| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000000740-ENSMUSG00000034796 |
CGP |
10090 |
8:123102350-123135182  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0006AP_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_0006AP_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000030585' => 'ribosomal protein L13',
'ENSDARG00000037084' => 'copine VII',
'ENSDARG00000080268' => 'Small nucleolar RNA MBII-202',
'ENSDARG00000084186' => 'Small nucleolar RNA MBII-202',
'ENSDARG00000085320' => 'Small nucleolar RNA MBII-202',
'ENSG00000167526' => 'ribosomal protein L13',
'ENSG00000178773' => 'copine VII',
'ENSG00000200084' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000000740' => 'ribosomal protein L13',
'ENSMUSG00000034796' => 'copine VII',
'ENSMUSG00000064450' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000098550' => 'microRNA 7079',
'ENSMUSG00000098582' => 'microRNA 7080'
),
'gene_name_arr' => array(
'ENSDARG00000030585' => 'rpl13',
'ENSDARG00000037084' => 'CPNE7',
'ENSDARG00000080268' => 'snoMBII-202',
'ENSDARG00000084186' => 'snoMBII-202',
'ENSDARG00000085320' => 'snoMBII-202',
'ENSG00000167526' => 'RPL13',
'ENSG00000178773' => 'CPNE7',
'ENSG00000200084' => 'SNORD68',
'ENSMUSG00000000740' => 'Rpl13',
'ENSMUSG00000034796' => 'Cpne7',
'ENSMUSG00000064450' => 'Snord68',
'ENSMUSG00000098550' => 'Mir7079',
'ENSMUSG00000098582' => 'Mir7080'
),
'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) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 14 => 'Brain',
(int) 21 => 'Breast',
(int) 30 => 'Colon',
(int) 34 => 'Heart',
(int) 42 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 63 => 'Muscle',
(int) 69 => 'Ovary',
(int) 81 => 'Placenta',
(int) 89 => '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) 45,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000047391' => array(
'start' => '69521681',
'end' => '69531116',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'rpl13-001'
),
'ENSDART00000149628' => array(
'start' => '69521721',
'end' => '69527575',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'rpl13-002'
),
'ENSDART00000149670' => array(
'start' => '69522965',
'end' => '69527576',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'rpl13-003'
),
'ENSDART00000091052' => array(
'start' => '69548086',
'end' => '69648039',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-201'
),
'ENSDART00000155249' => array(
'start' => '69540786',
'end' => '69648797',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-001'
),
'ENSDART00000118328' => array(
'start' => '69527371',
'end' => '69527453',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.1-201'
),
'ENSDART00000119586' => array(
'start' => '69525336',
'end' => '69525417',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.2-201'
),
'ENSDART00000120720' => array(
'start' => '69530134',
'end' => '69530210',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.3-201'
),
'ENST00000311528' => array(
'start' => '89560657',
'end' => '89566828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-001'
),
'ENST00000393099' => array(
'start' => '89560711',
'end' => '89564542',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-002'
),
'ENST00000399461' => array(
'start' => '89560904',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-003'
),
'ENST00000452368' => array(
'start' => '89560683',
'end' => '89563952',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-015'
),
'ENST00000467736' => array(
'start' => '89560711',
'end' => '89561710',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-006'
),
'ENST00000472354' => array(
'start' => '89562370',
'end' => '89563438',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-008'
),
'ENST00000484610' => array(
'start' => '89560679',
'end' => '89563067',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-004'
),
'ENST00000487034' => array(
'start' => '89560682',
'end' => '89561523',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-007'
),
'ENST00000491523' => array(
'start' => '89560677',
'end' => '89562393',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-005'
),
'ENST00000562879' => array(
'start' => '89560682',
'end' => '89563473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'RPL13-011'
),
'ENST00000563270' => array(
'start' => '89560681',
'end' => '89563032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-016'
),
'ENST00000563749' => array(
'start' => '89560677',
'end' => '89563043',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-010'
),
'ENST00000565571' => array(
'start' => '89560683',
'end' => '89561849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-018'
),
'ENST00000567815' => array(
'start' => '89560681',
'end' => '89563080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-009'
),
'ENST00000570149' => array(
'start' => '89562140',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-017'
),
'ENST00000268720' => array(
'start' => '89575768',
'end' => '89597246',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-002'
),
'ENST00000319518' => array(
'start' => '89575791',
