| Source ID |
Type |
Tax ID |
Position |
| POU3F1 |
UCNEbase |
7955 |
16:35549147-35843982  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007K7_0003 [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_0007K7_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007K7_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000200796' => 'RNA, U6 small nuclear 753, pseudogene',
'ENSG00000224592' => null,
'ENSG00000237290' => 'long intergenic non-protein coding RNA 1343',
'ENSG00000238063' => null,
'ENSG00000275350' => null,
'ENSMUSG00000051219' => 'RIKEN cDNA 3100002H09 gene',
'ENSMUSG00000073759' => 'RIKEN cDNA 4933407E24 gene',
'ENSMUSG00000084757' => 'RIKEN cDNA 1700057H15 gene',
'ENSMUSG00000086087' => 'predicted gene 12916',
'ENSMUSG00000086955' => 'RIKEN cDNA 1700021L23 gene',
'ENSMUSG00000086978' => 'RIKEN cDNA 4933435F18 gene',
'ENSMUSG00000088933' => 'predicted gene, 22983',
'ENSMUSG00000098760' => 'predicted gene 27247',
'ENSDARG00000089830' => '5S ribosomal RNA',
'ENSDARG00000092939' => 'si:dkey-258e8.1'
),
'gene_name_arr' => array(
'ENSG00000200796' => 'RNU6-753P',
'ENSG00000224592' => 'RP5-884C9.2',
'ENSG00000237290' => 'LINC01343',
'ENSG00000238063' => 'RP11-329N22.1',
'ENSG00000275350' => 'RP11-329N22.2',
'ENSMUSG00000051219' => '3100002H09Rik',
'ENSMUSG00000073759' => '4933407E24Rik',
'ENSMUSG00000084757' => '1700057H15Rik',
'ENSMUSG00000086087' => 'Gm12916',
'ENSMUSG00000086955' => '1700021L23Rik',
'ENSMUSG00000086978' => '4933435F18Rik',
'ENSMUSG00000088933' => 'Gm22983',
'ENSMUSG00000098760' => 'Gm27247',
'ENSDARG00000089830' => '5S_rRNA',
'ENSDARG00000092939' => 'si:dkey-258e8.1'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 14 => 'Breast',
(int) 16 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 21 => 'Liver',
(int) 24 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 30 => 'Placenta',
(int) 33 => '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) 20,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000363926' => array(
'start' => '38396659',
'end' => '38396765',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-753P-201'
),
'ENST00000428151' => array(
'start' => '38047425',
'end' => '38119025',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-884C9.2-001'
),
'ENST00000432922' => array(
'start' => '38047314',
'end' => '38105734',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-884C9.2-002'
),
'ENST00000431311' => array(
'start' => '38209034',
'end' => '38214767',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01343-001'
),
'ENST00000452971' => array(
'start' => '38475196',
'end' => '38476484',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-329N22.1-001'
),
'ENST00000611376' => array(
'start' => '38383838',
'end' => '38384422',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-329N22.2-001'
),
'ENSMUST00000053604' => array(
'start' => '124609931',
'end' => '124610803',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '3100002H09Rik-201'
),
'ENSMUST00000133499' => array(
'start' => '124569190',
'end' => '124574645',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933407E24Rik-001'
),
'ENSMUST00000127913' => array(
'start' => '124414416',
'end' => '124451295',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-003'
),
'ENSMUST00000143859' => array(
'start' => '124449902',
'end' => '124485959',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-002'
),
'ENSMUST00000148832' => array(
'start' => '124414416',
'end' => '124418858',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-004'
),
'ENSMUST00000156566' => array(
'start' => '124450235',
'end' => '124451285',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-001'
),
'ENSMUST00000139012' => array(
'start' => '124293693',
'end' => '124299848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12916-001'
),
'ENSMUST00000153719' => array(
'start' => '124302837',
'end' => '124311461',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700021L23Rik-001'
),
'ENSMUST00000125578' => array(
'start' => '124331406',
'end' => '124332467',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933435F18Rik-002'
),
'ENSMUST00000154878' => array(
'start' => '124326308',
'end' => '124332508',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933435F18Rik-001'
),
'ENSMUST00000158308' => array(
'start' => '124335578',
'end' => '124335681',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm22983-201'
),
'ENSMUST00000184062' => array(
