| Source ID |
Type |
Tax ID |
Position |
| hs941 |
VISTA |
10090 |
16:5363673-5964669  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_000882_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_000882_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000078328' => 'RNA binding protein, fox-1 homolog (C. elegans) 1',
'ENSG00000221257' => null,
'ENSG00000260338' => null,
'ENSG00000260411' => null,
'ENSG00000270440' => null,
'ENSG00000273648' => 'microRNA 8065',
'ENSG00000280000' => null
),
'gene_name_arr' => array(
'ENSG00000078328' => 'RBFOX1',
'ENSG00000221257' => 'AC012175.1',
'ENSG00000260338' => 'RP11-124K4.1',
'ENSG00000260411' => 'RP11-420N3.2',
'ENSG00000270440' => 'RP11-19H6.1',
'ENSG00000273648' => 'MIR8065',
'ENSG00000280000' => 'RP11-509E10.3'
),
'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) 4 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 13 => 'Breast',
(int) 19 => 'Colon',
(int) 23 => 'Heart',
(int) 29 => 'Kidney',
(int) 33 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 41 => 'Ovary',
(int) 44 => 'Placenta',
(int) 49 => '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) 28,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000311745' => array(
'start' => '7332750',
'end' => '7712504',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-001'
),
'ENST00000340209' => array(
'start' => '7332750',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-201'
),
'ENST00000355637' => array(
'start' => '7332750',
'end' => '7712504',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-002'
),
'ENST00000422070' => array(
'start' => '6019703',
'end' => '7709781',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-009'
),
'ENST00000436368' => array(
'start' => '7332750',
'end' => '7710844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-011'
),
'ENST00000535565' => array(
'start' => '6483179',
'end' => '7709776',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-005'
),
'ENST00000547338' => array(
'start' => '6773809',
'end' => '7710844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-008'
),
'ENST00000547372' => array(
'start' => '6019593',
'end' => '7711458',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-010'
),
'ENST00000547427' => array(
'start' => '6483324',
'end' => '7328793',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-012'
),
'ENST00000547605' => array(
'start' => '6019094',
'end' => '7653846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-014'
),
'ENST00000548749' => array(
'start' => '6019703',
'end' => '6723887',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-013'
),
'ENST00000550418' => array(
'start' => '6019131',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-003'
),
'ENST00000551752' => array(
'start' => '6483793',
'end' => '7653846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-007'
),
'ENST00000552089' => array(
'start' => '6483386',
'end' => '7710763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-006'
),
'ENST00000553186' => array(
'start' => '6019131',
'end' => '7710840',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-004'
),
'ENST00000564850' => array(
'start' => '7597217',
'end' => '7630626',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RBFOX1-015'
),
'ENST00000567470' => array(
'start' => '7653866',
'end' => '7710819',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-018'
),
'ENST00000569889' => array(
'start' => '7422778',
'end' => '7579785',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-017'
),
'ENST00000570188' => array(
'start' => '7664764',
'end' => '7710844',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RBFOX1-016'
),
'ENST00000570626' => array(
'start' => '7510122',
'end' => '7595641',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-019'
),
'ENST00000620507' => array(
'start' => '7332750',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-202'
),
'ENST00000408330' => array(
'start' => '5760687',
'end' => '5760788',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC012175.1-201'
),
'ENST00000561572' => array(
'start' => '5610300',
'end' => '5611293',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-124K4.1-002'
),
'ENST00000566218' => array(
'start' => '5601169',
'end' => '5616196',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-124K4.1-001'
),
'ENST00000585867' => array(
'start' => '5239815',
'end' => '5600151',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-420N3.2-002'
),
'ENST00000603755' => array(
'start' => '5838131',
'end' => '5838661',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-19H6.1-001'
),
'ENST00000620577' => array(
'start' => '5632467',
'end' => '5632566',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR8065-201'
),
'ENST00000624136' => array(
'start' => '6037210',
'end' => '6038977',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-509E10.3-001'
)
),
'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_000882_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000882_0001' => array(
'genes_in_region' => array(
'ENSG00000078328' => array(
[maximum depth reached]
),
'ENSG00000260411' => array(
[maximum depth reached]
),
'ENSG00000280000' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Muscle',
(int) 12 => 'Placenta',