'end' => '89597246',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-001'
),
'ENST00000525982' => array(
'start' => '89575782',
'end' => '89583714',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPNE7-003'
),
'ENST00000526232' => array(
'start' => '89595576',
'end' => '89596849',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-006'
),
'ENST00000529800' => array(
'start' => '89587043',
'end' => '89595423',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-004'
),
'ENST00000532500' => array(
'start' => '89584821',
'end' => '89587732',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPNE7-005'
),
'ENST00000564421' => array(
'start' => '89595770',
'end' => '89596845',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPNE7-009'
),
'ENST00000566398' => array(
'start' => '89594100',
'end' => '89596859',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPNE7-008'
),
'ENST00000568977' => array(
'start' => '89588804',
'end' => '89596816',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPNE7-010'
),
'ENST00000363214' => array(
'start' => '89561434',
'end' => '89561517',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORD68-201'
),
'ENSMUST00000000756' => array(
'start' => '123102350',
'end' => '123105244',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Rpl13-001'
),
'ENSMUST00000129311' => array(
'start' => '123102653',
'end' => '123105244',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-002'
),
'ENSMUST00000132275' => array(
'start' => '123102653',
'end' => '123104464',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-004'
),
'ENSMUST00000152444' => array(
'start' => '123102651',
'end' => '123103641',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-003'
),
'ENSMUST00000037900' => array(
'start' => '123117378',
'end' => '123135182',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpne7-001'
),
'ENSMUST00000123191' => array(
'start' => '123126517',
'end' => '123127373',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cpne7-005'
),
'ENSMUST00000127431' => array(
'start' => '123128623',
'end' => '123131892',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-004'
),
'ENSMUST00000131659' => array(
'start' => '123117447',
'end' => '123135182',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-002'
),
'ENSMUST00000134235' => array(
'start' => '123117374',
'end' => '123135180',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-003'
),
'ENSMUST00000082516' => array(
'start' => '123103038',
'end' => '123103123',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Snord68-201'
),
'ENSMUST00000184697' => array(
'start' => '123104975',
'end' => '123105043',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7079-201'
),
'ENSMUST00000184815' => array(
'start' => '123130106',
'end' => '123130172',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7080-201'
)
),
'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_0006AP_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0006AP_0001' => array(
'genes_in_region' => array(
'ENSDARG00000030585' => array(
[maximum depth reached]
),
'ENSDARG00000037084' => array(
[maximum depth reached]
),
'ENSDARG00000084186' => array(
[maximum depth reached]
),
'ENSDARG00000085320' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Brain',
(int) 15 => 'Heart',
(int) 16 => 'Muscle',
(int) 17 => 'Liver',
(int) 18 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000030585' => 'ribosomal protein L13',
'ENSDARG00000037084' => 'copine VII',
'ENSDARG00000080268' => 'Small nucleolar RNA MBII-202',
'ENSDARG00000084186' => 'Small nucleolar RNA MBII-202',
'ENSDARG00000085320' => 'Small nucleolar RNA MBII-202',
'ENSG00000167526' => 'ribosomal protein L13',
'ENSG00000178773' => 'copine VII',
'ENSG00000200084' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000000740' => 'ribosomal protein L13',
'ENSMUSG00000034796' => 'copine VII',
'ENSMUSG00000064450' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000098550' => 'microRNA 7079',
'ENSMUSG00000098582' => 'microRNA 7080'
)
$gene_name_arr = array(
'ENSDARG00000030585' => 'rpl13',
'ENSDARG00000037084' => 'CPNE7',
'ENSDARG00000080268' => 'snoMBII-202',
'ENSDARG00000084186' => 'snoMBII-202',
'ENSDARG00000085320' => 'snoMBII-202',
'ENSG00000167526' => 'RPL13',
'ENSG00000178773' => 'CPNE7',
'ENSG00000200084' => 'SNORD68',
'ENSMUSG00000000740' => 'Rpl13',
'ENSMUSG00000034796' => 'Cpne7',
'ENSMUSG00000064450' => 'Snord68',
'ENSMUSG00000098550' => 'Mir7079',
'ENSMUSG00000098582' => 'Mir7080'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AP_0001',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '69521681',
'seq_end' => '69648797',
'region_length' => '127116',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000030585-ENSDARG00000037084'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AP_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89560657',
'seq_end' => '89597246',
'region_length' => '36589',
'region_type' => 'CGP',
'el_id' => 'ENSG00000167526-ENSG00000178773'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AP_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123102350',
