) 24 => 'Colon',
(int) 26 => 'Heart',
(int) 31 => 'Kidney',
(int) 35 => 'Liver',
(int) 41 => 'Lung',
(int) 45 => 'Muscle',
(int) 50 => 'Ovary',
(int) 58 => 'Placenta',
(int) 63 => '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) 37,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000355233' => array(
'start' => '8314247',
'end' => '8733946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-201'
),
'ENST00000356435' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-202'
),
'ENST00000381196' => array(
'start' => '8314246',
'end' => '10033790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-002'
),
'ENST00000397606' => array(
'start' => '8317405',
'end' => '8733894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-006'
),
'ENST00000397611' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-203'
),
'ENST00000397617' => array(
'start' => '8314247',
'end' => '8733946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-204'
),
'ENST00000463477' => array(
'start' => '8528152',
'end' => '10612723',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-001'
),
'ENST00000471274' => array(
'start' => '8485763',
'end' => '8501059',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTPRD-005'
),
'ENST00000477552' => array(
'start' => '8484238',
'end' => '8485636',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PTPRD-007'
),
'ENST00000481079' => array(
'start' => '8633390',
'end' => '8857776',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-008'
),
'ENST00000486161' => array(
'start' => '8317404',
'end' => '8733894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-003'
),
'ENST00000488774' => array(
'start' => '8524949',
'end' => '8633460',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTPRD-004'
),
'ENST00000537002' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-205'
),
'ENST00000540109' => array(
'start' => '8317277',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-206'
),
'ENSMUST00000050757' => array(
'start' => '75944958',
'end' => '76344243',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-009'
),
'ENSMUST00000084467' => array(
'start' => '76140358',
'end' => '76325288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-010'
),
'ENSMUST00000098005' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-015'
),
'ENSMUST00000102834' => array(
'start' => '75941239',
'end' => '76133882',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-004'
),
'ENSMUST00000107287' => array(
'start' => '76139382',
'end' => '78211895',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-002'
),
'ENSMUST00000107289' => array(
'start' => '75941238',
'end' => '76449980',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-001'
),
'ENSMUST00000129550' => array(
'start' => '77917524',
'end' => '78211852',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-007'
),
'ENSMUST00000134604' => array(
'start' => '77925213',
'end' => '78211843',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-008'
),
'ENSMUST00000138955' => array(
'start' => '76593551',
'end' => '78211739',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-006'
),
'ENSMUST00000140422' => array(
'start' => '77351290',
'end' => '78211961',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-003'
),
'ENSMUST00000156656' => array(
'start' => '76591325',
'end' => '78211867',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-005'
),
'ENSMUST00000172811' => array(
'start' => '76099412',
'end' => '76107395',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ptprd-019'
),
'ENSMUST00000173376' => array(
'start' => '75944806',
'end' => '76594299',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-018'
),
'ENSMUST00000173560' => array(
'start' => '76082247',
'end' => '76101444',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-011'
),
'ENSMUST00000173592' => array(
'start' => '77193100',
'end' => '78211739',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-020'
),
'ENSMUST00000173662' => array(
'start' => '76084371',
'end' => '76086516',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-017'
),
'ENSMUST00000174023' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-016'
),
'ENSMUST00000174180' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-014'
),
'ENSMUST00000174531' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-021'
),
'ENSMUST00000174831' => array(
'start' => '75944958',
'end' => '76325243',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-013'
),
'ENSMUST00000174832' => array(
'start' => '76133158',
'end' => '76134143',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-012'
),
'ENSMUST00000117371' => array(
'start' => '75902260',
'end' => '75903155',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11241-001'
),
'ENSMUST00000118109' => array(
'start' => '75854518',
'end' => '75855346',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11256-001'
)
),
'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_0007LL_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007LL_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000028399' => array(
[maximum depth reached]
),
'ENSMUSG00000081844' => array(
[maximum depth reached]
),
'ENSMUSG00000084253' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Liver',
(int) 2 => 'Testis',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Placenta',
(int) 8 => 'Testis',
