| Source ID |
Type |
Tax ID |
Position |
| EN1 |
UCNEbase |
7955 |
1:6591069-6597708  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007KO_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_0007KO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000125629' => 'insulin induced gene 2',
'ENSG00000226856' => null,
'ENSMUSG00000003721' => 'insulin induced gene 2',
'ENSMUSG00000097881' => 'cerebellum expressed regulatory RNA',
'ENSMUSG00000101700' => 'predicted gene 29359',
'ENSMUSG00000101791' => 'RIKEN cDNA 2210011K15 gene'
),
'gene_name_arr' => array(
'ENSG00000125629' => 'INSIG2',
'ENSG00000226856' => 'AC093901.1',
'ENSMUSG00000003721' => 'Insig2',
'ENSMUSG00000097881' => 'Celrr',
'ENSMUSG00000101700' => 'RP23-36O22.1',
'ENSMUSG00000101791' => 'RP24-98O21.6'
),
'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) 11 => 'Bladder',
(int) 16 => 'Brain',
(int) 24 => 'Breast',
(int) 28 => 'Colon',
(int) 34 => 'Heart',
(int) 37 => 'Kidney',
(int) 44 => 'Liver',
(int) 50 => 'Lung',
(int) 54 => 'Muscle',
(int) 58 => 'Ovary',
(int) 67 => 'Placenta',
(int) 76 => '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) 31,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000245787' => array(
'start' => '118088474',
'end' => '118110028',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'INSIG2-001'
),
'ENST00000411929' => array(
'start' => '118088452',
'end' => '118108372',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'INSIG2-007'
),
'ENST00000467223' => array(
'start' => '118088550',
'end' => '118108390',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-004'
),
'ENST00000471186' => array(
'start' => '118088474',
'end' => '118110020',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-003'
),
'ENST00000479999' => array(
'start' => '118106659',
'end' => '118108467',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-006'
),
'ENST00000485520' => array(
'start' => '118088474',
'end' => '118110997',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-002'
),
'ENST00000488995' => array(
'start' => '118102538',
'end' => '118107142',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-005'
),
'ENST00000614681' => array(
'start' => '118096418',
'end' => '118108853',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'INSIG2-201'
),
'ENST00000414886' => array(
'start' => '118132128',
'end' => '118186386',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-001'
),
'ENST00000449075' => array(
'start' => '118182939',
'end' => '118186373',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-002'
),
'ENST00000449819' => array(
'start' => '118183021',
'end' => '118186386',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-003'
),
'ENSMUST00000003818' => array(
'start' => '121304353',
'end' => '121328024',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-002'
),
'ENSMUST00000071064' => array(
'start' => '121305522',
'end' => '121332589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-001'
),
'ENSMUST00000159085' => array(
'start' => '121305555',
'end' => '121327678',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-004'
),
'ENSMUST00000159125' => array(
'start' => '121319664',
'end' => '121327682',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-010'
),
'ENSMUST00000159192' => array(
'start' => '121306880',
'end' => '121312414',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-013'
),
'ENSMUST00000159528' => array(
'start' => '121305893',
'end' => '121307318',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-003'
),
'ENSMUST00000160688' => array(
'start' => '121305924',
'end' => '121327793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-007'
),
'ENSMUST00000160968' => array(
'start' => '121305538',
'end' => '121327746',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-005'
),
'ENSMUST00000161068' => array(
'start' => '121319761',
'end' => '121332550',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-006'
),
'ENSMUST00000161818' => array(
'start' => '121319734',
'end' => '121327688',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-009'
),
'ENSMUST00000162019' => array(
'start' => '121311845',
'end' => '121319728',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-012'
),
'ENSMUST00000162582' => array(
'start' => '121306937',
'end' => '121327765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-008'
),
'ENSMUST00000162790' => array(
'start' => '121307237',
'end' => '121323191',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-011'
),
'ENSMUST00000186915' => array(
'start' => '121305695',
'end' => '121327719',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-014'
),
'ENSMUST00000181183' => array(
'start' => '121087529',
'end' => '121088932',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-003'
),
'ENSMUST00000181433' => array(
'start' => '121087405',
'end' => '121120956',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-001'
),
'ENSMUST00000185678' => array(
'start' => '121087474',
'end' => '121178441',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-002'
),
'ENSMUST00000190612' => array(
'start' => '121087471',
'end' => '121117760',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-004'
),
'ENSMUST00000191007' => array(