'seq_end' => '123135182',
'region_length' => '32832',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000740-ENSMUSG00000034796'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 14 => 'Brain',
(int) 21 => 'Breast',
(int) 30 => 'Colon',
(int) 34 => 'Heart',
(int) 42 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 63 => 'Muscle',
(int) 69 => 'Ovary',
(int) 81 => 'Placenta',
(int) 89 => '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) 45
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000047391' => array(
'start' => '69521681',
'end' => '69531116',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'rpl13-001'
),
'ENSDART00000149628' => array(
'start' => '69521721',
'end' => '69527575',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'rpl13-002'
),
'ENSDART00000149670' => array(
'start' => '69522965',
'end' => '69527576',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'rpl13-003'
),
'ENSDART00000091052' => array(
'start' => '69548086',
'end' => '69648039',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-201'
),
'ENSDART00000155249' => array(
'start' => '69540786',
'end' => '69648797',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-001'
),
'ENSDART00000118328' => array(
'start' => '69527371',
'end' => '69527453',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.1-201'
),
'ENSDART00000119586' => array(
'start' => '69525336',
'end' => '69525417',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.2-201'
),
'ENSDART00000120720' => array(
'start' => '69530134',
'end' => '69530210',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.3-201'
),
'ENST00000311528' => array(
'start' => '89560657',
'end' => '89566828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-001'
),
'ENST00000393099' => array(
'start' => '89560711',
'end' => '89564542',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-002'
),
'ENST00000399461' => array(
'start' => '89560904',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-003'
),
'ENST00000452368' => array(
'start' => '89560683',
'end' => '89563952',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-015'
),
'ENST00000467736' => array(
'start' => '89560711',
'end' => '89561710',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-006'
),
'ENST00000472354' => array(
'start' => '89562370',
'end' => '89563438',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-008'
),
'ENST00000484610' => array(
'start' => '89560679',
'end' => '89563067',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-004'
),
'ENST00000487034' => array(
'start' => '89560682',
'end' => '89561523',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-007'
),
'ENST00000491523' => array(
'start' => '89560677',
'end' => '89562393',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-005'
),
'ENST00000562879' => array(
'start' => '89560682',
'end' => '89563473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'RPL13-011'
),
'ENST00000563270' => array(
'start' => '89560681',
'end' => '89563032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-016'
),
'ENST00000563749' => array(
'start' => '89560677',
'end' => '89563043',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-010'
),
'ENST00000565571' => array(
'start' => '89560683',
'end' => '89561849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-018'
),
'ENST00000567815' => array(
'start' => '89560681',
'end' => '89563080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-009'
),
'ENST00000570149' => array(
'start' => '89562140',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-017'
),
'ENST00000268720' => array(
'start' => '89575768',
'end' => '89597246',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-002'
),
'ENST00000319518' => array(
'start' => '89575791',
'end' => '89597246',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-001'
),
'ENST00000525982' => array(
'start' => '89575782',
'end' => '89583714',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPNE7-003'
),
'ENST00000526232' => array(
'start' => '89595576',
'end' => '89596849',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-006'
),
'ENST00000529800' => array(
'start' => '89587043',
'end' => '89595423',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-004'
),
'ENST00000532500' => array(
'start' => '89584821',
'end' => '89587732',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPNE7-005'
),
'ENST00000564421' => array(
'start' => '89595770',
'end' => '89596845',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPNE7-009'
),
'ENST00000566398' => array(
'start' => '89594100',
'end' => '89596859',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPNE7-008'
),
'ENST00000568977' => array(
'start' => '89588804',
'end' => '89596816',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPNE7-010'
),
'ENST00000363214' => array(
'start' => '89561434',
'end' => '89561517',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORD68-201'
),
'ENSMUST00000000756' => array(
'start' => '123102350',