'start' => '124528924',
'end' => '124657169',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27247-001'
),
'ENSDART00000125290' => array(
'start' => '35656812',
'end' => '35656926',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1804-201'
),
'ENSDART00000144119' => array(
'start' => '35829427',
'end' => '35855619',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:dkey-258e8.1-001'
)
),
'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_0007K7_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007K7_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007K7_0001' => array(
'genes_in_region' => array(
'ENSG00000224592' => array(
[maximum depth reached]
),
'ENSG00000237290' => array(
[maximum depth reached]
),
'ENSG00000238063' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Breast',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => 'Placenta',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis',
(int) 17 => 'Adrenal',
(int) 18 => 'Lung',
(int) 19 => 'Testis'
)
),
'CIL_0007K7_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000051219' => array(
[maximum depth reached]
),
'ENSMUSG00000073759' => array(
[maximum depth reached]
),
'ENSMUSG00000086087' => array(
[maximum depth reached]
),
'ENSMUSG00000086955' => array(
[maximum depth reached]
),
'ENSMUSG00000086978' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Liver',
(int) 2 => 'Placenta',
(int) 3 => 'Testis',
(int) 4 => 'Adipose',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Muscle',
(int) 13 => 'Ovary',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis',
(int) 17 => 'Testis',
(int) 18 => 'Brain',
(int) 19 => 'Testis',
(int) 20 => 'Adipose',
(int) 21 => 'Brain',
(int) 22 => 'Testis',
(int) 23 => 'Testis',
(int) 24 => 'Testis',
(int) 25 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000200796' => 'RNA, U6 small nuclear 753, pseudogene',
'ENSG00000224592' => null,
'ENSG00000237290' => 'long intergenic non-protein coding RNA 1343',
'ENSG00000238063' => null,
'ENSG00000275350' => null,
'ENSMUSG00000051219' => 'RIKEN cDNA 3100002H09 gene',
'ENSMUSG00000073759' => 'RIKEN cDNA 4933407E24 gene',
'ENSMUSG00000084757' => 'RIKEN cDNA 1700057H15 gene',
'ENSMUSG00000086087' => 'predicted gene 12916',
'ENSMUSG00000086955' => 'RIKEN cDNA 1700021L23 gene',
'ENSMUSG00000086978' => 'RIKEN cDNA 4933435F18 gene',
'ENSMUSG00000088933' => 'predicted gene, 22983',
'ENSMUSG00000098760' => 'predicted gene 27247',
'ENSDARG00000089830' => '5S ribosomal RNA',
'ENSDARG00000092939' => 'si:dkey-258e8.1'
)
$gene_name_arr = array(
'ENSG00000200796' => 'RNU6-753P',
'ENSG00000224592' => 'RP5-884C9.2',
'ENSG00000237290' => 'LINC01343',
'ENSG00000238063' => 'RP11-329N22.1',
'ENSG00000275350' => 'RP11-329N22.2',
'ENSMUSG00000051219' => '3100002H09Rik',
'ENSMUSG00000073759' => '4933407E24Rik',
'ENSMUSG00000084757' => '1700057H15Rik',
'ENSMUSG00000086087' => 'Gm12916',
'ENSMUSG00000086955' => '1700021L23Rik',
'ENSMUSG00000086978' => '4933435F18Rik',
'ENSMUSG00000088933' => 'Gm22983',
'ENSMUSG00000098760' => 'Gm27247',
'ENSDARG00000089830' => '5S_rRNA',
'ENSDARG00000092939' => 'si:dkey-258e8.1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007K7_0001',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '38095401',
'seq_end' => '38686502',
'region_length' => '591101',
'region_type' => 'UCNEbase',
'el_id' => 'POU3F1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007K7_0002',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '124086916',
'seq_end' => '124615945',
'region_length' => '529029',
'region_type' => 'UCNEbase',
'el_id' => 'POU3F1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007K7_0003',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '35549147',
'seq_end' => '35843982',
'region_length' => '294835',
'region_type' => 'UCNEbase',
'el_id' => 'POU3F1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 14 => 'Breast',
(int) 16 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 21 => 'Liver',
(int) 24 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 30 => 'Placenta',
(int) 33 => '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) 20
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000363926' => array(
'start' => '38396659',
'end' => '38396765',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-753P-201'
),
'ENST00000428151' => array(
'start' => '38047425',
'end' => '38119025',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-884C9.2-001'