(int) 13 => 'Breast',
(int) 14 => 'Heart',
(int) 15 => 'Muscle',
(int) 16 => 'Testis',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Muscle',
(int) 20 => 'Adipose',
(int) 21 => 'Placenta',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Placenta',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Kidney',
(int) 30 => 'Placenta',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Heart',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Ovary',
(int) 42 => 'Testis',
(int) 43 => 'Adipose',
(int) 44 => 'Adrenal',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000078328' => 'RNA binding protein, fox-1 homolog (C. elegans) 1',
'ENSG00000221257' => null,
'ENSG00000260338' => null,
'ENSG00000260411' => null,
'ENSG00000270440' => null,
'ENSG00000273648' => 'microRNA 8065',
'ENSG00000280000' => null
)
$gene_name_arr = array(
'ENSG00000078328' => 'RBFOX1',
'ENSG00000221257' => 'AC012175.1',
'ENSG00000260338' => 'RP11-124K4.1',
'ENSG00000260411' => 'RP11-420N3.2',
'ENSG00000270440' => 'RP11-19H6.1',
'ENSG00000273648' => 'MIR8065',
'ENSG00000280000' => 'RP11-509E10.3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000882_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '5441186',
'seq_end' => '6042172',
'region_length' => '600986',
'region_type' => 'VISTA',
'el_id' => 'hs941'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000882_0002',
'tax_id' => '10090',
'chromosome' => '16',
'seq_start' => '5363673',
'seq_end' => '5964669',
'region_length' => '600996',
'region_type' => 'VISTA',
'el_id' => 'hs941'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 13 => 'Breast',
(int) 19 => 'Colon',
(int) 23 => 'Heart',
(int) 29 => 'Kidney',
(int) 33 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 41 => 'Ovary',
(int) 44 => 'Placenta',
(int) 49 => '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) 28
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000311745' => array(
'start' => '7332750',
'end' => '7712504',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-001'
),
'ENST00000340209' => array(
'start' => '7332750',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-201'
),
'ENST00000355637' => array(
'start' => '7332750',
'end' => '7712504',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-002'
),
'ENST00000422070' => array(
'start' => '6019703',
'end' => '7709781',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-009'
),
'ENST00000436368' => array(
'start' => '7332750',
'end' => '7710844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-011'
),
'ENST00000535565' => array(
'start' => '6483179',
'end' => '7709776',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-005'
),
'ENST00000547338' => array(
'start' => '6773809',
'end' => '7710844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-008'
),
'ENST00000547372' => array(
'start' => '6019593',
'end' => '7711458',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-010'
),
'ENST00000547427' => array(
'start' => '6483324',
'end' => '7328793',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-012'
),
'ENST00000547605' => array(
'start' => '6019094',
'end' => '7653846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-014'
),
'ENST00000548749' => array(
'start' => '6019703',
'end' => '6723887',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-013'
),
'ENST00000550418' => array(
'start' => '6019131',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-003'
),
'ENST00000551752' => array(
'start' => '6483793',
'end' => '7653846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-007'
),
'ENST00000552089' => array(
'start' => '6483386',
'end' => '7710763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-006'
),
'ENST00000553186' => array(
'start' => '6019131',
'end' => '7710840',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-004'
),
'ENST00000564850' => array(
'start' => '7597217',
'end' => '7630626',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RBFOX1-015'
),
'ENST00000567470' => array(
'start' => '7653866',
'end' => '7710819',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-018'
),
'ENST00000569889' => array(
'start' => '7422778',
'end' => '7579785',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-017'
),
'ENST00000570188' => array(
'start' => '7664764',
'end' => '7710844',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RBFOX1-016'
),
'ENST00000570626' => array(
'start' => '7510122',
'end' => '7595641',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-019'
),
'ENST00000620507' => array(
'start' => '7332750',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-202'
),
'ENST00000408330' => array(
'start' => '5760687',
'end' => '5760788',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC012175.1-201'
),
'ENST00000561572' => array(
'start' => '5610300',
'end' => '5611293',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-124K4.1-002'
),
'ENST00000566218' => array(
'start' => '5601169',
'end' => '5616196',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-124K4.1-001'
),
'ENST00000585867' => array(
'start' => '5239815',
'end' => '5600151',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-420N3.2-002'
),
'ENST00000603755' => array(
'start' => '5838131',