'end' => '123105244',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Rpl13-001'
),
'ENSMUST00000129311' => array(
'start' => '123102653',
'end' => '123105244',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-002'
),
'ENSMUST00000132275' => array(
'start' => '123102653',
'end' => '123104464',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-004'
),
'ENSMUST00000152444' => array(
'start' => '123102651',
'end' => '123103641',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-003'
),
'ENSMUST00000037900' => array(
'start' => '123117378',
'end' => '123135182',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpne7-001'
),
'ENSMUST00000123191' => array(
'start' => '123126517',
'end' => '123127373',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cpne7-005'
),
'ENSMUST00000127431' => array(
'start' => '123128623',
'end' => '123131892',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-004'
),
'ENSMUST00000131659' => array(
'start' => '123117447',
'end' => '123135182',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-002'
),
'ENSMUST00000134235' => array(
'start' => '123117374',
'end' => '123135180',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-003'
),
'ENSMUST00000082516' => array(
'start' => '123103038',
'end' => '123103123',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Snord68-201'
),
'ENSMUST00000184697' => array(
'start' => '123104975',
'end' => '123105043',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7079-201'
),
'ENSMUST00000184815' => array(
'start' => '123130106',
'end' => '123130172',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7080-201'
)
)
$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_0006AP_0001' => array(
'genes_in_region' => array(
'ENSDARG00000030585' => array(
[maximum depth reached]
),
'ENSDARG00000037084' => array(
[maximum depth reached]
),
'ENSDARG00000084186' => array(
[maximum depth reached]
),
'ENSDARG00000085320' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Brain',
(int) 15 => 'Heart',
(int) 16 => 'Muscle',
(int) 17 => 'Liver',
(int) 18 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AP_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123102350',
'seq_end' => '123135182',
'region_length' => '32832',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000740-ENSMUSG00000034796'
)
)
$gene_el = array(
'ENSDART00000120720' => array(
'Heart' => array(
'average_FPKM' => '4.550',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000085320'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '4.550',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000120720'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0006AP_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000030585' => 'ribosomal protein L13',
'ENSDARG00000037084' => 'copine VII',
'ENSDARG00000080268' => 'Small nucleolar RNA MBII-202',
'ENSDARG00000084186' => 'Small nucleolar RNA MBII-202',
'ENSDARG00000085320' => 'Small nucleolar RNA MBII-202',
'ENSG00000167526' => 'ribosomal protein L13',
'ENSG00000178773' => 'copine VII',
'ENSG00000200084' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000000740' => 'ribosomal protein L13',
'ENSMUSG00000034796' => 'copine VII',
'ENSMUSG00000064450' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000098550' => 'microRNA 7079',
'ENSMUSG00000098582' => 'microRNA 7080'
),
'gene_name_arr' => array(
'ENSDARG00000030585' => 'rpl13',
'ENSDARG00000037084' => 'CPNE7',
'ENSDARG00000080268' => 'snoMBII-202',
'ENSDARG00000084186' => 'snoMBII-202',
'ENSDARG00000085320' => 'snoMBII-202',
'ENSG00000167526' => 'RPL13',
'ENSG00000178773' => 'CPNE7',
'ENSG00000200084' => 'SNORD68',
'ENSMUSG00000000740' => 'Rpl13',
'ENSMUSG00000034796' => 'Cpne7',
'ENSMUSG00000064450' => 'Snord68',
'ENSMUSG00000098550' => 'Mir7079',
'ENSMUSG00000098582' => 'Mir7080'
),
'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) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 14 => 'Brain',
(int) 21 => 'Breast',
(int) 30 => 'Colon',
(int) 34 => 'Heart',
(int) 42 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 63 => 'Muscle',
(int) 69 => 'Ovary',
(int) 81 => 'Placenta',
(int) 89 => '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) 45,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000047391' => array(
'start' => '69521681',
'end' => '69531116',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'rpl13-001'
),
'ENSDART00000149628' => array(
'start' => '69521721',
'end' => '69527575',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'rpl13-002'
),
'ENSDART00000149670' => array(
'start' => '69522965',
'end' => '69527576',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'rpl13-003'
),
'ENSDART00000091052' => array(
'start' => '69548086',
'end' => '69648039',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-201'
),
'ENSDART00000155249' => array(
'start' => '69540786',
'end' => '69648797',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-001'
),
'ENSDART00000118328' => array(
'start' => '69527371',
'end' => '69527453',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.1-201'
),
