| Source ID |
Type |
Tax ID |
Position |
| hs1384 |
VISTA |
10090 |
18:72424153-73026078  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0008ER_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_0008ER_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000187323' => 'DCC netrin 1 receptor',
'ENSG00000215457' => 'ribosomal protein S8 pseudogene 3',
'ENSG00000266335' => null,
'ENSMUSG00000080635' => 'predicted gene, 25509'
),
'gene_name_arr' => array(
'ENSG00000187323' => 'DCC',
'ENSG00000215457' => 'RPS8P3',
'ENSG00000266335' => 'RP11-25O3.1',
'ENSMUSG00000080635' => 'Gm25509'
),
'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) 2 => 'Adrenal',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 7 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 17 => 'Kidney',
(int) 20 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => '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) 21,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000304775' => array(
'start' => '52752162',
'end' => '53416557',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-002'
),
'ENST00000412726' => array(
'start' => '52752032',
'end' => '53535903',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-201'
),
'ENST00000442544' => array(
'start' => '52340172',
'end' => '53535899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-001'
),
'ENST00000577224' => array(
'start' => '53530297',
'end' => '53530451',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-017'
),
'ENST00000578080' => array(
'start' => '52752060',
'end' => '52759092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-004'
),
'ENST00000578949' => array(
'start' => '52934803',
'end' => '53157435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-012'
),
'ENST00000579349' => array(
'start' => '52752166',
'end' => '52906286',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-009'
),
'ENST00000579666' => array(
'start' => '52752174',
'end' => '52757281',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-005'
),
'ENST00000579702' => array(
'start' => '53499315',
'end' => '53526948',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCC-016'
),
'ENST00000579883' => array(
'start' => '52923799',
'end' => '53063613',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCC-014'
),
'ENST00000579941' => array(
'start' => '53391784',
'end' => '53416441',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-015'
),
'ENST00000580024' => array(
'start' => '52752159',
'end' => '52906267',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-010'
),
'ENST00000580146' => array(
'start' => '52940929',
'end' => '53157406',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-013'
),
'ENST00000581559' => array(
'start' => '52752167',
'end' => '52906256',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-003'
),
'ENST00000581580' => array(
'start' => '52934772',
'end' => '53530592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-011'
),
'ENST00000582595' => array(
'start' => '52752230',
'end' => '52754256',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-006'
),
'ENST00000582875' => array(
'start' => '52752161',
'end' => '52816889',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-007'
),
'ENST00000584710' => array(
'start' => '52923784',
'end' => '52931950',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-008'
),
'ENST00000462935' => array(
'start' => '51845007',
'end' => '51845628',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPS8P3-001'
),
'ENST00000582700' => array(
'start' => '52336361',
'end' => '52339025',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-25O3.1-001'
),
'ENSMUST00000116985' => array(
'start' => '72899882',
'end' => '72899987',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25509-201'
)
),
'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_0008ER_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008ER_0001' => array(
'genes_in_region' => array(
'ENSG00000187323' => array(
[maximum depth reached]
),
'ENSG00000215457' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Testis',
(int) 2 => 'Adrenal',
(int) 3 => 'Breast',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Adipose',
(int) 10 => 'Brain',
(int) 11 => 'Ovary',
(int) 12 => 'Colon',
(int) 13 => 'Lung',
(int) 14 => 'Bladder',
(int) 15 => 'Breast',
(int) 16 => 'Kidney',
(int) 17 => 'Placenta',
(int) 18 => 'Breast',
(int) 19 => 'Heart',
(int) 20 => 'Brain',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Heart',
(int) 30 => 'Kidney',
(int) 31 => 'Ovary',
(int) 32 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000187323' => 'DCC netrin 1 receptor',
'ENSG00000215457' => 'ribosomal protein S8 pseudogene 3',
'ENSG00000266335' => null,
'ENSMUSG00000080635' => 'predicted gene, 25509'
)
$gene_name_arr = array(
'ENSG00000187323' => 'DCC',
'ENSG00000215457' => 'RPS8P3',
'ENSG00000266335' => 'RP11-25O3.1',
'ENSMUSG00000080635' => 'Gm25509'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008ER_0001',
'tax_id' => '9606',
'chromosome' => '18',
'seq_start' => '51746215',
'seq_end' => '52348141',
