| Source ID |
Type |
Tax ID |
Position |
| mm639 |
VISTA |
10090 |
3:34802311-35403774  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00084C_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_00084C_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000240478' => null,
'ENSG00000241098' => 'uncharacterized LOC401103',
'ENSG00000242012' => null,
'ENSG00000242512' => 'long intergenic non-protein coding RNA 1206',
'ENSG00000244199' => null,
'ENSG00000244247' => null,
'ENSG00000252257' => 'RNA, 7SK small nuclear pseudogene 265',
'ENSMUSG00000093499' => 'predicted gene, 25442',
'ENSMUSG00000098862' => 'microRNA 6378'
),
'gene_name_arr' => array(
'ENSG00000240478' => 'RP11-416O18.2',
'ENSG00000241098' => 'FLJ46066',
'ENSG00000242012' => 'RP11-338L18.1',
'ENSG00000242512' => 'LINC01206',
'ENSG00000244199' => 'RP11-139K4.4',
'ENSG00000244247' => 'RP11-139K4.2',
'ENSG00000252257' => 'RN7SKP265',
'ENSMUSG00000093499' => 'Gm25442',
'ENSMUSG00000098862' => 'Mir6378'
),
'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) 7 => 'Brain',
(int) 11 => 'Breast',
(int) 13 => 'Colon',
(int) 16 => 'Heart',
(int) 21 => 'Kidney',
(int) 24 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 31 => '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) 24,
'longest_tissue_len' => (int) 7,
'transcript_data' => array(
'ENST00000462382' => array(
'start' => '182121884',
'end' => '182142137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-416O18.2-001'
),
'ENST00000496220' => array(
'start' => '182446970',
'end' => '182486364',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'FLJ46066-001'
),
'ENST00000473893' => array(
'start' => '182365147',
'end' => '182368256',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338L18.1-001'
),
'ENST00000467313' => array(
'start' => '181952374',
'end' => '181973345',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-004'
),
'ENST00000474045' => array(
'start' => '181952386',
'end' => '182003122',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-002'
),
'ENST00000476815' => array(
'start' => '181952404',
'end' => '181971879',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-005'
),
'ENST00000482787' => array(
'start' => '181952343',
'end' => '182010678',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-001'
),
'ENST00000490001' => array(
'start' => '181952373',
'end' => '182000262',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-003'
),
'ENST00000596820' => array(
'start' => '181952370',
'end' => '181972497',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-007'
),
'ENST00000600750' => array(
'start' => '181952349',
'end' => '181972497',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-006'
),
'ENST00000608042' => array(
'start' => '181971211',
'end' => '181973290',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-009'
),
'ENST00000608102' => array(
'start' => '181971214',
'end' => '181972470',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-010'
),
'ENST00000608336' => array(
'start' => '181967323',
'end' => '181972438',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-012'
),
'ENST00000609052' => array(
'start' => '181965983',
'end' => '181972492',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-013'
),
'ENST00000609168' => array(
'start' => '181971229',
'end' => '181973335',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-008'
),
'ENST00000609852' => array(
'start' => '181967858',
'end' => '181972470',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-011'
),
'ENST00000610910' => array(
'start' => '181952390',
'end' => '181963521',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-016'
),
'ENST00000614303' => array(
'start' => '181952378',
'end' => '181953734',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-014'
),
'ENST00000619662' => array(
'start' => '181952385',
'end' => '181957292',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-015'
),
'ENST00000498782' => array(
'start' => '182460417',
'end' => '182461072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-139K4.4-001'
),
'ENST00000489016' => array(
'start' => '182498264',
'end' => '182507124',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-139K4.2-001'
),
'ENST00000516448' => array(
'start' => '181968459',
'end' => '181968681',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SKP265-201'
),
'ENSMUST00000177270' => array(
'start' => '35325614',
'end' => '35325705',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25442-201'
),
'ENSMUST00000183357' => array(
'start' => '34922545',
'end' => '34922651',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir6378-201'
)
),
'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_00084C_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00084C_0001' => array(
