| Source ID |
Type |
Tax ID |
Position |
| FOXB2 |
UCNEbase |
7955 |
25:35215142-35242951  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007KF_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_0007KF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KF_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000106772' => 'prune homolog 2 (Drosophila)',
'ENSG00000229857' => null,
'ENSG00000230335' => 'DnaJ (Hsp40) homolog, subfamily B, member 5 pseudogene 1',
'ENSG00000236604' => 'lysophospholipase II pseudogene 3',
'ENSMUSG00000039126' => 'prune homolog 2 (Drosophila)',
'ENSDARG00000088148' => 'forkhead box B1a'
),
'gene_name_arr' => array(
'ENSG00000106772' => 'PRUNE2',
'ENSG00000229857' => 'RP11-159H20.3',
'ENSG00000230335' => 'DNAJB5P1',
'ENSG00000236604' => 'LYPLA2P3',
'ENSMUSG00000039126' => 'Prune2',
'ENSDARG00000088148' => 'foxb1a'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 11 => 'Brain',
(int) 17 => 'Breast',
(int) 20 => 'Colon',
(int) 24 => 'Heart',
(int) 27 => 'Kidney',
(int) 32 => 'Liver',
(int) 37 => 'Lung',
(int) 42 => 'Muscle',
(int) 45 => 'Ovary',
(int) 52 => 'Placenta',
(int) 58 => '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(
'ENST00000223609' => array(
'start' => '76611377',
'end' => '76692200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-201'
),
'ENST00000376713' => array(
'start' => '76788344',
'end' => '76906085',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-011'
),
'ENST00000376717' => array(
'start' => '76611376',
'end' => '76692193',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-007'
),
'ENST00000376718' => array(
'start' => '76611377',
'end' => '76906087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-003'
),
'ENST00000424866' => array(
'start' => '76614450',
'end' => '76652549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-010'
),
'ENST00000426088' => array(
'start' => '76614289',
'end' => '76710237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-006'
),
'ENST00000428286' => array(
'start' => '76611481',
'end' => '76906041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-202'
),
'ENST00000443509' => array(
'start' => '76611481',
'end' => '76906041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-203'
),
'ENST00000464414' => array(
'start' => '76614008',
'end' => '76615162',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-005'
),
'ENST00000466266' => array(
'start' => '76611376',
'end' => '76692200',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-004'
),
'ENST00000480674' => array(
'start' => '76651968',
'end' => '76703438',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-009'
),
'ENST00000488346' => array(
'start' => '76644497',
'end' => '76692167',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-001'
),
'ENST00000489555' => array(
'start' => '76846599',
'end' => '76869182',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-013'
),
'ENST00000492157' => array(
'start' => '76823248',
'end' => '76906087',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-012'
),
'ENST00000494975' => array(
'start' => '76641947',
'end' => '76645138',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-002'
),
'ENST00000451571' => array(
'start' => '76992099',
'end' => '76993108',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-159H20.3-001'
),
'ENST00000454004' => array(
'start' => '76931261',
'end' => '76932066',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'DNAJB5P1-001'
),
'ENST00000417429' => array(
'start' => '76970322',
'end' => '76971028',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'LYPLA2P3-001'
),
'ENSMUST00000087689' => array(
'start' => '16956118',
'end' => '17223932',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Prune2-201'
),
'ENSDART00000128240' => array(
'start' => '35229457',
'end' => '35230350',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'foxb1a-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_0007KF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KF_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007KF_0001' => array(
'genes_in_region' => array(
'ENSG00000106772' => array(
