Notice (8): Undefined index: CIL_0007KU_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_0007KU_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KU_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KU_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000182263' => 'fidgetin',
'ENSG00000200902' => 'RNA, U6 small nuclear 627, pseudogene',
'ENSG00000226847' => 'phosphoribosyl pyrophosphate synthetase 1 pseudogene 1',
'ENSG00000229641' => 'cytochrome P450, family 2, subfamily C, polypeptide 56, pseudogene',
'ENSG00000237844' => null,
'ENSG00000264074' => null,
'ENSMUSG00000075324' => 'fidgetin',
'ENSMUSG00000081065' => 'predicted gene 13576',
'ENSMUSG00000082127' => 'predicted gene 13577',
'ENSMUSG00000084104' => 'predicted gene 13578',
'ENSMUSG00000087702' => 'predicted gene 13575',
'ENSDARG00000008662' => 'fidgetin',
'ENSDARG00000079722' => 'Uncharacterized protein',
'ENSDARG00000088979' => 'cordon-bleu WH2 repeat protein-like 1'
),
'gene_name_arr' => array(
'ENSG00000182263' => 'FIGN',
'ENSG00000200902' => 'RNU6-627P',
'ENSG00000226847' => 'PRPS1P1',
'ENSG00000229641' => 'CYP2C56P',
'ENSG00000237844' => 'AC092684.1',
'ENSG00000264074' => 'AC110086.1',
'ENSMUSG00000075324' => 'Fign',
'ENSMUSG00000081065' => 'Gm13576',
'ENSMUSG00000082127' => 'Gm13577',
'ENSMUSG00000084104' => 'Gm13578',
'ENSMUSG00000087702' => 'Gm13575',
'ENSDARG00000008662' => 'fign',
'ENSDARG00000079722' => 'CABZ01053757.1',
'ENSDARG00000088979' => 'COBLL1 (1 of 2)'
),
'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]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 17 => 'Breast',
(int) 21 => 'Colon',
(int) 26 => 'Heart',
(int) 33 => 'Kidney',
(int) 40 => 'Liver',
(int) 47 => 'Lung',
(int) 51 => 'Muscle',
(int) 57 => 'Ovary',
(int) 62 => 'Placenta',
(int) 68 => '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) 19,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000333129' => array(
'start' => '163602611',
'end' => '163736007',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FIGN-001'
),
'ENST00000409634' => array(
'start' => '163593396',
'end' => '163736012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FIGN-004'
),
'ENST00000482917' => array(
'start' => '163611354',
'end' => '163735984',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FIGN-003'
),
'ENST00000364032' => array(
'start' => '163288995',
'end' => '163289096',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-627P-201'
),
'ENST00000445305' => array(
'start' => '164213539',
'end' => '164214414',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PRPS1P1-001'
),
'ENST00000440076' => array(
'start' => '164321933',
'end' => '164322223',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CYP2C56P-001'
),
'ENST00000429636' => array(
'start' => '163749573',
'end' => '164352223',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC092684.1-001'
),
'ENST00000581574' => array(
'start' => '164423525',
'end' => '164423606',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC110086.1-201'
),
'ENSMUST00000102728' => array(
'start' => '63977337',
'end' => '64098038',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Fign-002'
),
'ENSMUST00000126042' => array(
'start' => '63980447',
'end' => '64097988',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fign-004'
),
'ENSMUST00000131615' => array(
'start' => '63971507',
'end' => '64098012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fign-001'
),
'ENSMUST00000153538' => array(
'start' => '63980616',
'end' => '64098010',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fign-003'
),
'ENSMUST00000120851' => array(
'start' => '64569863',
'end' => '64570640',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13576-001'
),
'ENSMUST00000121365' => array(
'start' => '64474745',
'end' => '64474957',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13577-001'
),
'ENSMUST00000120849' => array(
'start' => '64867999',
'end' => '64868588',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13578-001'
),
'ENSMUST00000142353' => array(
'start' => '64382602',
'end' => '64393860',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm13575-001'
),
'ENSDART00000023105' => array(
'start' => '52086531',