(int) 9 => 'Adrenal',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Testis',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Adrenal',
(int) 25 => 'Breast',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Ovary',
(int) 36 => 'Brain',
(int) 37 => 'Ovary',
(int) 38 => 'Testis',
(int) 39 => 'Heart',
(int) 40 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000153707' => 'protein tyrosine phosphatase, receptor type, D',
'ENSMUSG00000028399' => 'protein tyrosine phosphatase, receptor type, D',
'ENSMUSG00000081844' => 'predicted gene 11241',
'ENSMUSG00000084253' => 'predicted gene 11256'
)
$gene_name_arr = array(
'ENSG00000153707' => 'PTPRD',
'ENSMUSG00000028399' => 'Ptprd',
'ENSMUSG00000081844' => 'Gm11241',
'ENSMUSG00000084253' => 'Gm11256'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0001',
'tax_id' => '9606',
'chromosome' => '9',
'seq_start' => '8095704',
'seq_end' => '8526809',
'region_length' => '431105',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0002',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '75700943',
'seq_end' => '76138737',
'region_length' => '437794',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0003',
'tax_id' => '7955',
'chromosome' => '22',
'seq_start' => '3479574',
'seq_end' => '3479770',
'region_length' => '196',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0004',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '76959895',
'seq_end' => '76964764',
'region_length' => '4869',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 19 => 'Breast',
(int) 24 => 'Colon',
(int) 26 => 'Heart',
(int) 31 => 'Kidney',
(int) 35 => 'Liver',
(int) 41 => 'Lung',
(int) 45 => 'Muscle',
(int) 50 => 'Ovary',
(int) 58 => 'Placenta',
(int) 63 => '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) 37
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000355233' => array(
'start' => '8314247',
'end' => '8733946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-201'
),
'ENST00000356435' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-202'
),
'ENST00000381196' => array(
'start' => '8314246',
'end' => '10033790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-002'
),
'ENST00000397606' => array(
'start' => '8317405',
'end' => '8733894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-006'
),
'ENST00000397611' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-203'
),
'ENST00000397617' => array(
'start' => '8314247',
'end' => '8733946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-204'
),
'ENST00000463477' => array(
'start' => '8528152',
'end' => '10612723',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-001'
),
'ENST00000471274' => array(
'start' => '8485763',
'end' => '8501059',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTPRD-005'
),
'ENST00000477552' => array(
'start' => '8484238',
'end' => '8485636',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PTPRD-007'
),
'ENST00000481079' => array(
'start' => '8633390',
'end' => '8857776',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-008'
),
'ENST00000486161' => array(
'start' => '8317404',
'end' => '8733894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-003'
),
'ENST00000488774' => array(
'start' => '8524949',
'end' => '8633460',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTPRD-004'
),
'ENST00000537002' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-205'
),
'ENST00000540109' => array(
'start' => '8317277',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-206'
),
'ENSMUST00000050757' => array(
'start' => '75944958',
'end' => '76344243',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-009'
),
'ENSMUST00000084467' => array(
'start' => '76140358',
'end' => '76325288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-010'
),
'ENSMUST00000098005' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-015'
),
'ENSMUST00000102834' => array(
'start' => '75941239',
'end' => '76133882',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-004'
),
'ENSMUST00000107287' => array(
'start' => '76139382',
'end' => '78211895',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-002'
),
'ENSMUST00000107289' => array(
'start' => '75941238',
'end' => '76449980',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-001'
),
'ENSMUST00000129550' => array(
'start' => '77917524',
'end' => '78211852',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-007'
),
'ENSMUST00000134604' => array(
'start' => '77925213',
'end' => '78211843',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-008'
),
'ENSMUST00000138955' => array(
'start' => '76593551',
'end' => '78211739',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-006'
),
'ENSMUST00000140422' => array(
'start' => '77351290',
'end' => '78211961',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-003'
),
'ENSMUST00000156656' => array(
'start' => '76591325',
'end' => '78211867',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-005'
),
'ENSMUST00000172811' => array(
'start' => '76099412',
'end' => '76107395',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ptprd-019'
),
'ENSMUST00000173376' => array(
'start' => '75944806',
'end' => '76594299',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-018'
),
'ENSMUST00000173560' => array(
'start' => '76082247',
'end' => '76101444',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-011'
),
'ENSMUST00000173592' => array(