'end' => '5838661',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-19H6.1-001'
),
'ENST00000620577' => array(
'start' => '5632467',
'end' => '5632566',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR8065-201'
),
'ENST00000624136' => array(
'start' => '6037210',
'end' => '6038977',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-509E10.3-001'
)
)
$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_000882_0001' => array(
'genes_in_region' => array(
'ENSG00000078328' => array(
[maximum depth reached]
),
'ENSG00000260411' => array(
[maximum depth reached]
),
'ENSG00000280000' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Muscle',
(int) 12 => 'Placenta',
(int) 13 => 'Breast',
(int) 14 => 'Heart',
(int) 15 => 'Muscle',
(int) 16 => 'Testis',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Muscle',
(int) 20 => 'Adipose',
(int) 21 => 'Placenta',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Placenta',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Kidney',
(int) 30 => 'Placenta',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Heart',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Ovary',
(int) 42 => 'Testis',
(int) 43 => 'Adipose',
(int) 44 => 'Adrenal',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000882_0002',
'tax_id' => '10090',
'chromosome' => '16',
'seq_start' => '5363673',
'seq_end' => '5964669',
'region_length' => '600996',
'region_type' => 'VISTA',
'el_id' => 'hs941'
)
)
$gene_el = array(
'ENST00000624136' => array(
'Adipose' => array(
'average_FPKM' => '0.172',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.171',
'stddev_FPKM' => '0.11'
),
'Breast' => array(
'average_FPKM' => '0.080',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.223',
'stddev_FPKM' => '0.15'
),
'Heart' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.126',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.087',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.005',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.089',
'stddev_FPKM' => '0.04'
)
)
)
$gene_key = 'ENSG00000280000'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.172',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.171',
'stddev_FPKM' => '0.11'
),
'Breast' => array(
'average_FPKM' => '0.080',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.223',
'stddev_FPKM' => '0.15'
),
'Heart' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.126',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.087',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.005',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.089',
'stddev_FPKM' => '0.04'
)
)
$tran_key = 'ENST00000624136'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_000882_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000078328' => 'RNA binding protein, fox-1 homolog (C. elegans) 1',
'ENSG00000221257' => null,
'ENSG00000260338' => null,
'ENSG00000260411' => null,
'ENSG00000270440' => null,
'ENSG00000273648' => 'microRNA 8065',
'ENSG00000280000' => null
),
'gene_name_arr' => array(
'ENSG00000078328' => 'RBFOX1',
'ENSG00000221257' => 'AC012175.1',
'ENSG00000260338' => 'RP11-124K4.1',
'ENSG00000260411' => 'RP11-420N3.2',
'ENSG00000270440' => 'RP11-19H6.1',
'ENSG00000273648' => 'MIR8065',
'ENSG00000280000' => 'RP11-509E10.3'
),
'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) 4 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 13 => 'Breast',
(int) 19 => 'Colon',
(int) 23 => 'Heart',
(int) 29 => 'Kidney',
(int) 33 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 41 => 'Ovary',
(int) 44 => 'Placenta',
(int) 49 => '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) 28,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000311745' => array(
'start' => '7332750',
'end' => '7712504',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-001'
),
'ENST00000340209' => array(
'start' => '7332750',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-201'
),
'ENST00000355637' => array(
'start' => '7332750',
'end' => '7712504',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-002'
),
'ENST00000422070' => array(
'start' => '6019703',
'end' => '7709781',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-009'
),
'ENST00000436368' => array(
'start' => '7332750',
'end' => '7710844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-011'
),
'ENST00000535565' => array(
'start' => '6483179',
'end' => '7709776',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-005'
),
'ENST00000547338' => array(
'start' => '6773809',
'end' => '7710844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-008'
),
'ENST00000547372' => array(
'start' => '6019593',
'end' => '7711458',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-010'
),
'ENST00000547427' => array(
'start' => '6483324',
'end' => '7328793',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-012'
),
'ENST00000547605' => array(
'start' => '6019094',
'end' => '7653846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-014'
),
'ENST00000548749' => array(
'start' => '6019703',
'end' => '6723887',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-013'
),
'ENST00000550418' => array(
'start' => '6019131',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-003'
),
'ENST00000551752' => array(
'start' => '6483793',