'end' => '52089435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'fign-201'
),
'ENSDART00000111381' => array(
'start' => '51926664',
'end' => '52019629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CABZ01053757.1-201'
),
'ENSDART00000121682' => array(
'start' => '51621835',
'end' => '51629141',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COBLL1 (1 of 2)-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_0007KU_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KU_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KU_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007KU_0001' => array(
'genes_in_region' => array(
'ENSG00000182263' => array(
[maximum depth reached]
),
'ENSG00000237844' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Ovary',
(int) 20 => 'Testis'
)
),
'CIL_0007KU_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000075324' => array(
[maximum depth reached]
),
'ENSMUSG00000082127' => array(
[maximum depth reached]
),
'ENSMUSG00000084104' => array(
[maximum depth reached]
),
'ENSMUSG00000087702' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Colon',
(int) 14 => 'Muscle',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Colon',
(int) 29 => 'Placenta',
(int) 30 => 'Brain',
(int) 31 => 'Liver',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Bladder',
(int) 35 => 'Brain',
(int) 36 => 'Liver',
(int) 37 => 'Placenta',
(int) 38 => 'Testis',
(int) 39 => 'Adipose'
)
),
'CIL_0007KU_0005' => array(
'genes_in_region' => array(
'ENSDARG00000008662' => array(
[maximum depth reached]
),
'ENSDARG00000079722' => array(
[maximum depth reached]
),
'ENSDARG00000088979' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Brain',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000182263' => 'fidgetin',
'ENSG00000200902' => 'RNA, U6 small nuclear 627, pseudogene',
'ENSG00000226847' => 'phosphoribosyl pyrophosphate synthetase 1 pseudogene 1',
'ENSG00000229641' => 'cytochrome P450, family 2, subfamily C, polypeptide 56, pseudogene',
'ENSG00000237844' => null,
'ENSG00000264074' => null,
'ENSMUSG00000075324' => 'fidgetin',
'ENSMUSG00000081065' => 'predicted gene 13576',
'ENSMUSG00000082127' => 'predicted gene 13577',
'ENSMUSG00000084104' => 'predicted gene 13578',
'ENSMUSG00000087702' => 'predicted gene 13575',
'ENSDARG00000008662' => 'fidgetin',
'ENSDARG00000079722' => 'Uncharacterized protein',
'ENSDARG00000088979' => 'cordon-bleu WH2 repeat protein-like 1'
)
$gene_name_arr = array(
'ENSG00000182263' => 'FIGN',
'ENSG00000200902' => 'RNU6-627P',
'ENSG00000226847' => 'PRPS1P1',
'ENSG00000229641' => 'CYP2C56P',
'ENSG00000237844' => 'AC092684.1',
'ENSG00000264074' => 'AC110086.1',
'ENSMUSG00000075324' => 'Fign',
'ENSMUSG00000081065' => 'Gm13576',
'ENSMUSG00000082127' => 'Gm13577',
'ENSMUSG00000084104' => 'Gm13578',
'ENSMUSG00000087702' => 'Gm13575',
'ENSDARG00000008662' => 'fign',
'ENSDARG00000079722' => 'CABZ01053757.1',
'ENSDARG00000088979' => 'COBLL1 (1 of 2)'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '163247304',
'seq_end' => '164450572',
'region_length' => '1203268',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0002',
'tax_id' => '10090',
'chromosome' => '2',
'seq_start' => '63574157',
'seq_end' => '64878215',
'region_length' => '1304058',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0003',
'tax_id' => '7955',
'chromosome' => '23',
'seq_start' => '27372307',
'seq_end' => '27372476',
'region_length' => '169',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0004',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '10324567',
'seq_end' => '10324815',
'region_length' => '248',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0005',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '51541313',
'seq_end' => '52197054',
'region_length' => '655741',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 17 => 'Breast',
(int) 21 => 'Colon',
(int) 26 => 'Heart',
(int) 33 => 'Kidney',
(int) 40 => 'Liver',
(int) 47 => 'Lung',
(int) 51 => 'Muscle',
(int) 57 => 'Ovary',
(int) 62 => 'Placenta',
(int) 68 => '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) 19
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000333129' => array(
'start' => '163602611',
'end' => '163736007',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FIGN-001'