'start' => '77193100',
'end' => '78211739',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-020'
),
'ENSMUST00000173662' => array(
'start' => '76084371',
'end' => '76086516',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-017'
),
'ENSMUST00000174023' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-016'
),
'ENSMUST00000174180' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-014'
),
'ENSMUST00000174531' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-021'
),
'ENSMUST00000174831' => array(
'start' => '75944958',
'end' => '76325243',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-013'
),
'ENSMUST00000174832' => array(
'start' => '76133158',
'end' => '76134143',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-012'
),
'ENSMUST00000117371' => array(
'start' => '75902260',
'end' => '75903155',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11241-001'
),
'ENSMUST00000118109' => array(
'start' => '75854518',
'end' => '75855346',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11256-001'
)
)
$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_0007LL_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000028399' => array(
[maximum depth reached]
),
'ENSMUSG00000081844' => array(
[maximum depth reached]
),
'ENSMUSG00000084253' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Liver',
(int) 2 => 'Testis',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Placenta',
(int) 8 => 'Testis',
(int) 9 => 'Adrenal',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Testis',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Adrenal',
(int) 25 => 'Breast',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Ovary',
(int) 36 => 'Brain',
(int) 37 => 'Ovary',
(int) 38 => 'Testis',
(int) 39 => 'Heart',
(int) 40 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0004',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '76959895',
'seq_end' => '76964764',
'region_length' => '4869',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
)
$gene_el = array(
'ENSMUST00000118109' => array(
'Heart' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.154',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000084253'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.154',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000118109'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007LL_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000153707' => 'protein tyrosine phosphatase, receptor type, D',
'ENSMUSG00000028399' => 'protein tyrosine phosphatase, receptor type, D',
'ENSMUSG00000081844' => 'predicted gene 11241',
'ENSMUSG00000084253' => 'predicted gene 11256'
),
'gene_name_arr' => array(
'ENSG00000153707' => 'PTPRD',
'ENSMUSG00000028399' => 'Ptprd',
'ENSMUSG00000081844' => 'Gm11241',
'ENSMUSG00000084253' => 'Gm11256'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 19 => 'Breast',
(int) 24 => 'Colon',
(int) 26 => 'Heart',
(int) 31 => 'Kidney',
(int) 35 => 'Liver',
(int) 41 => 'Lung',
(int) 45 => 'Muscle',
(int) 50 => 'Ovary',
(int) 58 => 'Placenta',
(int) 63 => '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) 37,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000355233' => array(
'start' => '8314247',
'end' => '8733946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-201'
),
'ENST00000356435' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-202'
),
'ENST00000381196' => array(
'start' => '8314246',
'end' => '10033790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-002'
),
'ENST00000397606' => array(
'start' => '8317405',
'end' => '8733894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-006'
),
'ENST00000397611' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-203'
),
'ENST00000397617' => array(
'start' => '8314247',
'end' => '8733946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-204'
),
'ENST00000463477' => array(
'start' => '8528152',
'end' => '10612723',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-001'
),
'ENST00000471274' => array(
'start' => '8485763',
'end' => '8501059',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTPRD-005'
),
'ENST00000477552' => array(
'start' => '8484238',
'end' => '8485636',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PTPRD-007'
),
'ENST00000481079' => array(
'start' => '8633390',
'end' => '8857776',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-008'
),
'ENST00000486161' => array(
'start' => '8317404',
'end' => '8733894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-003'
),
'ENST00000488774' => array(
'start' => '8524949',
'end' => '8633460',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTPRD-004'
),
'ENST00000537002' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-205'
),
'ENST00000540109' => array(
'start' => '8317277',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-206'
),
'ENSMUST00000050757' => array(
'start' => '75944958',
'end' => '76344243',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-009'
),
'ENSMUST00000084467' => array(
'start' => '76140358',
'end' => '76325288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-010'
),
'ENSMUST00000098005' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-015'
),
'ENSMUST00000102834' => array(
'start' => '75941239',
'end' => '76133882',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-004'
),
'ENSMUST00000107287' => array(
'start' => '76139382',