'end' => '7653846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-007'
),
'ENST00000552089' => array(
'start' => '6483386',
'end' => '7710763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-006'
),
'ENST00000553186' => array(
'start' => '6019131',
'end' => '7710840',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-004'
),
'ENST00000564850' => array(
'start' => '7597217',
'end' => '7630626',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RBFOX1-015'
),
'ENST00000567470' => array(
'start' => '7653866',
'end' => '7710819',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-018'
),
'ENST00000569889' => array(
'start' => '7422778',
'end' => '7579785',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-017'
),
'ENST00000570188' => array(
'start' => '7664764',
'end' => '7710844',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RBFOX1-016'
),
'ENST00000570626' => array(
'start' => '7510122',
'end' => '7595641',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-019'
),
'ENST00000620507' => array(
'start' => '7332750',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-202'
),
'ENST00000408330' => array(
'start' => '5760687',
'end' => '5760788',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC012175.1-201'
),
'ENST00000561572' => array(
'start' => '5610300',
'end' => '5611293',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-124K4.1-002'
),
'ENST00000566218' => array(
'start' => '5601169',
'end' => '5616196',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-124K4.1-001'
),
'ENST00000585867' => array(
'start' => '5239815',
'end' => '5600151',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-420N3.2-002'
),
'ENST00000603755' => array(
'start' => '5838131',
'end' => '5838661',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-19H6.1-001'
),
'ENST00000620577' => array(
'start' => '5632467',
'end' => '5632566',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR8065-201'
),
'ENST00000624136' => array(
'start' => '6037210',
'end' => '6038977',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-509E10.3-001'
)
),
'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_000882_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000882_0001' => array(
'genes_in_region' => array(
'ENSG00000078328' => array(
[maximum depth reached]
),
'ENSG00000260411' => array(
[maximum depth reached]
),
'ENSG00000280000' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Muscle',
(int) 12 => 'Placenta',
(int) 13 => 'Breast',
(int) 14 => 'Heart',
(int) 15 => 'Muscle',
(int) 16 => 'Testis',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Muscle',
(int) 20 => 'Adipose',
(int) 21 => 'Placenta',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Placenta',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Kidney',
(int) 30 => 'Placenta',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Heart',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Ovary',
(int) 42 => 'Testis',
(int) 43 => 'Adipose',
(int) 44 => 'Adrenal',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000078328' => 'RNA binding protein, fox-1 homolog (C. elegans) 1',
'ENSG00000221257' => null,
'ENSG00000260338' => null,
'ENSG00000260411' => null,
'ENSG00000270440' => null,
'ENSG00000273648' => 'microRNA 8065',
'ENSG00000280000' => null
)
$gene_name_arr = array(
'ENSG00000078328' => 'RBFOX1',
'ENSG00000221257' => 'AC012175.1',
'ENSG00000260338' => 'RP11-124K4.1',
'ENSG00000260411' => 'RP11-420N3.2',
'ENSG00000270440' => 'RP11-19H6.1',
'ENSG00000273648' => 'MIR8065',
'ENSG00000280000' => 'RP11-509E10.3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000882_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '5441186',
'seq_end' => '6042172',
'region_length' => '600986',
'region_type' => 'VISTA',
'el_id' => 'hs941'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000882_0002',
'tax_id' => '10090',
'chromosome' => '16',
'seq_start' => '5363673',
'seq_end' => '5964669',
'region_length' => '600996',
'region_type' => 'VISTA',
'el_id' => 'hs941'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 13 => 'Breast',
(int) 19 => 'Colon',
(int) 23 => 'Heart',
(int) 29 => 'Kidney',
(int) 33 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 41 => 'Ovary',
(int) 44 => 'Placenta',
(int) 49 => '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) 28
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000311745' => array(
'start' => '7332750',
'end' => '7712504',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-001'
),
'ENST00000340209' => array(
'start' => '7332750',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-201'
),
'ENST00000355637' => array(
'start' => '7332750',
'end' => '7712504',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-002'
),
'ENST00000422070' => array(
'start' => '6019703',
'end' => '7709781',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-009'
),
'ENST00000436368' => array(
'start' => '7332750',
'end' => '7710844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-011'
),
'ENST00000535565' => array(
'start' => '6483179',
'end' => '7709776',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-005'
),
'ENST00000547338' => array(
'start' => '6773809',