),
'ENST00000409634' => array(
'start' => '163593396',
'end' => '163736012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FIGN-004'
),
'ENST00000482917' => array(
'start' => '163611354',
'end' => '163735984',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FIGN-003'
),
'ENST00000364032' => array(
'start' => '163288995',
'end' => '163289096',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-627P-201'
),
'ENST00000445305' => array(
'start' => '164213539',
'end' => '164214414',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PRPS1P1-001'
),
'ENST00000440076' => array(
'start' => '164321933',
'end' => '164322223',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CYP2C56P-001'
),
'ENST00000429636' => array(
'start' => '163749573',
'end' => '164352223',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC092684.1-001'
),
'ENST00000581574' => array(
'start' => '164423525',
'end' => '164423606',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC110086.1-201'
),
'ENSMUST00000102728' => array(
'start' => '63977337',
'end' => '64098038',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Fign-002'
),
'ENSMUST00000126042' => array(
'start' => '63980447',
'end' => '64097988',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fign-004'
),
'ENSMUST00000131615' => array(
'start' => '63971507',
'end' => '64098012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fign-001'
),
'ENSMUST00000153538' => array(
'start' => '63980616',
'end' => '64098010',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fign-003'
),
'ENSMUST00000120851' => array(
'start' => '64569863',
'end' => '64570640',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13576-001'
),
'ENSMUST00000121365' => array(
'start' => '64474745',
'end' => '64474957',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13577-001'
),
'ENSMUST00000120849' => array(
'start' => '64867999',
'end' => '64868588',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13578-001'
),
'ENSMUST00000142353' => array(
'start' => '64382602',
'end' => '64393860',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm13575-001'
),
'ENSDART00000023105' => array(
'start' => '52086531',
'end' => '52089435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'fign-201'
),
'ENSDART00000111381' => array(
'start' => '51926664',
'end' => '52019629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CABZ01053757.1-201'
),
'ENSDART00000121682' => array(
'start' => '51621835',
'end' => '51629141',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COBLL1 (1 of 2)-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_0007KU_0001' => array(
'genes_in_region' => array(
'ENSG00000182263' => array(
[maximum depth reached]
),
'ENSG00000237844' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Ovary',
(int) 20 => 'Testis'
)
),
'CIL_0007KU_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000075324' => array(
[maximum depth reached]
),
'ENSMUSG00000082127' => array(
[maximum depth reached]
),
'ENSMUSG00000084104' => array(
[maximum depth reached]
),
'ENSMUSG00000087702' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Colon',
(int) 14 => 'Muscle',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Colon',
(int) 29 => 'Placenta',
(int) 30 => 'Brain',
(int) 31 => 'Liver',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Bladder',
(int) 35 => 'Brain',
(int) 36 => 'Liver',
(int) 37 => 'Placenta',
(int) 38 => 'Testis',
(int) 39 => 'Adipose'
)
),
'CIL_0007KU_0005' => array(
'genes_in_region' => array(
'ENSDARG00000008662' => array(
[maximum depth reached]
),
'ENSDARG00000079722' => array(
[maximum depth reached]
),
'ENSDARG00000088979' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Brain',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0003',
'tax_id' => '7955',
'chromosome' => '23',
'seq_start' => '27372307',
'seq_end' => '27372476',
'region_length' => '169',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
)
$gene_el = array(
'ENSMUST00000142353' => array(
'Adipose' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000087702'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000142353'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007KU_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KU_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KU_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000182263' => 'fidgetin',