'ENSDART00000119586' => array(
'start' => '69525336',
'end' => '69525417',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.2-201'
),
'ENSDART00000120720' => array(
'start' => '69530134',
'end' => '69530210',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.3-201'
),
'ENST00000311528' => array(
'start' => '89560657',
'end' => '89566828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-001'
),
'ENST00000393099' => array(
'start' => '89560711',
'end' => '89564542',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-002'
),
'ENST00000399461' => array(
'start' => '89560904',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-003'
),
'ENST00000452368' => array(
'start' => '89560683',
'end' => '89563952',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-015'
),
'ENST00000467736' => array(
'start' => '89560711',
'end' => '89561710',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-006'
),
'ENST00000472354' => array(
'start' => '89562370',
'end' => '89563438',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-008'
),
'ENST00000484610' => array(
'start' => '89560679',
'end' => '89563067',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-004'
),
'ENST00000487034' => array(
'start' => '89560682',
'end' => '89561523',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-007'
),
'ENST00000491523' => array(
'start' => '89560677',
'end' => '89562393',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-005'
),
'ENST00000562879' => array(
'start' => '89560682',
'end' => '89563473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'RPL13-011'
),
'ENST00000563270' => array(
'start' => '89560681',
'end' => '89563032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-016'
),
'ENST00000563749' => array(
'start' => '89560677',
'end' => '89563043',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-010'
),
'ENST00000565571' => array(
'start' => '89560683',
'end' => '89561849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-018'
),
'ENST00000567815' => array(
'start' => '89560681',
'end' => '89563080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-009'
),
'ENST00000570149' => array(
'start' => '89562140',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-017'
),
'ENST00000268720' => array(
'start' => '89575768',
'end' => '89597246',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-002'
),
'ENST00000319518' => array(
'start' => '89575791',
'end' => '89597246',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-001'
),
'ENST00000525982' => array(
'start' => '89575782',
'end' => '89583714',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPNE7-003'
),
'ENST00000526232' => array(
'start' => '89595576',
'end' => '89596849',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-006'
),
'ENST00000529800' => array(
'start' => '89587043',
'end' => '89595423',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-004'
),
'ENST00000532500' => array(
'start' => '89584821',
'end' => '89587732',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPNE7-005'
),
'ENST00000564421' => array(
'start' => '89595770',
'end' => '89596845',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPNE7-009'
),
'ENST00000566398' => array(
'start' => '89594100',
'end' => '89596859',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPNE7-008'
),
'ENST00000568977' => array(
'start' => '89588804',
'end' => '89596816',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPNE7-010'
),
'ENST00000363214' => array(
'start' => '89561434',
'end' => '89561517',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORD68-201'
),
'ENSMUST00000000756' => array(
'start' => '123102350',
'end' => '123105244',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Rpl13-001'
),
'ENSMUST00000129311' => array(
'start' => '123102653',
'end' => '123105244',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-002'
),
'ENSMUST00000132275' => array(
'start' => '123102653',
'end' => '123104464',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-004'
),
'ENSMUST00000152444' => array(
'start' => '123102651',
'end' => '123103641',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-003'
),
'ENSMUST00000037900' => array(
'start' => '123117378',
'end' => '123135182',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpne7-001'
),
'ENSMUST00000123191' => array(
'start' => '123126517',
'end' => '123127373',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cpne7-005'
),
'ENSMUST00000127431' => array(
'start' => '123128623',
'end' => '123131892',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-004'
),
'ENSMUST00000131659' => array(
'start' => '123117447',
'end' => '123135182',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-002'
),
'ENSMUST00000134235' => array(
'start' => '123117374',
'end' => '123135180',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-003'
),
'ENSMUST00000082516' => array(
'start' => '123103038',
'end' => '123103123',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Snord68-201'
),
'ENSMUST00000184697' => array(
'start' => '123104975',