),
'ENST00000432922' => array(
'start' => '38047314',
'end' => '38105734',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-884C9.2-002'
),
'ENST00000431311' => array(
'start' => '38209034',
'end' => '38214767',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01343-001'
),
'ENST00000452971' => array(
'start' => '38475196',
'end' => '38476484',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-329N22.1-001'
),
'ENST00000611376' => array(
'start' => '38383838',
'end' => '38384422',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-329N22.2-001'
),
'ENSMUST00000053604' => array(
'start' => '124609931',
'end' => '124610803',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '3100002H09Rik-201'
),
'ENSMUST00000133499' => array(
'start' => '124569190',
'end' => '124574645',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933407E24Rik-001'
),
'ENSMUST00000127913' => array(
'start' => '124414416',
'end' => '124451295',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-003'
),
'ENSMUST00000143859' => array(
'start' => '124449902',
'end' => '124485959',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-002'
),
'ENSMUST00000148832' => array(
'start' => '124414416',
'end' => '124418858',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-004'
),
'ENSMUST00000156566' => array(
'start' => '124450235',
'end' => '124451285',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-001'
),
'ENSMUST00000139012' => array(
'start' => '124293693',
'end' => '124299848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12916-001'
),
'ENSMUST00000153719' => array(
'start' => '124302837',
'end' => '124311461',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700021L23Rik-001'
),
'ENSMUST00000125578' => array(
'start' => '124331406',
'end' => '124332467',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933435F18Rik-002'
),
'ENSMUST00000154878' => array(
'start' => '124326308',
'end' => '124332508',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933435F18Rik-001'
),
'ENSMUST00000158308' => array(
'start' => '124335578',
'end' => '124335681',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm22983-201'
),
'ENSMUST00000184062' => array(
'start' => '124528924',
'end' => '124657169',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27247-001'
),
'ENSDART00000125290' => array(
'start' => '35656812',
'end' => '35656926',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1804-201'
),
'ENSDART00000144119' => array(
'start' => '35829427',
'end' => '35855619',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:dkey-258e8.1-001'
)
)
$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_0007K7_0001' => array(
'genes_in_region' => array(
'ENSG00000224592' => array(
[maximum depth reached]
),
'ENSG00000237290' => array(
[maximum depth reached]
),
'ENSG00000238063' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Breast',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => 'Placenta',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis',
(int) 17 => 'Adrenal',
(int) 18 => 'Lung',
(int) 19 => 'Testis'
)
),
'CIL_0007K7_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000051219' => array(
[maximum depth reached]
),
'ENSMUSG00000073759' => array(
[maximum depth reached]
),
'ENSMUSG00000086087' => array(
[maximum depth reached]
),
'ENSMUSG00000086955' => array(
[maximum depth reached]
),
'ENSMUSG00000086978' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Liver',
(int) 2 => 'Placenta',
(int) 3 => 'Testis',
(int) 4 => 'Adipose',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Muscle',
(int) 13 => 'Ovary',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis',
(int) 17 => 'Testis',
(int) 18 => 'Brain',
(int) 19 => 'Testis',
(int) 20 => 'Adipose',
(int) 21 => 'Brain',
(int) 22 => 'Testis',
(int) 23 => 'Testis',
(int) 24 => 'Testis',
(int) 25 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007K7_0003',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '35549147',
'seq_end' => '35843982',
'region_length' => '294835',
'region_type' => 'UCNEbase',
'el_id' => 'POU3F1'
)
)
$gene_el = array(
'ENSMUST00000125578' => array(
'Testis' => array(
'average_FPKM' => '1.268',
'stddev_FPKM' => '0.42'
)
),
'ENSMUST00000154878' => array(
'Testis' => array(