[maximum depth reached]
),
'ENSG00000229857' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Liver',
(int) 5 => 'Ovary',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Brain',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Colon',
(int) 19 => 'Heart',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Colon',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Lung',
(int) 38 => 'Muscle',
(int) 39 => 'Ovary',
(int) 40 => 'Placenta',
(int) 41 => 'Testis',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Ovary',
(int) 46 => 'Adrenal',
(int) 47 => 'Kidney',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta'
)
),
'CIL_0007KF_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000039126' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000106772' => 'prune homolog 2 (Drosophila)',
'ENSG00000229857' => null,
'ENSG00000230335' => 'DnaJ (Hsp40) homolog, subfamily B, member 5 pseudogene 1',
'ENSG00000236604' => 'lysophospholipase II pseudogene 3',
'ENSMUSG00000039126' => 'prune homolog 2 (Drosophila)',
'ENSDARG00000088148' => 'forkhead box B1a'
)
$gene_name_arr = array(
'ENSG00000106772' => 'PRUNE2',
'ENSG00000229857' => 'RP11-159H20.3',
'ENSG00000230335' => 'DNAJB5P1',
'ENSG00000236604' => 'LYPLA2P3',
'ENSMUSG00000039126' => 'Prune2',
'ENSDARG00000088148' => 'foxb1a'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0001',
'tax_id' => '9606',
'chromosome' => '9',
'seq_start' => '76802153',
'seq_end' => '77013234',
'region_length' => '211081',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0002',
'tax_id' => '10090',
'chromosome' => '19',
'seq_start' => '16879655',
'seq_end' => '17039871',
'region_length' => '160216',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0003',
'tax_id' => '7955',
'chromosome' => '25',
'seq_start' => '35215142',
'seq_end' => '35242951',
'region_length' => '27809',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0004',
'tax_id' => '7955',
'chromosome' => '8',
'seq_start' => '39596786',
'seq_end' => '39603930',
'region_length' => '7144',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 11 => 'Brain',
(int) 17 => 'Breast',
(int) 20 => 'Colon',
(int) 24 => 'Heart',
(int) 27 => 'Kidney',
(int) 32 => 'Liver',
(int) 37 => 'Lung',
(int) 42 => 'Muscle',
(int) 45 => 'Ovary',
(int) 52 => 'Placenta',
(int) 58 => '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(
'ENST00000223609' => array(
'start' => '76611377',
'end' => '76692200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-201'
),
'ENST00000376713' => array(
'start' => '76788344',
'end' => '76906085',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-011'
),
'ENST00000376717' => array(
'start' => '76611376',
'end' => '76692193',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-007'
),
'ENST00000376718' => array(
'start' => '76611377',
'end' => '76906087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-003'
),
'ENST00000424866' => array(
'start' => '76614450',
'end' => '76652549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-010'
),
'ENST00000426088' => array(
'start' => '76614289',
'end' => '76710237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-006'
),
'ENST00000428286' => array(
'start' => '76611481',
'end' => '76906041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-202'
),
'ENST00000443509' => array(
'start' => '76611481',
'end' => '76906041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-203'
),
'ENST00000464414' => array(
'start' => '76614008',
'end' => '76615162',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-005'
),
'ENST00000466266' => array(
'start' => '76611376',
'end' => '76692200',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-004'
),
'ENST00000480674' => array(
'start' => '76651968',
'end' => '76703438',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-009'
),
'ENST00000488346' => array(
'start' => '76644497',
'end' => '76692167',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-001'
),
'ENST00000489555' => array(
'start' => '76846599',
'end' => '76869182',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-013'
),
'ENST00000492157' => array(
'start' => '76823248',