'region_length' => '601926',
'region_type' => 'VISTA',
'el_id' => 'hs1384'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008ER_0002',
'tax_id' => '10090',
'chromosome' => '18',
'seq_start' => '72424153',
'seq_end' => '73026078',
'region_length' => '601925',
'region_type' => 'VISTA',
'el_id' => 'hs1384'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 7 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 17 => 'Kidney',
(int) 20 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => '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) 21
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000304775' => array(
'start' => '52752162',
'end' => '53416557',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-002'
),
'ENST00000412726' => array(
'start' => '52752032',
'end' => '53535903',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-201'
),
'ENST00000442544' => array(
'start' => '52340172',
'end' => '53535899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-001'
),
'ENST00000577224' => array(
'start' => '53530297',
'end' => '53530451',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-017'
),
'ENST00000578080' => array(
'start' => '52752060',
'end' => '52759092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-004'
),
'ENST00000578949' => array(
'start' => '52934803',
'end' => '53157435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-012'
),
'ENST00000579349' => array(
'start' => '52752166',
'end' => '52906286',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-009'
),
'ENST00000579666' => array(
'start' => '52752174',
'end' => '52757281',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-005'
),
'ENST00000579702' => array(
'start' => '53499315',
'end' => '53526948',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCC-016'
),
'ENST00000579883' => array(
'start' => '52923799',
'end' => '53063613',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCC-014'
),
'ENST00000579941' => array(
'start' => '53391784',
'end' => '53416441',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-015'
),
'ENST00000580024' => array(
'start' => '52752159',
'end' => '52906267',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-010'
),
'ENST00000580146' => array(
'start' => '52940929',
'end' => '53157406',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-013'
),
'ENST00000581559' => array(
'start' => '52752167',
'end' => '52906256',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-003'
),
'ENST00000581580' => array(
'start' => '52934772',
'end' => '53530592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-011'
),
'ENST00000582595' => array(
'start' => '52752230',
'end' => '52754256',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-006'
),
'ENST00000582875' => array(
'start' => '52752161',
'end' => '52816889',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-007'
),
'ENST00000584710' => array(
'start' => '52923784',
'end' => '52931950',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-008'
),
'ENST00000462935' => array(
'start' => '51845007',
'end' => '51845628',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPS8P3-001'
),
'ENST00000582700' => array(
'start' => '52336361',
'end' => '52339025',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-25O3.1-001'
),
'ENSMUST00000116985' => array(
'start' => '72899882',
'end' => '72899987',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25509-201'
)
)
$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_0008ER_0001' => array(
'genes_in_region' => array(
'ENSG00000187323' => array(
[maximum depth reached]
),
'ENSG00000215457' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Testis',
(int) 2 => 'Adrenal',
(int) 3 => 'Breast',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Adipose',
(int) 10 => 'Brain',
(int) 11 => 'Ovary',
(int) 12 => 'Colon',
(int) 13 => 'Lung',
(int) 14 => 'Bladder',
(int) 15 => 'Breast',
(int) 16 => 'Kidney',
(int) 17 => 'Placenta',
(int) 18 => 'Breast',
(int) 19 => 'Heart',
(int) 20 => 'Brain',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Heart',
(int) 30 => 'Kidney',
(int) 31 => 'Ovary',
(int) 32 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008ER_0002',
'tax_id' => '10090',
'chromosome' => '18',
'seq_start' => '72424153',
'seq_end' => '73026078',
'region_length' => '601925',
'region_type' => 'VISTA',
'el_id' => 'hs1384'
)
)
$gene_el = array(
'ENST00000462935' => array(
'Adipose' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.058',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.081',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.029',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.128',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.025',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000215457'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.058',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.081',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.029',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.128',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.025',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000462935'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0008ER_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000187323' => 'DCC netrin 1 receptor',