'average_FPKM' => '0.013',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000086978'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '0.013',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000154878'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007K7_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007K7_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000200796' => 'RNA, U6 small nuclear 753, pseudogene',
'ENSG00000224592' => null,
'ENSG00000237290' => 'long intergenic non-protein coding RNA 1343',
'ENSG00000238063' => null,
'ENSG00000275350' => null,
'ENSMUSG00000051219' => 'RIKEN cDNA 3100002H09 gene',
'ENSMUSG00000073759' => 'RIKEN cDNA 4933407E24 gene',
'ENSMUSG00000084757' => 'RIKEN cDNA 1700057H15 gene',
'ENSMUSG00000086087' => 'predicted gene 12916',
'ENSMUSG00000086955' => 'RIKEN cDNA 1700021L23 gene',
'ENSMUSG00000086978' => 'RIKEN cDNA 4933435F18 gene',
'ENSMUSG00000088933' => 'predicted gene, 22983',
'ENSMUSG00000098760' => 'predicted gene 27247',
'ENSDARG00000089830' => '5S ribosomal RNA',
'ENSDARG00000092939' => 'si:dkey-258e8.1'
),
'gene_name_arr' => array(
'ENSG00000200796' => 'RNU6-753P',
'ENSG00000224592' => 'RP5-884C9.2',
'ENSG00000237290' => 'LINC01343',
'ENSG00000238063' => 'RP11-329N22.1',
'ENSG00000275350' => 'RP11-329N22.2',
'ENSMUSG00000051219' => '3100002H09Rik',
'ENSMUSG00000073759' => '4933407E24Rik',
'ENSMUSG00000084757' => '1700057H15Rik',
'ENSMUSG00000086087' => 'Gm12916',
'ENSMUSG00000086955' => '1700021L23Rik',
'ENSMUSG00000086978' => '4933435F18Rik',
'ENSMUSG00000088933' => 'Gm22983',
'ENSMUSG00000098760' => 'Gm27247',
'ENSDARG00000089830' => '5S_rRNA',
'ENSDARG00000092939' => 'si:dkey-258e8.1'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 14 => 'Breast',
(int) 16 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 21 => 'Liver',
(int) 24 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 30 => 'Placenta',
(int) 33 => '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) 20,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000363926' => array(
'start' => '38396659',
'end' => '38396765',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-753P-201'
),
'ENST00000428151' => array(
'start' => '38047425',
'end' => '38119025',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-884C9.2-001'
),
'ENST00000432922' => array(
'start' => '38047314',
'end' => '38105734',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-884C9.2-002'
),
'ENST00000431311' => array(
'start' => '38209034',
'end' => '38214767',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01343-001'
),
'ENST00000452971' => array(
'start' => '38475196',
'end' => '38476484',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-329N22.1-001'
),
'ENST00000611376' => array(
'start' => '38383838',
'end' => '38384422',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-329N22.2-001'
),
'ENSMUST00000053604' => array(
'start' => '124609931',
'end' => '124610803',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '3100002H09Rik-201'
),
'ENSMUST00000133499' => array(
'start' => '124569190',
'end' => '124574645',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933407E24Rik-001'
),
'ENSMUST00000127913' => array(
'start' => '124414416',
'end' => '124451295',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-003'
),
'ENSMUST00000143859' => array(
'start' => '124449902',
'end' => '124485959',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-002'
),
'ENSMUST00000148832' => array(
'start' => '124414416',
'end' => '124418858',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-004'
),
'ENSMUST00000156566' => array(
'start' => '124450235',
'end' => '124451285',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-001'
),
'ENSMUST00000139012' => array(
'start' => '124293693',
'end' => '124299848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12916-001'
),
'ENSMUST00000153719' => array(
'start' => '124302837',
'end' => '124311461',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700021L23Rik-001'
),
'ENSMUST00000125578' => array(
'start' => '124331406',
'end' => '124332467',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933435F18Rik-002'
),
'ENSMUST00000154878' => array(
'start' => '124326308',
'end' => '124332508',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933435F18Rik-001'
),
'ENSMUST00000158308' => array(
'start' => '124335578',
'end' => '124335681',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm22983-201'
),
'ENSMUST00000184062' => array(
'start' => '124528924',
'end' => '124657169',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27247-001'
),
'ENSDART00000125290' => array(