'start' => '121224276',
'end' => '121227526',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-36O22.1-001'
),
'ENSMUST00000190690' => array(
'start' => '121355116',
'end' => '121359900',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-98O21.6-001'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0007KO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007KO_0001' => array(
'genes_in_region' => array(
'ENSG00000125629' => array(
[maximum depth reached]
),
'ENSG00000226856' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Colon',
(int) 16 => 'Adipose',
(int) 17 => 'Adrenal',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Colon',
(int) 21 => 'Heart',
(int) 22 => 'Kidney',
(int) 23 => 'Lung',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis',
(int) 31 => 'Breast',
(int) 32 => 'Liver',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Adrenal',
(int) 36 => 'Liver',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Ovary',
(int) 43 => 'Testis'
)
),
'CIL_0007KO_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000003721' => array(
[maximum depth reached]
),
'ENSMUSG00000097881' => array(
[maximum depth reached]
),
'ENSMUSG00000101700' => array(
[maximum depth reached]
),
'ENSMUSG00000101791' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Lung',
(int) 18 => 'Testis',
(int) 19 => 'Brain',
(int) 20 => 'Kidney',
(int) 21 => 'Adipose',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Ovary',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Testis',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Liver',
(int) 33 => 'Testis',
(int) 34 => 'Adipose',
(int) 35 => 'Bladder',
(int) 36 => 'Brain',
(int) 37 => 'Colon',
(int) 38 => 'Kidney',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000125629' => 'insulin induced gene 2',
'ENSG00000226856' => null,
'ENSMUSG00000003721' => 'insulin induced gene 2',
'ENSMUSG00000097881' => 'cerebellum expressed regulatory RNA',
'ENSMUSG00000101700' => 'predicted gene 29359',
'ENSMUSG00000101791' => 'RIKEN cDNA 2210011K15 gene'
)
$gene_name_arr = array(
'ENSG00000125629' => 'INSIG2',
'ENSG00000226856' => 'AC093901.1',
'ENSMUSG00000003721' => 'Insig2',
'ENSMUSG00000097881' => 'Celrr',
'ENSMUSG00000101700' => 'RP23-36O22.1',
'ENSMUSG00000101791' => 'RP24-98O21.6'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KO_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '118051989',
'seq_end' => '118547477',
'region_length' => '495488',
'region_type' => 'UCNEbase',
'el_id' => 'EN1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KO_0002',
'tax_id' => '10090',
'chromosome' => '1',
'seq_start' => '120886247',
'seq_end' => '121392907',
'region_length' => '506660',
'region_type' => 'UCNEbase',
'el_id' => 'EN1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KO_0003',
'tax_id' => '7955',
'chromosome' => '1',
'seq_start' => '6591069',
'seq_end' => '6597708',
'region_length' => '6639',
'region_type' => 'UCNEbase',
'el_id' => 'EN1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 16 => 'Brain',
(int) 24 => 'Breast',
(int) 28 => 'Colon',
(int) 34 => 'Heart',
(int) 37 => 'Kidney',
(int) 44 => 'Liver',
(int) 50 => 'Lung',
(int) 54 => 'Muscle',
(int) 58 => 'Ovary',
(int) 67 => 'Placenta',
(int) 76 => '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) 31
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000245787' => array(
'start' => '118088474',
'end' => '118110028',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'INSIG2-001'
),
'ENST00000411929' => array(
'start' => '118088452',
'end' => '118108372',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'INSIG2-007'
),
'ENST00000467223' => array(
'start' => '118088550',
'end' => '118108390',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-004'
),
'ENST00000471186' => array(
'start' => '118088474',
'end' => '118110020',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-003'
),
'ENST00000479999' => array(
'start' => '118106659',
'end' => '118108467',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-006'
),
'ENST00000485520' => array(
'start' => '118088474',
'end' => '118110997',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-002'
),
'ENST00000488995' => array(
'start' => '118102538',
'end' => '118107142',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-005'
),
'ENST00000614681' => array(
'start' => '118096418',
'end' => '118108853',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'INSIG2-201'
),
'ENST00000414886' => array(
'start' => '118132128',
'end' => '118186386',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-001'
),
'ENST00000449075' => array(
'start' => '118182939',
'end' => '118186373',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-002'
),
'ENST00000449819' => array(
'start' => '118183021',
'end' => '118186386',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-003'
),
'ENSMUST00000003818' => array(
'start' => '121304353',
'end' => '121328024',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-002'
),
'ENSMUST00000071064' => array(
'start' => '121305522',
'end' => '121332589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-001'
),
'ENSMUST00000159085' => array(
'start' => '121305555',