'end' => '76906087',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-012'
),
'ENST00000494975' => array(
'start' => '76641947',
'end' => '76645138',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-002'
),
'ENST00000451571' => array(
'start' => '76992099',
'end' => '76993108',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-159H20.3-001'
),
'ENST00000454004' => array(
'start' => '76931261',
'end' => '76932066',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'DNAJB5P1-001'
),
'ENST00000417429' => array(
'start' => '76970322',
'end' => '76971028',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'LYPLA2P3-001'
),
'ENSMUST00000087689' => array(
'start' => '16956118',
'end' => '17223932',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Prune2-201'
),
'ENSDART00000128240' => array(
'start' => '35229457',
'end' => '35230350',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'foxb1a-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_0007KF_0001' => array(
'genes_in_region' => array(
'ENSG00000106772' => array(
[maximum depth reached]
),
'ENSG00000229857' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Liver',
(int) 5 => 'Ovary',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Brain',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Colon',
(int) 19 => 'Heart',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Colon',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Lung',
(int) 38 => 'Muscle',
(int) 39 => 'Ovary',
(int) 40 => 'Placenta',
(int) 41 => 'Testis',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Ovary',
(int) 46 => 'Adrenal',
(int) 47 => 'Kidney',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta'
)
),
'CIL_0007KF_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000039126' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0003',
'tax_id' => '7955',
'chromosome' => '25',
'seq_start' => '35215142',
'seq_end' => '35242951',
'region_length' => '27809',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
)
$gene_el = array(
'ENSMUST00000087689' => array(
'Adipose' => array(
'average_FPKM' => '2.238',
'stddev_FPKM' => '1.67'
),
'Adrenal' => array(
'average_FPKM' => '0.885',
'stddev_FPKM' => '0.24'
),
'Bladder' => array(
'average_FPKM' => '3.357',
'stddev_FPKM' => '2.04'
),
'Brain' => array(
'average_FPKM' => '0.720',
'stddev_FPKM' => '0.48'
),
'Breast' => array(
'average_FPKM' => '1.181',
'stddev_FPKM' => '0.43'
),
'Colon' => array(
'average_FPKM' => '0.410',
'stddev_FPKM' => '0.26'
),
'Heart' => array(
'average_FPKM' => '5.212',
'stddev_FPKM' => '1.13'
),
'Kidney' => array(
'average_FPKM' => '0.155',
'stddev_FPKM' => '0.07'
),
'Liver' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.01'
),
'Lung' => array(
'average_FPKM' => '0.571',
'stddev_FPKM' => '0.17'
),
'Muscle' => array(
'average_FPKM' => '0.310',
'stddev_FPKM' => '0.16'
),
'Ovary' => array(
'average_FPKM' => '1.114',
'stddev_FPKM' => '0.54'
),
'Placenta' => array(
'average_FPKM' => '2.693',
'stddev_FPKM' => '1.28'
),
'Testis' => array(
'average_FPKM' => '0.103',
'stddev_FPKM' => '0.02'
)
)
)
$gene_key = 'ENSMUSG00000039126'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '2.238',
'stddev_FPKM' => '1.67'
),
'Adrenal' => array(
'average_FPKM' => '0.885',
'stddev_FPKM' => '0.24'
),
'Bladder' => array(
'average_FPKM' => '3.357',
'stddev_FPKM' => '2.04'
),
'Brain' => array(
'average_FPKM' => '0.720',
'stddev_FPKM' => '0.48'
),
'Breast' => array(
'average_FPKM' => '1.181',
'stddev_FPKM' => '0.43'
),
'Colon' => array(
'average_FPKM' => '0.410',
'stddev_FPKM' => '0.26'
),
'Heart' => array(
'average_FPKM' => '5.212',
'stddev_FPKM' => '1.13'
),
'Kidney' => array(
'average_FPKM' => '0.155',
'stddev_FPKM' => '0.07'
),
'Liver' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.01'
),
'Lung' => array(
'average_FPKM' => '0.571',
'stddev_FPKM' => '0.17'
),
'Muscle' => array(
'average_FPKM' => '0.310',
'stddev_FPKM' => '0.16'
),
'Ovary' => array(
'average_FPKM' => '1.114',
'stddev_FPKM' => '0.54'
),
'Placenta' => array(
'average_FPKM' => '2.693',
'stddev_FPKM' => '1.28'
),
'Testis' => array(
'average_FPKM' => '0.103',
'stddev_FPKM' => '0.02'
)
)