'end' => '78211895',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-002'
),
'ENSMUST00000107289' => array(
'start' => '75941238',
'end' => '76449980',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-001'
),
'ENSMUST00000129550' => array(
'start' => '77917524',
'end' => '78211852',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-007'
),
'ENSMUST00000134604' => array(
'start' => '77925213',
'end' => '78211843',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-008'
),
'ENSMUST00000138955' => array(
'start' => '76593551',
'end' => '78211739',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-006'
),
'ENSMUST00000140422' => array(
'start' => '77351290',
'end' => '78211961',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-003'
),
'ENSMUST00000156656' => array(
'start' => '76591325',
'end' => '78211867',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-005'
),
'ENSMUST00000172811' => array(
'start' => '76099412',
'end' => '76107395',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ptprd-019'
),
'ENSMUST00000173376' => array(
'start' => '75944806',
'end' => '76594299',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-018'
),
'ENSMUST00000173560' => array(
'start' => '76082247',
'end' => '76101444',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-011'
),
'ENSMUST00000173592' => array(
'start' => '77193100',
'end' => '78211739',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-020'
),
'ENSMUST00000173662' => array(
'start' => '76084371',
'end' => '76086516',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-017'
),
'ENSMUST00000174023' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-016'
),
'ENSMUST00000174180' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-014'
),
'ENSMUST00000174531' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-021'
),
'ENSMUST00000174831' => array(
'start' => '75944958',
'end' => '76325243',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-013'
),
'ENSMUST00000174832' => array(
'start' => '76133158',
'end' => '76134143',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-012'
),
'ENSMUST00000117371' => array(
'start' => '75902260',
'end' => '75903155',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11241-001'
),
'ENSMUST00000118109' => array(
'start' => '75854518',
'end' => '75855346',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11256-001'
)
),
'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_0007LL_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007LL_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000028399' => array(
[maximum depth reached]
),
'ENSMUSG00000081844' => array(
[maximum depth reached]
),
'ENSMUSG00000084253' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Liver',
(int) 2 => 'Testis',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Placenta',
(int) 8 => 'Testis',
(int) 9 => 'Adrenal',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Testis',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Adrenal',
(int) 25 => 'Breast',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Ovary',
(int) 36 => 'Brain',
(int) 37 => 'Ovary',
(int) 38 => 'Testis',
(int) 39 => 'Heart',
(int) 40 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000153707' => 'protein tyrosine phosphatase, receptor type, D',
'ENSMUSG00000028399' => 'protein tyrosine phosphatase, receptor type, D',
'ENSMUSG00000081844' => 'predicted gene 11241',
'ENSMUSG00000084253' => 'predicted gene 11256'
)
$gene_name_arr = array(
'ENSG00000153707' => 'PTPRD',
'ENSMUSG00000028399' => 'Ptprd',
'ENSMUSG00000081844' => 'Gm11241',
'ENSMUSG00000084253' => 'Gm11256'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0001',
'tax_id' => '9606',
'chromosome' => '9',
'seq_start' => '8095704',
'seq_end' => '8526809',
'region_length' => '431105',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0002',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '75700943',
'seq_end' => '76138737',
'region_length' => '437794',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0003',
'tax_id' => '7955',
'chromosome' => '22',
'seq_start' => '3479574',
'seq_end' => '3479770',
'region_length' => '196',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0004',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '76959895',
'seq_end' => '76964764',
'region_length' => '4869',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 19 => 'Breast',
(int) 24 => 'Colon',
(int) 26 => 'Heart',
(int) 31 => 'Kidney',
(int) 35 => 'Liver',
(int) 41 => 'Lung',
(int) 45 => 'Muscle',
(int) 50 => 'Ovary',
(int) 58 => 'Placenta',
(int) 63 => '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) 37
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000355233' => array(
'start' => '8314247',
'end' => '8733946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-201'
),
'ENST00000356435' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-202'
),
'ENST00000381196' => array(
'start' => '8314246',
'end' => '10033790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-002'
),
'ENST00000397606' => array(
'start' => '8317405',
'end' => '8733894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-006'
),
'ENST00000397611' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-203'
),
'ENST00000397617' => array(
'start' => '8314247',
'end' => '8733946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-204'
),