'start' => '35656812',
'end' => '35656926',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1804-201'
),
'ENSDART00000144119' => array(
'start' => '35829427',
'end' => '35855619',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:dkey-258e8.1-001'
)
),
'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_0007K7_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007K7_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007K7_0001' => array(
'genes_in_region' => array(
'ENSG00000224592' => array(
[maximum depth reached]
),
'ENSG00000237290' => array(
[maximum depth reached]
),
'ENSG00000238063' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Breast',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => 'Placenta',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis',
(int) 17 => 'Adrenal',
(int) 18 => 'Lung',
(int) 19 => 'Testis'
)
),
'CIL_0007K7_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000051219' => array(
[maximum depth reached]
),
'ENSMUSG00000073759' => array(
[maximum depth reached]
),
'ENSMUSG00000086087' => array(
[maximum depth reached]
),
'ENSMUSG00000086955' => array(
[maximum depth reached]
),
'ENSMUSG00000086978' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Liver',
(int) 2 => 'Placenta',
(int) 3 => 'Testis',
(int) 4 => 'Adipose',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Muscle',
(int) 13 => 'Ovary',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis',
(int) 17 => 'Testis',
(int) 18 => 'Brain',
(int) 19 => 'Testis',
(int) 20 => 'Adipose',
(int) 21 => 'Brain',
(int) 22 => 'Testis',
(int) 23 => 'Testis',
(int) 24 => 'Testis',
(int) 25 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000200796' => 'RNA, U6 small nuclear 753, pseudogene',
'ENSG00000224592' => null,
'ENSG00000237290' => 'long intergenic non-protein coding RNA 1343',
'ENSG00000238063' => null,
'ENSG00000275350' => null,
'ENSMUSG00000051219' => 'RIKEN cDNA 3100002H09 gene',
'ENSMUSG00000073759' => 'RIKEN cDNA 4933407E24 gene',
'ENSMUSG00000084757' => 'RIKEN cDNA 1700057H15 gene',
'ENSMUSG00000086087' => 'predicted gene 12916',
'ENSMUSG00000086955' => 'RIKEN cDNA 1700021L23 gene',
'ENSMUSG00000086978' => 'RIKEN cDNA 4933435F18 gene',
'ENSMUSG00000088933' => 'predicted gene, 22983',
'ENSMUSG00000098760' => 'predicted gene 27247',
'ENSDARG00000089830' => '5S ribosomal RNA',
'ENSDARG00000092939' => 'si:dkey-258e8.1'
)
$gene_name_arr = array(
'ENSG00000200796' => 'RNU6-753P',
'ENSG00000224592' => 'RP5-884C9.2',
'ENSG00000237290' => 'LINC01343',
'ENSG00000238063' => 'RP11-329N22.1',
'ENSG00000275350' => 'RP11-329N22.2',
'ENSMUSG00000051219' => '3100002H09Rik',
'ENSMUSG00000073759' => '4933407E24Rik',
'ENSMUSG00000084757' => '1700057H15Rik',
'ENSMUSG00000086087' => 'Gm12916',
'ENSMUSG00000086955' => '1700021L23Rik',
'ENSMUSG00000086978' => '4933435F18Rik',
'ENSMUSG00000088933' => 'Gm22983',
'ENSMUSG00000098760' => 'Gm27247',
'ENSDARG00000089830' => '5S_rRNA',
'ENSDARG00000092939' => 'si:dkey-258e8.1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007K7_0001',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '38095401',
'seq_end' => '38686502',
'region_length' => '591101',
'region_type' => 'UCNEbase',
'el_id' => 'POU3F1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007K7_0002',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '124086916',
'seq_end' => '124615945',
'region_length' => '529029',
'region_type' => 'UCNEbase',
'el_id' => 'POU3F1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007K7_0003',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '35549147',
'seq_end' => '35843982',
'region_length' => '294835',
'region_type' => 'UCNEbase',
'el_id' => 'POU3F1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 14 => 'Breast',
(int) 16 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 21 => 'Liver',
(int) 24 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 30 => 'Placenta',
(int) 33 => '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) 20
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000363926' => array(
'start' => '38396659',
'end' => '38396765',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-753P-201'
),
'ENST00000428151' => array(
'start' => '38047425',
'end' => '38119025',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-884C9.2-001'
),
'ENST00000432922' => array(
'start' => '38047314',
'end' => '38105734',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-884C9.2-002'