'end' => '121327678',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-004'
),
'ENSMUST00000159125' => array(
'start' => '121319664',
'end' => '121327682',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-010'
),
'ENSMUST00000159192' => array(
'start' => '121306880',
'end' => '121312414',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-013'
),
'ENSMUST00000159528' => array(
'start' => '121305893',
'end' => '121307318',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-003'
),
'ENSMUST00000160688' => array(
'start' => '121305924',
'end' => '121327793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-007'
),
'ENSMUST00000160968' => array(
'start' => '121305538',
'end' => '121327746',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-005'
),
'ENSMUST00000161068' => array(
'start' => '121319761',
'end' => '121332550',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-006'
),
'ENSMUST00000161818' => array(
'start' => '121319734',
'end' => '121327688',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-009'
),
'ENSMUST00000162019' => array(
'start' => '121311845',
'end' => '121319728',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-012'
),
'ENSMUST00000162582' => array(
'start' => '121306937',
'end' => '121327765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-008'
),
'ENSMUST00000162790' => array(
'start' => '121307237',
'end' => '121323191',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-011'
),
'ENSMUST00000186915' => array(
'start' => '121305695',
'end' => '121327719',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-014'
),
'ENSMUST00000181183' => array(
'start' => '121087529',
'end' => '121088932',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-003'
),
'ENSMUST00000181433' => array(
'start' => '121087405',
'end' => '121120956',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-001'
),
'ENSMUST00000185678' => array(
'start' => '121087474',
'end' => '121178441',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-002'
),
'ENSMUST00000190612' => array(
'start' => '121087471',
'end' => '121117760',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-004'
),
'ENSMUST00000191007' => array(
'start' => '121224276',
'end' => '121227526',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-36O22.1-001'
),
'ENSMUST00000190690' => array(
'start' => '121355116',
'end' => '121359900',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-98O21.6-001'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0007KO_0001' => array(
'genes_in_region' => array(
'ENSG00000125629' => array(
[maximum depth reached]
),
'ENSG00000226856' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Colon',
(int) 16 => 'Adipose',
(int) 17 => 'Adrenal',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Colon',
(int) 21 => 'Heart',
(int) 22 => 'Kidney',
(int) 23 => 'Lung',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis',
(int) 31 => 'Breast',
(int) 32 => 'Liver',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Adrenal',
(int) 36 => 'Liver',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Ovary',
(int) 43 => 'Testis'
)
),
'CIL_0007KO_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000003721' => array(
[maximum depth reached]
),
'ENSMUSG00000097881' => array(
[maximum depth reached]
),
'ENSMUSG00000101700' => array(
[maximum depth reached]
),
'ENSMUSG00000101791' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Lung',
(int) 18 => 'Testis',
(int) 19 => 'Brain',
(int) 20 => 'Kidney',
(int) 21 => 'Adipose',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Ovary',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Testis',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Liver',
(int) 33 => 'Testis',
(int) 34 => 'Adipose',
(int) 35 => 'Bladder',
(int) 36 => 'Brain',
(int) 37 => 'Colon',
(int) 38 => 'Kidney',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KO_0003',
'tax_id' => '7955',
'chromosome' => '1',
'seq_start' => '6591069',
'seq_end' => '6597708',
'region_length' => '6639',
'region_type' => 'UCNEbase',
'el_id' => 'EN1'
)
)
$gene_el = array(
'ENSMUST00000190690' => array(
'Adipose' => array(
'average_FPKM' => '0.021',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.014',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.035',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.37'
),
'Kidney' => array(
'average_FPKM' => '0.022',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.013',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.016',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.157',
'stddev_FPKM' => '0.09'
),
'Testis' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000101791'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.021',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.014',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.035',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.37'
),
'Kidney' => array(
'average_FPKM' => '0.022',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.013',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.016',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.157',
'stddev_FPKM' => '0.09'
),