'ENST00000463477' => array(
'start' => '8528152',
'end' => '10612723',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-001'
),
'ENST00000471274' => array(
'start' => '8485763',
'end' => '8501059',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTPRD-005'
),
'ENST00000477552' => array(
'start' => '8484238',
'end' => '8485636',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'PTPRD-007'
),
'ENST00000481079' => array(
'start' => '8633390',
'end' => '8857776',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-008'
),
'ENST00000486161' => array(
'start' => '8317404',
'end' => '8733894',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-003'
),
'ENST00000488774' => array(
'start' => '8524949',
'end' => '8633460',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PTPRD-004'
),
'ENST00000537002' => array(
'start' => '8314247',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-205'
),
'ENST00000540109' => array(
'start' => '8317277',
'end' => '8733949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PTPRD-206'
),
'ENSMUST00000050757' => array(
'start' => '75944958',
'end' => '76344243',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-009'
),
'ENSMUST00000084467' => array(
'start' => '76140358',
'end' => '76325288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-010'
),
'ENSMUST00000098005' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-015'
),
'ENSMUST00000102834' => array(
'start' => '75941239',
'end' => '76133882',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-004'
),
'ENSMUST00000107287' => array(
'start' => '76139382',
'end' => '78211895',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-002'
),
'ENSMUST00000107289' => array(
'start' => '75941238',
'end' => '76449980',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-001'
),
'ENSMUST00000129550' => array(
'start' => '77917524',
'end' => '78211852',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-007'
),
'ENSMUST00000134604' => array(
'start' => '77925213',
'end' => '78211843',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-008'
),
'ENSMUST00000138955' => array(
'start' => '76593551',
'end' => '78211739',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-006'
),
'ENSMUST00000140422' => array(
'start' => '77351290',
'end' => '78211961',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-003'
),
'ENSMUST00000156656' => array(
'start' => '76591325',
'end' => '78211867',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ptprd-005'
),
'ENSMUST00000172811' => array(
'start' => '76099412',
'end' => '76107395',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ptprd-019'
),
'ENSMUST00000173376' => array(
'start' => '75944806',
'end' => '76594299',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-018'
),
'ENSMUST00000173560' => array(
'start' => '76082247',
'end' => '76101444',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-011'
),
'ENSMUST00000173592' => array(
'start' => '77193100',
'end' => '78211739',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ptprd-020'
),
'ENSMUST00000173662' => array(
'start' => '76084371',
'end' => '76086516',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-017'
),
'ENSMUST00000174023' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-016'
),
'ENSMUST00000174180' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-014'
),
'ENSMUST00000174531' => array(
'start' => '75944958',
'end' => '76325264',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-021'
),
'ENSMUST00000174831' => array(
'start' => '75944958',
'end' => '76325243',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-013'
),
'ENSMUST00000174832' => array(
'start' => '76133158',
'end' => '76134143',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ptprd-012'
),
'ENSMUST00000117371' => array(
'start' => '75902260',
'end' => '75903155',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11241-001'
),
'ENSMUST00000118109' => array(
'start' => '75854518',
'end' => '75855346',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm11256-001'
)
)
$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_0007LL_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000028399' => array(
[maximum depth reached]
),
'ENSMUSG00000081844' => array(
[maximum depth reached]
),
'ENSMUSG00000084253' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Liver',
(int) 2 => 'Testis',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Placenta',
(int) 8 => 'Testis',
(int) 9 => 'Adrenal',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Testis',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Adrenal',
(int) 25 => 'Breast',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Ovary',
(int) 36 => 'Brain',
(int) 37 => 'Ovary',
(int) 38 => 'Testis',
(int) 39 => 'Heart',
(int) 40 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LL_0004',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '76959895',
'seq_end' => '76964764',
'region_length' => '4869',
'region_type' => 'UCNEbase',
'el_id' => 'PTPRD'
)
)
$gene_el = array(
'ENSMUST00000118109' => array(
'Heart' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.154',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000084253'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.154',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000118109'
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
(Ptprd)