'genes_in_region' => array(
'ENSG00000242012' => array(
[maximum depth reached]
),
'ENSG00000242512' => array(
[maximum depth reached]
),
'ENSG00000244199' => array(
[maximum depth reached]
),
'ENSG00000244247' => array(
[maximum depth reached]
),
'ENSG00000252257' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Breast',
(int) 2 => 'Adrenal',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Ovary',
(int) 7 => 'Adipose',
(int) 8 => 'Brain',
(int) 9 => 'Colon',
(int) 10 => 'Heart',
(int) 11 => 'Ovary',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Heart',
(int) 20 => 'Liver',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Heart',
(int) 27 => 'Kidney',
(int) 28 => 'Liver',
(int) 29 => 'Muscle',
(int) 30 => 'Adrenal',
(int) 31 => 'Brain',
(int) 32 => 'Kidney',
(int) 33 => 'Testis',
(int) 34 => 'Testis',
(int) 35 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000240478' => null,
'ENSG00000241098' => 'uncharacterized LOC401103',
'ENSG00000242012' => null,
'ENSG00000242512' => 'long intergenic non-protein coding RNA 1206',
'ENSG00000244199' => null,
'ENSG00000244247' => null,
'ENSG00000252257' => 'RNA, 7SK small nuclear pseudogene 265',
'ENSMUSG00000093499' => 'predicted gene, 25442',
'ENSMUSG00000098862' => 'microRNA 6378'
)
$gene_name_arr = array(
'ENSG00000240478' => 'RP11-416O18.2',
'ENSG00000241098' => 'FLJ46066',
'ENSG00000242012' => 'RP11-338L18.1',
'ENSG00000242512' => 'LINC01206',
'ENSG00000244199' => 'RP11-139K4.4',
'ENSG00000244247' => 'RP11-139K4.2',
'ENSG00000252257' => 'RN7SKP265',
'ENSMUSG00000093499' => 'Gm25442',
'ENSMUSG00000098862' => 'Mir6378'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00084C_0001',
'tax_id' => '9606',
'chromosome' => '3',
'seq_start' => '181957553',
'seq_end' => '182559100',
'region_length' => '601547',
'region_type' => 'VISTA',
'el_id' => 'mm639'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00084C_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '34802311',
'seq_end' => '35403774',
'region_length' => '601463',
'region_type' => 'VISTA',
'el_id' => 'mm639'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 7 => 'Brain',
(int) 11 => 'Breast',
(int) 13 => 'Colon',
(int) 16 => 'Heart',
(int) 21 => 'Kidney',
(int) 24 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 31 => '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) 24
$longest_tissue_len = (int) 7
$transcript_data = array(
'ENST00000462382' => array(
'start' => '182121884',
'end' => '182142137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-416O18.2-001'
),
'ENST00000496220' => array(
'start' => '182446970',
'end' => '182486364',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'FLJ46066-001'
),
'ENST00000473893' => array(
'start' => '182365147',
'end' => '182368256',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338L18.1-001'
),
'ENST00000467313' => array(
'start' => '181952374',
'end' => '181973345',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-004'
),
'ENST00000474045' => array(
'start' => '181952386',
'end' => '182003122',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-002'
),
'ENST00000476815' => array(
'start' => '181952404',
'end' => '181971879',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-005'
),
'ENST00000482787' => array(
'start' => '181952343',
'end' => '182010678',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-001'
),
'ENST00000490001' => array(
'start' => '181952373',
'end' => '182000262',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-003'
),
'ENST00000596820' => array(
'start' => '181952370',
'end' => '181972497',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-007'
),
'ENST00000600750' => array(
'start' => '181952349',
'end' => '181972497',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-006'
),
'ENST00000608042' => array(
'start' => '181971211',
'end' => '181973290',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-009'
),
'ENST00000608102' => array(
'start' => '181971214',
'end' => '181972470',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-010'
),
'ENST00000608336' => array(
'start' => '181967323',
'end' => '181972438',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-012'
),
'ENST00000609052' => array(
'start' => '181965983',
'end' => '181972492',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-013'
),
'ENST00000609168' => array(
'start' => '181971229',
'end' => '181973335',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-008'
),
'ENST00000609852' => array(
'start' => '181967858',
'end' => '181972470',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-011'
),
'ENST00000610910' => array(
'start' => '181952390',
'end' => '181963521',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-016'