'ENSG00000200902' => 'RNA, U6 small nuclear 627, pseudogene',
'ENSG00000226847' => 'phosphoribosyl pyrophosphate synthetase 1 pseudogene 1',
'ENSG00000229641' => 'cytochrome P450, family 2, subfamily C, polypeptide 56, pseudogene',
'ENSG00000237844' => null,
'ENSG00000264074' => null,
'ENSMUSG00000075324' => 'fidgetin',
'ENSMUSG00000081065' => 'predicted gene 13576',
'ENSMUSG00000082127' => 'predicted gene 13577',
'ENSMUSG00000084104' => 'predicted gene 13578',
'ENSMUSG00000087702' => 'predicted gene 13575',
'ENSDARG00000008662' => 'fidgetin',
'ENSDARG00000079722' => 'Uncharacterized protein',
'ENSDARG00000088979' => 'cordon-bleu WH2 repeat protein-like 1'
),
'gene_name_arr' => array(
'ENSG00000182263' => 'FIGN',
'ENSG00000200902' => 'RNU6-627P',
'ENSG00000226847' => 'PRPS1P1',
'ENSG00000229641' => 'CYP2C56P',
'ENSG00000237844' => 'AC092684.1',
'ENSG00000264074' => 'AC110086.1',
'ENSMUSG00000075324' => 'Fign',
'ENSMUSG00000081065' => 'Gm13576',
'ENSMUSG00000082127' => 'Gm13577',
'ENSMUSG00000084104' => 'Gm13578',
'ENSMUSG00000087702' => 'Gm13575',
'ENSDARG00000008662' => 'fign',
'ENSDARG00000079722' => 'CABZ01053757.1',
'ENSDARG00000088979' => 'COBLL1 (1 of 2)'
),
'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]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 17 => 'Breast',
(int) 21 => 'Colon',
(int) 26 => 'Heart',
(int) 33 => 'Kidney',
(int) 40 => 'Liver',
(int) 47 => 'Lung',
(int) 51 => 'Muscle',
(int) 57 => 'Ovary',
(int) 62 => 'Placenta',
(int) 68 => '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) 19,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000333129' => array(
'start' => '163602611',
'end' => '163736007',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FIGN-001'
),
'ENST00000409634' => array(
'start' => '163593396',
'end' => '163736012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FIGN-004'
),
'ENST00000482917' => array(
'start' => '163611354',
'end' => '163735984',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FIGN-003'
),
'ENST00000364032' => array(
'start' => '163288995',
'end' => '163289096',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-627P-201'
),
'ENST00000445305' => array(
'start' => '164213539',
'end' => '164214414',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PRPS1P1-001'
),
'ENST00000440076' => array(
'start' => '164321933',
'end' => '164322223',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CYP2C56P-001'
),
'ENST00000429636' => array(
'start' => '163749573',
'end' => '164352223',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC092684.1-001'
),
'ENST00000581574' => array(
'start' => '164423525',
'end' => '164423606',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC110086.1-201'
),
'ENSMUST00000102728' => array(
'start' => '63977337',
'end' => '64098038',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Fign-002'
),
'ENSMUST00000126042' => array(
'start' => '63980447',
'end' => '64097988',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fign-004'
),
'ENSMUST00000131615' => array(
'start' => '63971507',
'end' => '64098012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fign-001'
),
'ENSMUST00000153538' => array(
'start' => '63980616',
'end' => '64098010',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fign-003'
),
'ENSMUST00000120851' => array(
'start' => '64569863',
'end' => '64570640',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13576-001'
),
'ENSMUST00000121365' => array(
'start' => '64474745',
'end' => '64474957',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13577-001'
),
'ENSMUST00000120849' => array(
'start' => '64867999',
'end' => '64868588',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13578-001'
),
'ENSMUST00000142353' => array(
'start' => '64382602',
'end' => '64393860',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm13575-001'
),
'ENSDART00000023105' => array(
'start' => '52086531',
'end' => '52089435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'fign-201'
),
'ENSDART00000111381' => array(
'start' => '51926664',
'end' => '52019629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CABZ01053757.1-201'