'end' => '123105043',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7079-201'
),
'ENSMUST00000184815' => array(
'start' => '123130106',
'end' => '123130172',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7080-201'
)
),
'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_0006AP_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0006AP_0001' => array(
'genes_in_region' => array(
'ENSDARG00000030585' => array(
[maximum depth reached]
),
'ENSDARG00000037084' => array(
[maximum depth reached]
),
'ENSDARG00000084186' => array(
[maximum depth reached]
),
'ENSDARG00000085320' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Brain',
(int) 15 => 'Heart',
(int) 16 => 'Muscle',
(int) 17 => 'Liver',
(int) 18 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000030585' => 'ribosomal protein L13',
'ENSDARG00000037084' => 'copine VII',
'ENSDARG00000080268' => 'Small nucleolar RNA MBII-202',
'ENSDARG00000084186' => 'Small nucleolar RNA MBII-202',
'ENSDARG00000085320' => 'Small nucleolar RNA MBII-202',
'ENSG00000167526' => 'ribosomal protein L13',
'ENSG00000178773' => 'copine VII',
'ENSG00000200084' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000000740' => 'ribosomal protein L13',
'ENSMUSG00000034796' => 'copine VII',
'ENSMUSG00000064450' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000098550' => 'microRNA 7079',
'ENSMUSG00000098582' => 'microRNA 7080'
)
$gene_name_arr = array(
'ENSDARG00000030585' => 'rpl13',
'ENSDARG00000037084' => 'CPNE7',
'ENSDARG00000080268' => 'snoMBII-202',
'ENSDARG00000084186' => 'snoMBII-202',
'ENSDARG00000085320' => 'snoMBII-202',
'ENSG00000167526' => 'RPL13',
'ENSG00000178773' => 'CPNE7',
'ENSG00000200084' => 'SNORD68',
'ENSMUSG00000000740' => 'Rpl13',
'ENSMUSG00000034796' => 'Cpne7',
'ENSMUSG00000064450' => 'Snord68',
'ENSMUSG00000098550' => 'Mir7079',
'ENSMUSG00000098582' => 'Mir7080'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AP_0001',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '69521681',
'seq_end' => '69648797',
'region_length' => '127116',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000030585-ENSDARG00000037084'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AP_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89560657',
'seq_end' => '89597246',
'region_length' => '36589',
'region_type' => 'CGP',
'el_id' => 'ENSG00000167526-ENSG00000178773'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AP_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123102350',
'seq_end' => '123135182',
'region_length' => '32832',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000740-ENSMUSG00000034796'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 14 => 'Brain',
(int) 21 => 'Breast',
(int) 30 => 'Colon',
(int) 34 => 'Heart',
(int) 42 => 'Kidney',
(int) 51 => 'Liver',
(int) 59 => 'Lung',
(int) 63 => 'Muscle',
(int) 69 => 'Ovary',
(int) 81 => 'Placenta',
(int) 89 => '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) 45
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000047391' => array(
'start' => '69521681',
'end' => '69531116',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'rpl13-001'
),
'ENSDART00000149628' => array(
'start' => '69521721',
'end' => '69527575',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'rpl13-002'
),
'ENSDART00000149670' => array(
'start' => '69522965',
'end' => '69527576',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'rpl13-003'
),
'ENSDART00000091052' => array(
'start' => '69548086',
'end' => '69648039',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-201'
),
'ENSDART00000155249' => array(
'start' => '69540786',
'end' => '69648797',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-001'
),
'ENSDART00000118328' => array(
'start' => '69527371',
'end' => '69527453',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.1-201'
),
'ENSDART00000119586' => array(
'start' => '69525336',
'end' => '69525417',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.2-201'
),
'ENSDART00000120720' => array(
'start' => '69530134',
'end' => '69530210',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'snoMBII-202.3-201'
),
'ENST00000311528' => array(
'start' => '89560657',
'end' => '89566828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-001'
),
'ENST00000393099' => array(
'start' => '89560711',
'end' => '89564542',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-002'
),
'ENST00000399461' => array(
'start' => '89560904',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-003'
),
'ENST00000452368' => array(
'start' => '89560683',
'end' => '89563952',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-015'
),
'ENST00000467736' => array(
'start' => '89560711',
'end' => '89561710',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-006'
),
'ENST00000472354' => array(
'start' => '89562370',
'end' => '89563438',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-008'
),
'ENST00000484610' => array(
'start' => '89560679',
'end' => '89563067',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-004'
),
'ENST00000487034' => array(
'start' => '89560682',