'Testis' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000190690'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007KO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000125629' => 'insulin induced gene 2',
'ENSG00000226856' => null,
'ENSMUSG00000003721' => 'insulin induced gene 2',
'ENSMUSG00000097881' => 'cerebellum expressed regulatory RNA',
'ENSMUSG00000101700' => 'predicted gene 29359',
'ENSMUSG00000101791' => 'RIKEN cDNA 2210011K15 gene'
),
'gene_name_arr' => array(
'ENSG00000125629' => 'INSIG2',
'ENSG00000226856' => 'AC093901.1',
'ENSMUSG00000003721' => 'Insig2',
'ENSMUSG00000097881' => 'Celrr',
'ENSMUSG00000101700' => 'RP23-36O22.1',
'ENSMUSG00000101791' => 'RP24-98O21.6'
),
'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) 11 => 'Bladder',
(int) 16 => 'Brain',
(int) 24 => 'Breast',
(int) 28 => 'Colon',
(int) 34 => 'Heart',
(int) 37 => 'Kidney',
(int) 44 => 'Liver',
(int) 50 => 'Lung',
(int) 54 => 'Muscle',
(int) 58 => 'Ovary',
(int) 67 => 'Placenta',
(int) 76 => '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) 31,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000245787' => array(
'start' => '118088474',
'end' => '118110028',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'INSIG2-001'
),
'ENST00000411929' => array(
'start' => '118088452',
'end' => '118108372',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'INSIG2-007'
),
'ENST00000467223' => array(
'start' => '118088550',
'end' => '118108390',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-004'
),
'ENST00000471186' => array(
'start' => '118088474',
'end' => '118110020',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-003'
),
'ENST00000479999' => array(
'start' => '118106659',
'end' => '118108467',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-006'
),
'ENST00000485520' => array(
'start' => '118088474',
'end' => '118110997',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-002'
),
'ENST00000488995' => array(
'start' => '118102538',
'end' => '118107142',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-005'
),
'ENST00000614681' => array(
'start' => '118096418',
'end' => '118108853',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'INSIG2-201'
),
'ENST00000414886' => array(
'start' => '118132128',
'end' => '118186386',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-001'
),
'ENST00000449075' => array(
'start' => '118182939',
'end' => '118186373',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-002'
),
'ENST00000449819' => array(
'start' => '118183021',
'end' => '118186386',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-003'
),
'ENSMUST00000003818' => array(
'start' => '121304353',
'end' => '121328024',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-002'
),
'ENSMUST00000071064' => array(
'start' => '121305522',
'end' => '121332589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-001'
),
'ENSMUST00000159085' => array(
'start' => '121305555',
'end' => '121327678',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-004'
),
'ENSMUST00000159125' => array(
'start' => '121319664',
'end' => '121327682',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-010'
),
'ENSMUST00000159192' => array(
'start' => '121306880',
'end' => '121312414',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-013'
),
'ENSMUST00000159528' => array(
'start' => '121305893',
'end' => '121307318',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-003'
),
'ENSMUST00000160688' => array(
'start' => '121305924',
'end' => '121327793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-007'
),
'ENSMUST00000160968' => array(
'start' => '121305538',
'end' => '121327746',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-005'
),
'ENSMUST00000161068' => array(
'start' => '121319761',
'end' => '121332550',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-006'
),
'ENSMUST00000161818' => array(
'start' => '121319734',
'end' => '121327688',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-009'
),
'ENSMUST00000162019' => array(
'start' => '121311845',
'end' => '121319728',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-012'
),
'ENSMUST00000162582' => array(
'start' => '121306937',
'end' => '121327765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-008'
),
'ENSMUST00000162790' => array(
'start' => '121307237',
'end' => '121323191',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-011'
),
'ENSMUST00000186915' => array(
'start' => '121305695',
'end' => '121327719',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-014'
),
'ENSMUST00000181183' => array(
'start' => '121087529',
'end' => '121088932',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-003'
),
'ENSMUST00000181433' => array(
'start' => '121087405',
'end' => '121120956',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-001'
),
'ENSMUST00000185678' => array(
'start' => '121087474',
'end' => '121178441',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-002'
),
'ENSMUST00000190612' => array(
'start' => '121087471',
'end' => '121117760',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-004'
),
'ENSMUST00000191007' => array(
'start' => '121224276',
'end' => '121227526',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-36O22.1-001'
),
'ENSMUST00000190690' => array(