),
'ENSDART00000121682' => array(
'start' => '51621835',
'end' => '51629141',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COBLL1 (1 of 2)-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_0007KU_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KU_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KU_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007KU_0001' => array(
'genes_in_region' => array(
'ENSG00000182263' => array(
[maximum depth reached]
),
'ENSG00000237844' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Ovary',
(int) 20 => 'Testis'
)
),
'CIL_0007KU_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000075324' => array(
[maximum depth reached]
),
'ENSMUSG00000082127' => array(
[maximum depth reached]
),
'ENSMUSG00000084104' => array(
[maximum depth reached]
),
'ENSMUSG00000087702' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Colon',
(int) 14 => 'Muscle',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Colon',
(int) 29 => 'Placenta',
(int) 30 => 'Brain',
(int) 31 => 'Liver',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Bladder',
(int) 35 => 'Brain',
(int) 36 => 'Liver',
(int) 37 => 'Placenta',
(int) 38 => 'Testis',
(int) 39 => 'Adipose'
)
),
'CIL_0007KU_0005' => array(
'genes_in_region' => array(
'ENSDARG00000008662' => array(
[maximum depth reached]
),
'ENSDARG00000079722' => array(
[maximum depth reached]
),
'ENSDARG00000088979' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Brain',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000182263' => 'fidgetin',
'ENSG00000200902' => 'RNA, U6 small nuclear 627, pseudogene',
'ENSG00000226847' => 'phosphoribosyl pyrophosphate synthetase 1 pseudogene 1',
'ENSG00000229641' => 'cytochrome P450, family 2, subfamily C, polypeptide 56, pseudogene',
'ENSG00000237844' => null,
'ENSG00000264074' => null,
'ENSMUSG00000075324' => 'fidgetin',
'ENSMUSG00000081065' => 'predicted gene 13576',
'ENSMUSG00000082127' => 'predicted gene 13577',
'ENSMUSG00000084104' => 'predicted gene 13578',
'ENSMUSG00000087702' => 'predicted gene 13575',
'ENSDARG00000008662' => 'fidgetin',
'ENSDARG00000079722' => 'Uncharacterized protein',
'ENSDARG00000088979' => 'cordon-bleu WH2 repeat protein-like 1'
)
$gene_name_arr = array(
'ENSG00000182263' => 'FIGN',
'ENSG00000200902' => 'RNU6-627P',
'ENSG00000226847' => 'PRPS1P1',
'ENSG00000229641' => 'CYP2C56P',
'ENSG00000237844' => 'AC092684.1',
'ENSG00000264074' => 'AC110086.1',
'ENSMUSG00000075324' => 'Fign',
'ENSMUSG00000081065' => 'Gm13576',
'ENSMUSG00000082127' => 'Gm13577',
'ENSMUSG00000084104' => 'Gm13578',
'ENSMUSG00000087702' => 'Gm13575',
'ENSDARG00000008662' => 'fign',
'ENSDARG00000079722' => 'CABZ01053757.1',
'ENSDARG00000088979' => 'COBLL1 (1 of 2)'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '163247304',
'seq_end' => '164450572',
'region_length' => '1203268',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0002',
'tax_id' => '10090',
'chromosome' => '2',
'seq_start' => '63574157',
'seq_end' => '64878215',
'region_length' => '1304058',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0003',
'tax_id' => '7955',
'chromosome' => '23',
'seq_start' => '27372307',
'seq_end' => '27372476',
'region_length' => '169',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0004',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '10324567',
'seq_end' => '10324815',
'region_length' => '248',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0005',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '51541313',
'seq_end' => '52197054',
'region_length' => '655741',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 17 => 'Breast',
(int) 21 => 'Colon',
(int) 26 => 'Heart',
(int) 33 => 'Kidney',
(int) 40 => 'Liver',
(int) 47 => 'Lung',
(int) 51 => 'Muscle',
(int) 57 => 'Ovary',
(int) 62 => 'Placenta',
(int) 68 => '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) 19
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000333129' => array(
'start' => '163602611',
'end' => '163736007',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FIGN-001'
),
'ENST00000409634' => array(
'start' => '163593396',
'end' => '163736012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FIGN-004'
),