'end' => '89561523',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-007'
),
'ENST00000491523' => array(
'start' => '89560677',
'end' => '89562393',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-005'
),
'ENST00000562879' => array(
'start' => '89560682',
'end' => '89563473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'RPL13-011'
),
'ENST00000563270' => array(
'start' => '89560681',
'end' => '89563032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-016'
),
'ENST00000563749' => array(
'start' => '89560677',
'end' => '89563043',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-010'
),
'ENST00000565571' => array(
'start' => '89560683',
'end' => '89561849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-018'
),
'ENST00000567815' => array(
'start' => '89560681',
'end' => '89563080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-009'
),
'ENST00000570149' => array(
'start' => '89562140',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-017'
),
'ENST00000268720' => array(
'start' => '89575768',
'end' => '89597246',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-002'
),
'ENST00000319518' => array(
'start' => '89575791',
'end' => '89597246',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-001'
),
'ENST00000525982' => array(
'start' => '89575782',
'end' => '89583714',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPNE7-003'
),
'ENST00000526232' => array(
'start' => '89595576',
'end' => '89596849',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-006'
),
'ENST00000529800' => array(
'start' => '89587043',
'end' => '89595423',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPNE7-004'
),
'ENST00000532500' => array(
'start' => '89584821',
'end' => '89587732',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPNE7-005'
),
'ENST00000564421' => array(
'start' => '89595770',
'end' => '89596845',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPNE7-009'
),
'ENST00000566398' => array(
'start' => '89594100',
'end' => '89596859',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CPNE7-008'
),
'ENST00000568977' => array(
'start' => '89588804',
'end' => '89596816',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CPNE7-010'
),
'ENST00000363214' => array(
'start' => '89561434',
'end' => '89561517',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORD68-201'
),
'ENSMUST00000000756' => array(
'start' => '123102350',
'end' => '123105244',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Rpl13-001'
),
'ENSMUST00000129311' => array(
'start' => '123102653',
'end' => '123105244',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-002'
),
'ENSMUST00000132275' => array(
'start' => '123102653',
'end' => '123104464',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-004'
),
'ENSMUST00000152444' => array(
'start' => '123102651',
'end' => '123103641',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-003'
),
'ENSMUST00000037900' => array(
'start' => '123117378',
'end' => '123135182',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpne7-001'
),
'ENSMUST00000123191' => array(
'start' => '123126517',
'end' => '123127373',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cpne7-005'
),
'ENSMUST00000127431' => array(
'start' => '123128623',
'end' => '123131892',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-004'
),
'ENSMUST00000131659' => array(
'start' => '123117447',
'end' => '123135182',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-002'
),
'ENSMUST00000134235' => array(
'start' => '123117374',
'end' => '123135180',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cpne7-003'
),
'ENSMUST00000082516' => array(
'start' => '123103038',
'end' => '123103123',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Snord68-201'
),
'ENSMUST00000184697' => array(
'start' => '123104975',
'end' => '123105043',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7079-201'
),
'ENSMUST00000184815' => array(
'start' => '123130106',
'end' => '123130172',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7080-201'
)
)
$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_0006AP_0001' => array(
'genes_in_region' => array(
'ENSDARG00000030585' => array(
[maximum depth reached]
),
'ENSDARG00000037084' => array(
[maximum depth reached]
),
'ENSDARG00000084186' => array(
[maximum depth reached]
),
'ENSDARG00000085320' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Brain',
(int) 15 => 'Heart',
(int) 16 => 'Muscle',
(int) 17 => 'Liver',
(int) 18 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AP_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123102350',
'seq_end' => '123135182',
'region_length' => '32832',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000740-ENSMUSG00000034796'
)
)
$gene_el = array(
'ENSDART00000120720' => array(
'Heart' => array(
'average_FPKM' => '4.550',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000085320'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '4.550',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000120720'
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
(rpl13)