),
'ENST00000614303' => array(
'start' => '181952378',
'end' => '181953734',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-014'
),
'ENST00000619662' => array(
'start' => '181952385',
'end' => '181957292',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-015'
),
'ENST00000498782' => array(
'start' => '182460417',
'end' => '182461072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-139K4.4-001'
),
'ENST00000489016' => array(
'start' => '182498264',
'end' => '182507124',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-139K4.2-001'
),
'ENST00000516448' => array(
'start' => '181968459',
'end' => '181968681',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SKP265-201'
),
'ENSMUST00000177270' => array(
'start' => '35325614',
'end' => '35325705',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25442-201'
),
'ENSMUST00000183357' => array(
'start' => '34922545',
'end' => '34922651',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir6378-201'
)
)
$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_00084C_0001' => array(
'genes_in_region' => array(
'ENSG00000242012' => array(
[maximum depth reached]
),
'ENSG00000242512' => array(
[maximum depth reached]
),
'ENSG00000244199' => array(
[maximum depth reached]
),
'ENSG00000244247' => array(
[maximum depth reached]
),
'ENSG00000252257' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Breast',
(int) 2 => 'Adrenal',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Ovary',
(int) 7 => 'Adipose',
(int) 8 => 'Brain',
(int) 9 => 'Colon',
(int) 10 => 'Heart',
(int) 11 => 'Ovary',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Heart',
(int) 20 => 'Liver',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Heart',
(int) 27 => 'Kidney',
(int) 28 => 'Liver',
(int) 29 => 'Muscle',
(int) 30 => 'Adrenal',
(int) 31 => 'Brain',
(int) 32 => 'Kidney',
(int) 33 => 'Testis',
(int) 34 => 'Testis',
(int) 35 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00084C_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '34802311',
'seq_end' => '35403774',
'region_length' => '601463',
'region_type' => 'VISTA',
'el_id' => 'mm639'
)
)
$gene_el = array(
'ENST00000516448' => array(
'Testis' => array(
'average_FPKM' => '1.053',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000252257'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '1.053',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000516448'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00084C_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000240478' => null,
'ENSG00000241098' => 'uncharacterized LOC401103',
'ENSG00000242012' => null,
'ENSG00000242512' => 'long intergenic non-protein coding RNA 1206',
'ENSG00000244199' => null,
'ENSG00000244247' => null,
'ENSG00000252257' => 'RNA, 7SK small nuclear pseudogene 265',
'ENSMUSG00000093499' => 'predicted gene, 25442',
'ENSMUSG00000098862' => 'microRNA 6378'
),
'gene_name_arr' => array(
'ENSG00000240478' => 'RP11-416O18.2',
'ENSG00000241098' => 'FLJ46066',
'ENSG00000242012' => 'RP11-338L18.1',
'ENSG00000242512' => 'LINC01206',
'ENSG00000244199' => 'RP11-139K4.4',
'ENSG00000244247' => 'RP11-139K4.2',
'ENSG00000252257' => 'RN7SKP265',
'ENSMUSG00000093499' => 'Gm25442',
'ENSMUSG00000098862' => 'Mir6378'
),
'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) 7 => 'Brain',
(int) 11 => 'Breast',
(int) 13 => 'Colon',
(int) 16 => 'Heart',
(int) 21 => 'Kidney',
(int) 24 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 31 => '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) 24,
'longest_tissue_len' => (int) 7,
'transcript_data' => array(
'ENST00000462382' => array(
'start' => '182121884',
'end' => '182142137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-416O18.2-001'
),
'ENST00000496220' => array(
'start' => '182446970',
'end' => '182486364',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'FLJ46066-001'
),
'ENST00000473893' => array(
'start' => '182365147',
'end' => '182368256',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338L18.1-001'
),
'ENST00000467313' => array(
'start' => '181952374',
'end' => '181973345',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-004'
),
'ENST00000474045' => array(
'start' => '181952386',
'end' => '182003122',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-002'
),
'ENST00000476815' => array(
'start' => '181952404',
'end' => '181971879',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-005'
),
'ENST00000482787' => array(
'start' => '181952343',
'end' => '182010678',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-001'
),
'ENST00000490001' => array(
'start' => '181952373',
'end' => '182000262',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-003'
),
'ENST00000596820' => array(
'start' => '181952370',