$tran_key = 'ENSMUST00000087689'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007KF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KF_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000106772' => 'prune homolog 2 (Drosophila)',
'ENSG00000229857' => null,
'ENSG00000230335' => 'DnaJ (Hsp40) homolog, subfamily B, member 5 pseudogene 1',
'ENSG00000236604' => 'lysophospholipase II pseudogene 3',
'ENSMUSG00000039126' => 'prune homolog 2 (Drosophila)',
'ENSDARG00000088148' => 'forkhead box B1a'
),
'gene_name_arr' => array(
'ENSG00000106772' => 'PRUNE2',
'ENSG00000229857' => 'RP11-159H20.3',
'ENSG00000230335' => 'DNAJB5P1',
'ENSG00000236604' => 'LYPLA2P3',
'ENSMUSG00000039126' => 'Prune2',
'ENSDARG00000088148' => 'foxb1a'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 11 => 'Brain',
(int) 17 => 'Breast',
(int) 20 => 'Colon',
(int) 24 => 'Heart',
(int) 27 => 'Kidney',
(int) 32 => 'Liver',
(int) 37 => 'Lung',
(int) 42 => 'Muscle',
(int) 45 => 'Ovary',
(int) 52 => 'Placenta',
(int) 58 => '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(
'ENST00000223609' => array(
'start' => '76611377',
'end' => '76692200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-201'
),
'ENST00000376713' => array(
'start' => '76788344',
'end' => '76906085',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-011'
),
'ENST00000376717' => array(
'start' => '76611376',
'end' => '76692193',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-007'
),
'ENST00000376718' => array(
'start' => '76611377',
'end' => '76906087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-003'
),
'ENST00000424866' => array(
'start' => '76614450',
'end' => '76652549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-010'
),
'ENST00000426088' => array(
'start' => '76614289',
'end' => '76710237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-006'
),
'ENST00000428286' => array(
'start' => '76611481',
'end' => '76906041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-202'
),
'ENST00000443509' => array(
'start' => '76611481',
'end' => '76906041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-203'
),
'ENST00000464414' => array(
'start' => '76614008',
'end' => '76615162',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-005'
),
'ENST00000466266' => array(
'start' => '76611376',
'end' => '76692200',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-004'
),
'ENST00000480674' => array(
'start' => '76651968',
'end' => '76703438',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-009'
),
'ENST00000488346' => array(
'start' => '76644497',
'end' => '76692167',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-001'
),
'ENST00000489555' => array(
'start' => '76846599',
'end' => '76869182',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-013'
),
'ENST00000492157' => array(
'start' => '76823248',
'end' => '76906087',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-012'
),
'ENST00000494975' => array(
'start' => '76641947',
'end' => '76645138',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-002'
),
'ENST00000451571' => array(
'start' => '76992099',
'end' => '76993108',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-159H20.3-001'
),
'ENST00000454004' => array(
'start' => '76931261',
'end' => '76932066',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'DNAJB5P1-001'
),
'ENST00000417429' => array(
'start' => '76970322',
'end' => '76971028',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'LYPLA2P3-001'
),
'ENSMUST00000087689' => array(
'start' => '16956118',
'end' => '17223932',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Prune2-201'
),
'ENSDART00000128240' => array(
'start' => '35229457',
'end' => '35230350',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'foxb1a-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_0007KF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KF_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007KF_0001' => array(
'genes_in_region' => array(
'ENSG00000106772' => array(
[maximum depth reached]
),
'ENSG00000229857' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Liver',