'ENSG00000215457' => 'ribosomal protein S8 pseudogene 3',
'ENSG00000266335' => null,
'ENSMUSG00000080635' => 'predicted gene, 25509'
),
'gene_name_arr' => array(
'ENSG00000187323' => 'DCC',
'ENSG00000215457' => 'RPS8P3',
'ENSG00000266335' => 'RP11-25O3.1',
'ENSMUSG00000080635' => 'Gm25509'
),
'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) 2 => 'Adrenal',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 7 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 17 => 'Kidney',
(int) 20 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => '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) 21,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000304775' => array(
'start' => '52752162',
'end' => '53416557',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-002'
),
'ENST00000412726' => array(
'start' => '52752032',
'end' => '53535903',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-201'
),
'ENST00000442544' => array(
'start' => '52340172',
'end' => '53535899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-001'
),
'ENST00000577224' => array(
'start' => '53530297',
'end' => '53530451',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-017'
),
'ENST00000578080' => array(
'start' => '52752060',
'end' => '52759092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-004'
),
'ENST00000578949' => array(
'start' => '52934803',
'end' => '53157435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-012'
),
'ENST00000579349' => array(
'start' => '52752166',
'end' => '52906286',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-009'
),
'ENST00000579666' => array(
'start' => '52752174',
'end' => '52757281',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-005'
),
'ENST00000579702' => array(
'start' => '53499315',
'end' => '53526948',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCC-016'
),
'ENST00000579883' => array(
'start' => '52923799',
'end' => '53063613',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCC-014'
),
'ENST00000579941' => array(
'start' => '53391784',
'end' => '53416441',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-015'
),
'ENST00000580024' => array(
'start' => '52752159',
'end' => '52906267',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-010'
),
'ENST00000580146' => array(
'start' => '52940929',
'end' => '53157406',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-013'
),
'ENST00000581559' => array(
'start' => '52752167',
'end' => '52906256',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-003'
),
'ENST00000581580' => array(
'start' => '52934772',
'end' => '53530592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-011'
),
'ENST00000582595' => array(
'start' => '52752230',
'end' => '52754256',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-006'
),
'ENST00000582875' => array(
'start' => '52752161',
'end' => '52816889',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-007'
),
'ENST00000584710' => array(
'start' => '52923784',
'end' => '52931950',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-008'
),
'ENST00000462935' => array(
'start' => '51845007',
'end' => '51845628',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPS8P3-001'
),
'ENST00000582700' => array(
'start' => '52336361',
'end' => '52339025',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-25O3.1-001'
),
'ENSMUST00000116985' => array(
'start' => '72899882',
'end' => '72899987',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25509-201'
)
),
'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_0008ER_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008ER_0001' => array(
'genes_in_region' => array(
'ENSG00000187323' => array(
[maximum depth reached]
),
'ENSG00000215457' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Testis',
(int) 2 => 'Adrenal',
(int) 3 => 'Breast',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Adipose',
(int) 10 => 'Brain',
(int) 11 => 'Ovary',
(int) 12 => 'Colon',
(int) 13 => 'Lung',
(int) 14 => 'Bladder',
(int) 15 => 'Breast',
(int) 16 => 'Kidney',
(int) 17 => 'Placenta',
(int) 18 => 'Breast',
(int) 19 => 'Heart',
(int) 20 => 'Brain',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Heart',
(int) 30 => 'Kidney',
(int) 31 => 'Ovary',
(int) 32 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000187323' => 'DCC netrin 1 receptor',
'ENSG00000215457' => 'ribosomal protein S8 pseudogene 3',
'ENSG00000266335' => null,
'ENSMUSG00000080635' => 'predicted gene, 25509'
)
$gene_name_arr = array(
'ENSG00000187323' => 'DCC',
'ENSG00000215457' => 'RPS8P3',
'ENSG00000266335' => 'RP11-25O3.1',
'ENSMUSG00000080635' => 'Gm25509'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008ER_0001',
'tax_id' => '9606',
'chromosome' => '18',
'seq_start' => '51746215',
'seq_end' => '52348141',
'region_length' => '601926',
'region_type' => 'VISTA',
'el_id' => 'hs1384'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008ER_0002',