'end' => '181972497',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-007'
),
'ENST00000600750' => array(
'start' => '181952349',
'end' => '181972497',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-006'
),
'ENST00000608042' => array(
'start' => '181971211',
'end' => '181973290',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-009'
),
'ENST00000608102' => array(
'start' => '181971214',
'end' => '181972470',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-010'
),
'ENST00000608336' => array(
'start' => '181967323',
'end' => '181972438',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-012'
),
'ENST00000609052' => array(
'start' => '181965983',
'end' => '181972492',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-013'
),
'ENST00000609168' => array(
'start' => '181971229',
'end' => '181973335',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-008'
),
'ENST00000609852' => array(
'start' => '181967858',
'end' => '181972470',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-011'
),
'ENST00000610910' => array(
'start' => '181952390',
'end' => '181963521',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-016'
),
'ENST00000614303' => array(
'start' => '181952378',
'end' => '181953734',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-014'
),
'ENST00000619662' => array(
'start' => '181952385',
'end' => '181957292',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-015'
),
'ENST00000498782' => array(
'start' => '182460417',
'end' => '182461072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-139K4.4-001'
),
'ENST00000489016' => array(
'start' => '182498264',
'end' => '182507124',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-139K4.2-001'
),
'ENST00000516448' => array(
'start' => '181968459',
'end' => '181968681',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SKP265-201'
),
'ENSMUST00000177270' => array(
'start' => '35325614',
'end' => '35325705',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25442-201'
),
'ENSMUST00000183357' => array(
'start' => '34922545',
'end' => '34922651',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir6378-201'
)
),
'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_00084C_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00084C_0001' => array(
'genes_in_region' => array(
'ENSG00000242012' => array(
[maximum depth reached]
),
'ENSG00000242512' => array(
[maximum depth reached]
),
'ENSG00000244199' => array(
[maximum depth reached]
),
'ENSG00000244247' => array(
[maximum depth reached]
),
'ENSG00000252257' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Breast',
(int) 2 => 'Adrenal',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Ovary',
(int) 7 => 'Adipose',
(int) 8 => 'Brain',
(int) 9 => 'Colon',
(int) 10 => 'Heart',
(int) 11 => 'Ovary',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Heart',
(int) 20 => 'Liver',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Heart',
(int) 27 => 'Kidney',
(int) 28 => 'Liver',
(int) 29 => 'Muscle',
(int) 30 => 'Adrenal',
(int) 31 => 'Brain',
(int) 32 => 'Kidney',
(int) 33 => 'Testis',
(int) 34 => 'Testis',
(int) 35 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000240478' => null,
'ENSG00000241098' => 'uncharacterized LOC401103',
'ENSG00000242012' => null,
'ENSG00000242512' => 'long intergenic non-protein coding RNA 1206',
'ENSG00000244199' => null,
'ENSG00000244247' => null,
'ENSG00000252257' => 'RNA, 7SK small nuclear pseudogene 265',
'ENSMUSG00000093499' => 'predicted gene, 25442',
'ENSMUSG00000098862' => 'microRNA 6378'
)
$gene_name_arr = array(
'ENSG00000240478' => 'RP11-416O18.2',
'ENSG00000241098' => 'FLJ46066',
'ENSG00000242012' => 'RP11-338L18.1',
'ENSG00000242512' => 'LINC01206',
'ENSG00000244199' => 'RP11-139K4.4',
'ENSG00000244247' => 'RP11-139K4.2',
'ENSG00000252257' => 'RN7SKP265',
'ENSMUSG00000093499' => 'Gm25442',
'ENSMUSG00000098862' => 'Mir6378'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00084C_0001',
'tax_id' => '9606',
'chromosome' => '3',
'seq_start' => '181957553',
'seq_end' => '182559100',
'region_length' => '601547',
'region_type' => 'VISTA',
'el_id' => 'mm639'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00084C_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '34802311',
'seq_end' => '35403774',
'region_length' => '601463',
'region_type' => 'VISTA',
'el_id' => 'mm639'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 7 => 'Brain',
(int) 11 => 'Breast',
(int) 13 => 'Colon',
(int) 16 => 'Heart',
(int) 21 => 'Kidney',
(int) 24 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 31 => '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) 24
$longest_tissue_len = (int) 7
$transcript_data = array(
'ENST00000462382' => array(
'start' => '182121884',