(int) 5 => 'Ovary',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Brain',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Colon',
(int) 19 => 'Heart',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Colon',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Lung',
(int) 38 => 'Muscle',
(int) 39 => 'Ovary',
(int) 40 => 'Placenta',
(int) 41 => 'Testis',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Ovary',
(int) 46 => 'Adrenal',
(int) 47 => 'Kidney',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta'
)
),
'CIL_0007KF_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000039126' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000106772' => 'prune homolog 2 (Drosophila)',
'ENSG00000229857' => null,
'ENSG00000230335' => 'DnaJ (Hsp40) homolog, subfamily B, member 5 pseudogene 1',
'ENSG00000236604' => 'lysophospholipase II pseudogene 3',
'ENSMUSG00000039126' => 'prune homolog 2 (Drosophila)',
'ENSDARG00000088148' => 'forkhead box B1a'
)
$gene_name_arr = array(
'ENSG00000106772' => 'PRUNE2',
'ENSG00000229857' => 'RP11-159H20.3',
'ENSG00000230335' => 'DNAJB5P1',
'ENSG00000236604' => 'LYPLA2P3',
'ENSMUSG00000039126' => 'Prune2',
'ENSDARG00000088148' => 'foxb1a'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0001',
'tax_id' => '9606',
'chromosome' => '9',
'seq_start' => '76802153',
'seq_end' => '77013234',
'region_length' => '211081',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0002',
'tax_id' => '10090',
'chromosome' => '19',
'seq_start' => '16879655',
'seq_end' => '17039871',
'region_length' => '160216',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0003',
'tax_id' => '7955',
'chromosome' => '25',
'seq_start' => '35215142',
'seq_end' => '35242951',
'region_length' => '27809',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0004',
'tax_id' => '7955',
'chromosome' => '8',
'seq_start' => '39596786',
'seq_end' => '39603930',
'region_length' => '7144',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 11 => 'Brain',
(int) 17 => 'Breast',
(int) 20 => 'Colon',
(int) 24 => 'Heart',
(int) 27 => 'Kidney',
(int) 32 => 'Liver',
(int) 37 => 'Lung',
(int) 42 => 'Muscle',
(int) 45 => 'Ovary',
(int) 52 => 'Placenta',
(int) 58 => '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(
'ENST00000223609' => array(
'start' => '76611377',
'end' => '76692200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-201'
),
'ENST00000376713' => array(
'start' => '76788344',
'end' => '76906085',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-011'
),
'ENST00000376717' => array(
'start' => '76611376',
'end' => '76692193',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-007'
),
'ENST00000376718' => array(
'start' => '76611377',
'end' => '76906087',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-003'
),
'ENST00000424866' => array(
'start' => '76614450',
'end' => '76652549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-010'
),
'ENST00000426088' => array(
'start' => '76614289',
'end' => '76710237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-006'
),
'ENST00000428286' => array(
'start' => '76611481',
'end' => '76906041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-202'
),
'ENST00000443509' => array(
'start' => '76611481',
'end' => '76906041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PRUNE2-203'
),
'ENST00000464414' => array(
'start' => '76614008',
'end' => '76615162',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-005'
),
'ENST00000466266' => array(
'start' => '76611376',
'end' => '76692200',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-004'
),
'ENST00000480674' => array(
'start' => '76651968',
'end' => '76703438',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-009'
),
'ENST00000488346' => array(
'start' => '76644497',
'end' => '76692167',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-001'
),
'ENST00000489555' => array(
'start' => '76846599',
'end' => '76869182',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-013'
),
'ENST00000492157' => array(
'start' => '76823248',
'end' => '76906087',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-012'
),
'ENST00000494975' => array(
'start' => '76641947',