'ENST00000482917' => array(
'start' => '163611354',
'end' => '163735984',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FIGN-003'
),
'ENST00000364032' => array(
'start' => '163288995',
'end' => '163289096',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-627P-201'
),
'ENST00000445305' => array(
'start' => '164213539',
'end' => '164214414',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PRPS1P1-001'
),
'ENST00000440076' => array(
'start' => '164321933',
'end' => '164322223',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CYP2C56P-001'
),
'ENST00000429636' => array(
'start' => '163749573',
'end' => '164352223',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC092684.1-001'
),
'ENST00000581574' => array(
'start' => '164423525',
'end' => '164423606',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC110086.1-201'
),
'ENSMUST00000102728' => array(
'start' => '63977337',
'end' => '64098038',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Fign-002'
),
'ENSMUST00000126042' => array(
'start' => '63980447',
'end' => '64097988',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fign-004'
),
'ENSMUST00000131615' => array(
'start' => '63971507',
'end' => '64098012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fign-001'
),
'ENSMUST00000153538' => array(
'start' => '63980616',
'end' => '64098010',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fign-003'
),
'ENSMUST00000120851' => array(
'start' => '64569863',
'end' => '64570640',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13576-001'
),
'ENSMUST00000121365' => array(
'start' => '64474745',
'end' => '64474957',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13577-001'
),
'ENSMUST00000120849' => array(
'start' => '64867999',
'end' => '64868588',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13578-001'
),
'ENSMUST00000142353' => array(
'start' => '64382602',
'end' => '64393860',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm13575-001'
),
'ENSDART00000023105' => array(
'start' => '52086531',
'end' => '52089435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'fign-201'
),
'ENSDART00000111381' => array(
'start' => '51926664',
'end' => '52019629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CABZ01053757.1-201'
),
'ENSDART00000121682' => array(
'start' => '51621835',
'end' => '51629141',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'COBLL1 (1 of 2)-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_0007KU_0001' => array(
'genes_in_region' => array(
'ENSG00000182263' => array(
[maximum depth reached]
),
'ENSG00000237844' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Ovary',
(int) 20 => 'Testis'
)
),
'CIL_0007KU_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000075324' => array(
[maximum depth reached]
),
'ENSMUSG00000082127' => array(
[maximum depth reached]
),
'ENSMUSG00000084104' => array(
[maximum depth reached]
),
'ENSMUSG00000087702' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Colon',
(int) 14 => 'Muscle',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Colon',
(int) 29 => 'Placenta',
(int) 30 => 'Brain',
(int) 31 => 'Liver',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Bladder',
(int) 35 => 'Brain',
(int) 36 => 'Liver',
(int) 37 => 'Placenta',
(int) 38 => 'Testis',
(int) 39 => 'Adipose'
)
),
'CIL_0007KU_0005' => array(
'genes_in_region' => array(
'ENSDARG00000008662' => array(
[maximum depth reached]
),
'ENSDARG00000079722' => array(
[maximum depth reached]
),
'ENSDARG00000088979' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Brain',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KU_0003',
'tax_id' => '7955',
'chromosome' => '23',
'seq_start' => '27372307',
'seq_end' => '27372476',
'region_length' => '169',
'region_type' => 'UCNEbase',
'el_id' => 'FIGN'
)
)
$gene_el = array(
'ENSMUST00000142353' => array(
'Adipose' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000087702'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.052',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000142353'
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
| Source ID |
Type |
Tax ID |
Position |
| FIGN |
UCNEbase |
7955 |
23:27372307-27372476  |
| Gene | Transcript | Position | Biotype |
|---|
(FIGN)