'end' => '182142137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-416O18.2-001'
),
'ENST00000496220' => array(
'start' => '182446970',
'end' => '182486364',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'FLJ46066-001'
),
'ENST00000473893' => array(
'start' => '182365147',
'end' => '182368256',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338L18.1-001'
),
'ENST00000467313' => array(
'start' => '181952374',
'end' => '181973345',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-004'
),
'ENST00000474045' => array(
'start' => '181952386',
'end' => '182003122',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-002'
),
'ENST00000476815' => array(
'start' => '181952404',
'end' => '181971879',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-005'
),
'ENST00000482787' => array(
'start' => '181952343',
'end' => '182010678',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-001'
),
'ENST00000490001' => array(
'start' => '181952373',
'end' => '182000262',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-003'
),
'ENST00000596820' => array(
'start' => '181952370',
'end' => '181972497',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-007'
),
'ENST00000600750' => array(
'start' => '181952349',
'end' => '181972497',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-006'
),
'ENST00000608042' => array(
'start' => '181971211',
'end' => '181973290',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-009'
),
'ENST00000608102' => array(
'start' => '181971214',
'end' => '181972470',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-010'
),
'ENST00000608336' => array(
'start' => '181967323',
'end' => '181972438',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-012'
),
'ENST00000609052' => array(
'start' => '181965983',
'end' => '181972492',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-013'
),
'ENST00000609168' => array(
'start' => '181971229',
'end' => '181973335',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-008'
),
'ENST00000609852' => array(
'start' => '181967858',
'end' => '181972470',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-011'
),
'ENST00000610910' => array(
'start' => '181952390',
'end' => '181963521',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-016'
),
'ENST00000614303' => array(
'start' => '181952378',
'end' => '181953734',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-014'
),
'ENST00000619662' => array(
'start' => '181952385',
'end' => '181957292',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01206-015'
),
'ENST00000498782' => array(
'start' => '182460417',
'end' => '182461072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-139K4.4-001'
),
'ENST00000489016' => array(
'start' => '182498264',
'end' => '182507124',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-139K4.2-001'
),
'ENST00000516448' => array(
'start' => '181968459',
'end' => '181968681',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SKP265-201'
),
'ENSMUST00000177270' => array(
'start' => '35325614',
'end' => '35325705',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25442-201'
),
'ENSMUST00000183357' => array(
'start' => '34922545',
'end' => '34922651',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir6378-201'
)
)
$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_00084C_0001' => array(
'genes_in_region' => array(
'ENSG00000242012' => array(
[maximum depth reached]
),
'ENSG00000242512' => array(
[maximum depth reached]
),
'ENSG00000244199' => array(
[maximum depth reached]
),
'ENSG00000244247' => array(
[maximum depth reached]
),
'ENSG00000252257' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Breast',
(int) 2 => 'Adrenal',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Ovary',
(int) 7 => 'Adipose',
(int) 8 => 'Brain',
(int) 9 => 'Colon',
(int) 10 => 'Heart',
(int) 11 => 'Ovary',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Heart',
(int) 20 => 'Liver',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Heart',
(int) 27 => 'Kidney',
(int) 28 => 'Liver',
(int) 29 => 'Muscle',
(int) 30 => 'Adrenal',
(int) 31 => 'Brain',
(int) 32 => 'Kidney',
(int) 33 => 'Testis',
(int) 34 => 'Testis',
(int) 35 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00084C_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '34802311',
'seq_end' => '35403774',
'region_length' => '601463',
'region_type' => 'VISTA',
'el_id' => 'mm639'
)
)
$gene_el = array(
'ENST00000516448' => array(
'Testis' => array(
'average_FPKM' => '1.053',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000252257'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '1.053',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000516448'
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
(RP11-338L18.1)