'end' => '76645138',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PRUNE2-002'
),
'ENST00000451571' => array(
'start' => '76992099',
'end' => '76993108',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-159H20.3-001'
),
'ENST00000454004' => array(
'start' => '76931261',
'end' => '76932066',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'DNAJB5P1-001'
),
'ENST00000417429' => array(
'start' => '76970322',
'end' => '76971028',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'LYPLA2P3-001'
),
'ENSMUST00000087689' => array(
'start' => '16956118',
'end' => '17223932',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Prune2-201'
),
'ENSDART00000128240' => array(
'start' => '35229457',
'end' => '35230350',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'foxb1a-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_0007KF_0001' => array(
'genes_in_region' => array(
'ENSG00000106772' => array(
[maximum depth reached]
),
'ENSG00000229857' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Colon',
(int) 4 => 'Liver',
(int) 5 => 'Ovary',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Brain',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Colon',
(int) 19 => 'Heart',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Colon',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Lung',
(int) 38 => 'Muscle',
(int) 39 => 'Ovary',
(int) 40 => 'Placenta',
(int) 41 => 'Testis',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Ovary',
(int) 46 => 'Adrenal',
(int) 47 => 'Kidney',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta'
)
),
'CIL_0007KF_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000039126' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KF_0003',
'tax_id' => '7955',
'chromosome' => '25',
'seq_start' => '35215142',
'seq_end' => '35242951',
'region_length' => '27809',
'region_type' => 'UCNEbase',
'el_id' => 'FOXB2'
)
)
$gene_el = array(
'ENSMUST00000087689' => array(
'Adipose' => array(
'average_FPKM' => '2.238',
'stddev_FPKM' => '1.67'
),
'Adrenal' => array(
'average_FPKM' => '0.885',
'stddev_FPKM' => '0.24'
),
'Bladder' => array(
'average_FPKM' => '3.357',
'stddev_FPKM' => '2.04'
),
'Brain' => array(
'average_FPKM' => '0.720',
'stddev_FPKM' => '0.48'
),
'Breast' => array(
'average_FPKM' => '1.181',
'stddev_FPKM' => '0.43'
),
'Colon' => array(
'average_FPKM' => '0.410',
'stddev_FPKM' => '0.26'
),
'Heart' => array(
'average_FPKM' => '5.212',
'stddev_FPKM' => '1.13'
),
'Kidney' => array(
'average_FPKM' => '0.155',
'stddev_FPKM' => '0.07'
),
'Liver' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.01'
),
'Lung' => array(
'average_FPKM' => '0.571',
'stddev_FPKM' => '0.17'
),
'Muscle' => array(
'average_FPKM' => '0.310',
'stddev_FPKM' => '0.16'
),
'Ovary' => array(
'average_FPKM' => '1.114',
'stddev_FPKM' => '0.54'
),
'Placenta' => array(
'average_FPKM' => '2.693',
'stddev_FPKM' => '1.28'
),
'Testis' => array(
'average_FPKM' => '0.103',
'stddev_FPKM' => '0.02'
)
)
)
$gene_key = 'ENSMUSG00000039126'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '2.238',
'stddev_FPKM' => '1.67'
),
'Adrenal' => array(
'average_FPKM' => '0.885',
'stddev_FPKM' => '0.24'
),
'Bladder' => array(
'average_FPKM' => '3.357',
'stddev_FPKM' => '2.04'
),
'Brain' => array(
'average_FPKM' => '0.720',
'stddev_FPKM' => '0.48'
),
'Breast' => array(
'average_FPKM' => '1.181',
'stddev_FPKM' => '0.43'
),
'Colon' => array(
'average_FPKM' => '0.410',
'stddev_FPKM' => '0.26'
),
'Heart' => array(
'average_FPKM' => '5.212',
'stddev_FPKM' => '1.13'
),
'Kidney' => array(
'average_FPKM' => '0.155',
'stddev_FPKM' => '0.07'
),
'Liver' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.01'
),
'Lung' => array(
'average_FPKM' => '0.571',
'stddev_FPKM' => '0.17'
),
'Muscle' => array(
'average_FPKM' => '0.310',
'stddev_FPKM' => '0.16'
),
'Ovary' => array(
'average_FPKM' => '1.114',
'stddev_FPKM' => '0.54'
),
'Placenta' => array(
'average_FPKM' => '2.693',
'stddev_FPKM' => '1.28'
),
'Testis' => array(
'average_FPKM' => '0.103',
'stddev_FPKM' => '0.02'
)
)
$tran_key = 'ENSMUST00000087689'
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
(PRUNE2)