'start' => '121355116',
'end' => '121359900',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-98O21.6-001'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0007KO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007KO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007KO_0001' => array(
'genes_in_region' => array(
'ENSG00000125629' => array(
[maximum depth reached]
),
'ENSG00000226856' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Colon',
(int) 16 => 'Adipose',
(int) 17 => 'Adrenal',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Colon',
(int) 21 => 'Heart',
(int) 22 => 'Kidney',
(int) 23 => 'Lung',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis',
(int) 31 => 'Breast',
(int) 32 => 'Liver',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Adrenal',
(int) 36 => 'Liver',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Ovary',
(int) 43 => 'Testis'
)
),
'CIL_0007KO_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000003721' => array(
[maximum depth reached]
),
'ENSMUSG00000097881' => array(
[maximum depth reached]
),
'ENSMUSG00000101700' => array(
[maximum depth reached]
),
'ENSMUSG00000101791' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Lung',
(int) 18 => 'Testis',
(int) 19 => 'Brain',
(int) 20 => 'Kidney',
(int) 21 => 'Adipose',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Ovary',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Testis',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Liver',
(int) 33 => 'Testis',
(int) 34 => 'Adipose',
(int) 35 => 'Bladder',
(int) 36 => 'Brain',
(int) 37 => 'Colon',
(int) 38 => 'Kidney',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000125629' => 'insulin induced gene 2',
'ENSG00000226856' => null,
'ENSMUSG00000003721' => 'insulin induced gene 2',
'ENSMUSG00000097881' => 'cerebellum expressed regulatory RNA',
'ENSMUSG00000101700' => 'predicted gene 29359',
'ENSMUSG00000101791' => 'RIKEN cDNA 2210011K15 gene'
)
$gene_name_arr = array(
'ENSG00000125629' => 'INSIG2',
'ENSG00000226856' => 'AC093901.1',
'ENSMUSG00000003721' => 'Insig2',
'ENSMUSG00000097881' => 'Celrr',
'ENSMUSG00000101700' => 'RP23-36O22.1',
'ENSMUSG00000101791' => 'RP24-98O21.6'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KO_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '118051989',
'seq_end' => '118547477',
'region_length' => '495488',
'region_type' => 'UCNEbase',
'el_id' => 'EN1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KO_0002',
'tax_id' => '10090',
'chromosome' => '1',
'seq_start' => '120886247',
'seq_end' => '121392907',
'region_length' => '506660',
'region_type' => 'UCNEbase',
'el_id' => 'EN1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KO_0003',
'tax_id' => '7955',
'chromosome' => '1',
'seq_start' => '6591069',
'seq_end' => '6597708',
'region_length' => '6639',
'region_type' => 'UCNEbase',
'el_id' => 'EN1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 16 => 'Brain',
(int) 24 => 'Breast',
(int) 28 => 'Colon',
(int) 34 => 'Heart',
(int) 37 => 'Kidney',
(int) 44 => 'Liver',
(int) 50 => 'Lung',
(int) 54 => 'Muscle',
(int) 58 => 'Ovary',
(int) 67 => 'Placenta',
(int) 76 => '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) 31
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000245787' => array(
'start' => '118088474',
'end' => '118110028',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'INSIG2-001'
),
'ENST00000411929' => array(
'start' => '118088452',
'end' => '118108372',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'INSIG2-007'
),
'ENST00000467223' => array(
'start' => '118088550',
'end' => '118108390',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-004'
),
'ENST00000471186' => array(
'start' => '118088474',
'end' => '118110020',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-003'
),
'ENST00000479999' => array(
'start' => '118106659',
'end' => '118108467',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-006'
),
'ENST00000485520' => array(
'start' => '118088474',
'end' => '118110997',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-002'
),
'ENST00000488995' => array(
'start' => '118102538',
'end' => '118107142',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'INSIG2-005'
),
'ENST00000614681' => array(
'start' => '118096418',
'end' => '118108853',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'INSIG2-201'
),
'ENST00000414886' => array(
'start' => '118132128',
'end' => '118186386',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-001'
),
'ENST00000449075' => array(
'start' => '118182939',
'end' => '118186373',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-002'
),
'ENST00000449819' => array(
'start' => '118183021',
'end' => '118186386',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC093901.1-003'
),
'ENSMUST00000003818' => array(
'start' => '121304353',
'end' => '121328024',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-002'
),
'ENSMUST00000071064' => array(
'start' => '121305522',
'end' => '121332589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-001'
),
'ENSMUST00000159085' => array(
'start' => '121305555',
'end' => '121327678',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-004'
),