'tax_id' => '10090',
'chromosome' => '18',
'seq_start' => '72424153',
'seq_end' => '73026078',
'region_length' => '601925',
'region_type' => 'VISTA',
'el_id' => 'hs1384'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 7 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 17 => 'Kidney',
(int) 20 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => '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) 21
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000304775' => array(
'start' => '52752162',
'end' => '53416557',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-002'
),
'ENST00000412726' => array(
'start' => '52752032',
'end' => '53535903',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-201'
),
'ENST00000442544' => array(
'start' => '52340172',
'end' => '53535899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-001'
),
'ENST00000577224' => array(
'start' => '53530297',
'end' => '53530451',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-017'
),
'ENST00000578080' => array(
'start' => '52752060',
'end' => '52759092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-004'
),
'ENST00000578949' => array(
'start' => '52934803',
'end' => '53157435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-012'
),
'ENST00000579349' => array(
'start' => '52752166',
'end' => '52906286',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-009'
),
'ENST00000579666' => array(
'start' => '52752174',
'end' => '52757281',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-005'
),
'ENST00000579702' => array(
'start' => '53499315',
'end' => '53526948',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCC-016'
),
'ENST00000579883' => array(
'start' => '52923799',
'end' => '53063613',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCC-014'
),
'ENST00000579941' => array(
'start' => '53391784',
'end' => '53416441',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-015'
),
'ENST00000580024' => array(
'start' => '52752159',
'end' => '52906267',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-010'
),
'ENST00000580146' => array(
'start' => '52940929',
'end' => '53157406',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-013'
),
'ENST00000581559' => array(
'start' => '52752167',
'end' => '52906256',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DCC-003'
),
'ENST00000581580' => array(
'start' => '52934772',
'end' => '53530592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-011'
),
'ENST00000582595' => array(
'start' => '52752230',
'end' => '52754256',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-006'
),
'ENST00000582875' => array(
'start' => '52752161',
'end' => '52816889',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCC-007'
),
'ENST00000584710' => array(
'start' => '52923784',
'end' => '52931950',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DCC-008'
),
'ENST00000462935' => array(
'start' => '51845007',
'end' => '51845628',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPS8P3-001'
),
'ENST00000582700' => array(
'start' => '52336361',
'end' => '52339025',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-25O3.1-001'
),
'ENSMUST00000116985' => array(
'start' => '72899882',
'end' => '72899987',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25509-201'
)
)
$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_0008ER_0001' => array(
'genes_in_region' => array(
'ENSG00000187323' => array(
[maximum depth reached]
),
'ENSG00000215457' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Testis',
(int) 2 => 'Adrenal',
(int) 3 => 'Breast',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Adipose',
(int) 10 => 'Brain',
(int) 11 => 'Ovary',
(int) 12 => 'Colon',
(int) 13 => 'Lung',
(int) 14 => 'Bladder',
(int) 15 => 'Breast',
(int) 16 => 'Kidney',
(int) 17 => 'Placenta',
(int) 18 => 'Breast',
(int) 19 => 'Heart',
(int) 20 => 'Brain',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Heart',
(int) 30 => 'Kidney',
(int) 31 => 'Ovary',
(int) 32 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008ER_0002',
'tax_id' => '10090',
'chromosome' => '18',
'seq_start' => '72424153',
'seq_end' => '73026078',
'region_length' => '601925',
'region_type' => 'VISTA',
'el_id' => 'hs1384'
)
)
$gene_el = array(
'ENST00000462935' => array(
'Adipose' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.058',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.081',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.029',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.128',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.025',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000215457'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.058',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.081',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.029',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.128',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.025',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000462935'
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
(DCC)