'end' => '7710844',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-008'
),
'ENST00000547372' => array(
'start' => '6019593',
'end' => '7711458',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-010'
),
'ENST00000547427' => array(
'start' => '6483324',
'end' => '7328793',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-012'
),
'ENST00000547605' => array(
'start' => '6019094',
'end' => '7653846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-014'
),
'ENST00000548749' => array(
'start' => '6019703',
'end' => '6723887',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-013'
),
'ENST00000550418' => array(
'start' => '6019131',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-003'
),
'ENST00000551752' => array(
'start' => '6483793',
'end' => '7653846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-007'
),
'ENST00000552089' => array(
'start' => '6483386',
'end' => '7710763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-006'
),
'ENST00000553186' => array(
'start' => '6019131',
'end' => '7710840',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-004'
),
'ENST00000564850' => array(
'start' => '7597217',
'end' => '7630626',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RBFOX1-015'
),
'ENST00000567470' => array(
'start' => '7653866',
'end' => '7710819',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-018'
),
'ENST00000569889' => array(
'start' => '7422778',
'end' => '7579785',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RBFOX1-017'
),
'ENST00000570188' => array(
'start' => '7664764',
'end' => '7710844',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RBFOX1-016'
),
'ENST00000570626' => array(
'start' => '7510122',
'end' => '7595641',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-019'
),
'ENST00000620507' => array(
'start' => '7332750',
'end' => '7713338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RBFOX1-202'
),
'ENST00000408330' => array(
'start' => '5760687',
'end' => '5760788',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC012175.1-201'
),
'ENST00000561572' => array(
'start' => '5610300',
'end' => '5611293',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-124K4.1-002'
),
'ENST00000566218' => array(
'start' => '5601169',
'end' => '5616196',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-124K4.1-001'
),
'ENST00000585867' => array(
'start' => '5239815',
'end' => '5600151',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-420N3.2-002'
),
'ENST00000603755' => array(
'start' => '5838131',
'end' => '5838661',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-19H6.1-001'
),
'ENST00000620577' => array(
'start' => '5632467',
'end' => '5632566',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR8065-201'
),
'ENST00000624136' => array(
'start' => '6037210',
'end' => '6038977',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-509E10.3-001'
)
)
$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_000882_0001' => array(
'genes_in_region' => array(
'ENSG00000078328' => array(
[maximum depth reached]
),
'ENSG00000260411' => array(
[maximum depth reached]
),
'ENSG00000280000' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Muscle',
(int) 12 => 'Placenta',
(int) 13 => 'Breast',
(int) 14 => 'Heart',
(int) 15 => 'Muscle',
(int) 16 => 'Testis',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Muscle',
(int) 20 => 'Adipose',
(int) 21 => 'Placenta',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Placenta',
(int) 27 => 'Breast',
(int) 28 => 'Colon',
(int) 29 => 'Kidney',
(int) 30 => 'Placenta',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Heart',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Ovary',
(int) 42 => 'Testis',
(int) 43 => 'Adipose',
(int) 44 => 'Adrenal',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000882_0002',
'tax_id' => '10090',
'chromosome' => '16',
'seq_start' => '5363673',
'seq_end' => '5964669',
'region_length' => '600996',
'region_type' => 'VISTA',
'el_id' => 'hs941'
)
)
$gene_el = array(
'ENST00000624136' => array(
'Adipose' => array(
'average_FPKM' => '0.172',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.171',
'stddev_FPKM' => '0.11'
),
'Breast' => array(
'average_FPKM' => '0.080',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.223',
'stddev_FPKM' => '0.15'
),
'Heart' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.126',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.087',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.005',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.089',
'stddev_FPKM' => '0.04'
)
)
)
$gene_key = 'ENSG00000280000'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.172',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.171',
'stddev_FPKM' => '0.11'
),
'Breast' => array(
'average_FPKM' => '0.080',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.223',
'stddev_FPKM' => '0.15'
),
'Heart' => array(
'average_FPKM' => '0.048',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.126',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.087',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.005',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.089',
'stddev_FPKM' => '0.04'
)
)
$tran_key = 'ENST00000624136'
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
(RBFOX1)