),
'ENST00000431311' => array(
'start' => '38209034',
'end' => '38214767',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01343-001'
),
'ENST00000452971' => array(
'start' => '38475196',
'end' => '38476484',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-329N22.1-001'
),
'ENST00000611376' => array(
'start' => '38383838',
'end' => '38384422',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-329N22.2-001'
),
'ENSMUST00000053604' => array(
'start' => '124609931',
'end' => '124610803',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '3100002H09Rik-201'
),
'ENSMUST00000133499' => array(
'start' => '124569190',
'end' => '124574645',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933407E24Rik-001'
),
'ENSMUST00000127913' => array(
'start' => '124414416',
'end' => '124451295',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-003'
),
'ENSMUST00000143859' => array(
'start' => '124449902',
'end' => '124485959',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-002'
),
'ENSMUST00000148832' => array(
'start' => '124414416',
'end' => '124418858',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-004'
),
'ENSMUST00000156566' => array(
'start' => '124450235',
'end' => '124451285',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700057H15Rik-001'
),
'ENSMUST00000139012' => array(
'start' => '124293693',
'end' => '124299848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm12916-001'
),
'ENSMUST00000153719' => array(
'start' => '124302837',
'end' => '124311461',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700021L23Rik-001'
),
'ENSMUST00000125578' => array(
'start' => '124331406',
'end' => '124332467',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933435F18Rik-002'
),
'ENSMUST00000154878' => array(
'start' => '124326308',
'end' => '124332508',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '4933435F18Rik-001'
),
'ENSMUST00000158308' => array(
'start' => '124335578',
'end' => '124335681',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm22983-201'
),
'ENSMUST00000184062' => array(
'start' => '124528924',
'end' => '124657169',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27247-001'
),
'ENSDART00000125290' => array(
'start' => '35656812',
'end' => '35656926',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1804-201'
),
'ENSDART00000144119' => array(
'start' => '35829427',
'end' => '35855619',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:dkey-258e8.1-001'
)
)
$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_0007K7_0001' => array(
'genes_in_region' => array(
'ENSG00000224592' => array(
[maximum depth reached]
),
'ENSG00000237290' => array(
[maximum depth reached]
),
'ENSG00000238063' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Breast',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Ovary',
(int) 13 => 'Placenta',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis',
(int) 17 => 'Adrenal',
(int) 18 => 'Lung',
(int) 19 => 'Testis'
)
),
'CIL_0007K7_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000051219' => array(
[maximum depth reached]
),
'ENSMUSG00000073759' => array(
[maximum depth reached]
),
'ENSMUSG00000086087' => array(
[maximum depth reached]
),
'ENSMUSG00000086955' => array(
[maximum depth reached]
),
'ENSMUSG00000086978' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Liver',
(int) 2 => 'Placenta',
(int) 3 => 'Testis',
(int) 4 => 'Adipose',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Muscle',
(int) 13 => 'Ovary',
(int) 14 => 'Testis',
(int) 15 => 'Brain',
(int) 16 => 'Testis',
(int) 17 => 'Testis',
(int) 18 => 'Brain',
(int) 19 => 'Testis',
(int) 20 => 'Adipose',
(int) 21 => 'Brain',
(int) 22 => 'Testis',
(int) 23 => 'Testis',
(int) 24 => 'Testis',
(int) 25 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007K7_0003',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '35549147',
'seq_end' => '35843982',
'region_length' => '294835',
'region_type' => 'UCNEbase',
'el_id' => 'POU3F1'
)
)
$gene_el = array(
'ENSMUST00000125578' => array(
'Testis' => array(
'average_FPKM' => '1.268',
'stddev_FPKM' => '0.42'
)
),
'ENSMUST00000154878' => array(
'Testis' => array(
'average_FPKM' => '0.013',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000086978'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '0.013',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000154878'
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
(RP5-884C9.2)