'ENSMUST00000159125' => array(
'start' => '121319664',
'end' => '121327682',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-010'
),
'ENSMUST00000159192' => array(
'start' => '121306880',
'end' => '121312414',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-013'
),
'ENSMUST00000159528' => array(
'start' => '121305893',
'end' => '121307318',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-003'
),
'ENSMUST00000160688' => array(
'start' => '121305924',
'end' => '121327793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-007'
),
'ENSMUST00000160968' => array(
'start' => '121305538',
'end' => '121327746',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-005'
),
'ENSMUST00000161068' => array(
'start' => '121319761',
'end' => '121332550',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-006'
),
'ENSMUST00000161818' => array(
'start' => '121319734',
'end' => '121327688',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-009'
),
'ENSMUST00000162019' => array(
'start' => '121311845',
'end' => '121319728',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Insig2-012'
),
'ENSMUST00000162582' => array(
'start' => '121306937',
'end' => '121327765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-008'
),
'ENSMUST00000162790' => array(
'start' => '121307237',
'end' => '121323191',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-011'
),
'ENSMUST00000186915' => array(
'start' => '121305695',
'end' => '121327719',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Insig2-014'
),
'ENSMUST00000181183' => array(
'start' => '121087529',
'end' => '121088932',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-003'
),
'ENSMUST00000181433' => array(
'start' => '121087405',
'end' => '121120956',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-001'
),
'ENSMUST00000185678' => array(
'start' => '121087474',
'end' => '121178441',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-002'
),
'ENSMUST00000190612' => array(
'start' => '121087471',
'end' => '121117760',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Celrr-004'
),
'ENSMUST00000191007' => array(
'start' => '121224276',
'end' => '121227526',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-36O22.1-001'
),
'ENSMUST00000190690' => array(
'start' => '121355116',
'end' => '121359900',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-98O21.6-001'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0007KO_0001' => array(
'genes_in_region' => array(
'ENSG00000125629' => array(
[maximum depth reached]
),
'ENSG00000226856' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Colon',
(int) 16 => 'Adipose',
(int) 17 => 'Adrenal',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Colon',
(int) 21 => 'Heart',
(int) 22 => 'Kidney',
(int) 23 => 'Lung',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis',
(int) 31 => 'Breast',
(int) 32 => 'Liver',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Adrenal',
(int) 36 => 'Liver',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Ovary',
(int) 43 => 'Testis'
)
),
'CIL_0007KO_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000003721' => array(
[maximum depth reached]
),
'ENSMUSG00000097881' => array(
[maximum depth reached]
),
'ENSMUSG00000101700' => array(
[maximum depth reached]
),
'ENSMUSG00000101791' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Lung',
(int) 18 => 'Testis',
(int) 19 => 'Brain',
(int) 20 => 'Kidney',
(int) 21 => 'Adipose',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Ovary',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Testis',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Liver',
(int) 33 => 'Testis',
(int) 34 => 'Adipose',
(int) 35 => 'Bladder',
(int) 36 => 'Brain',
(int) 37 => 'Colon',
(int) 38 => 'Kidney',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007KO_0003',
'tax_id' => '7955',
'chromosome' => '1',
'seq_start' => '6591069',
'seq_end' => '6597708',
'region_length' => '6639',
'region_type' => 'UCNEbase',
'el_id' => 'EN1'
)
)
$gene_el = array(
'ENSMUST00000190690' => array(
'Adipose' => array(
'average_FPKM' => '0.021',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.014',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.035',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.37'
),
'Kidney' => array(
'average_FPKM' => '0.022',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.013',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.016',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.157',
'stddev_FPKM' => '0.09'
),
'Testis' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000101791'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.021',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.014',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.035',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.37'
),
'Kidney' => array(
'average_FPKM' => '0.022',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.013',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.016',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.157',
'stddev_FPKM' => '0.09'
),
'Testis' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000190690'
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
(INSIG2)