| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000006517-ENSMUSG00000006587 |
CGP |
10090 |
8:122433596-122460692  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00032X_0002 [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_00032X_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000167508' => 'mevalonate (diphospho) decarboxylase',
'ENSG00000185669' => 'snail family zinc finger 3',
'ENSG00000260630' => 'SNAI3 antisense RNA 1',
'ENSMUSG00000006517' => 'mevalonate (diphospho) decarboxylase',
'ENSMUSG00000006587' => 'snail family zinc finger 3'
),
'gene_name_arr' => array(
'ENSG00000167508' => 'MVD',
'ENSG00000185669' => 'SNAI3',
'ENSG00000260630' => 'SNAI3-AS1',
'ENSMUSG00000006517' => 'Mvd',
'ENSMUSG00000006587' => 'Snai3'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 11 => 'Brain',
(int) 20 => 'Breast',
(int) 26 => 'Colon',
(int) 33 => 'Heart',
(int) 39 => 'Kidney',
(int) 46 => 'Liver',
(int) 53 => 'Lung',
(int) 61 => 'Muscle',
(int) 66 => 'Ovary',
(int) 74 => 'Placenta',
(int) 80 => '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) 27,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000301012' => array(
'start' => '88651935',
'end' => '88663110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-001'
),
'ENST00000561895' => array(
'start' => '88652510',
'end' => '88654985',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-004'
),
'ENST00000562651' => array(
'start' => '88657436',
'end' => '88660872',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-011'
),
'ENST00000562741' => array(
'start' => '88662102',
'end' => '88663161',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-014'
),
'ENST00000562981' => array(
'start' => '88652354',
'end' => '88653584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-003'
),
'ENST00000563170' => array(
'start' => '88656121',
'end' => '88663065',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-012'
),
'ENST00000563463' => array(
'start' => '88658973',
'end' => '88663079',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-016'
),
'ENST00000563785' => array(
'start' => '88655834',
'end' => '88663094',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-006'
),
'ENST00000565149' => array(
'start' => '88651935',
'end' => '88657266',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-002'
),
'ENST00000565610' => array(
'start' => '88657944',
'end' => '88663148',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-017'
),
'ENST00000565720' => array(
'start' => '88656261',
'end' => '88657507',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-005'
),
'ENST00000565842' => array(
'start' => '88662115',
'end' => '88663046',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-015'
),
'ENST00000566636' => array(
'start' => '88656170',
'end' => '88658783',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-010'
),
'ENST00000567064' => array(
'start' => '88655657',
'end' => '88663091',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-013'
),
'ENST00000568133' => array(
'start' => '88655663',
'end' => '88663082',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-009'
),
'ENST00000568709' => array(
'start' => '88656105',
'end' => '88663029',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-008'
),
'ENST00000569177' => array(
'start' => '88655385',
'end' => '88663137',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-007'
),
'ENST00000620002' => array(
'start' => '88651940',
'end' => '88663110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-201'
),
'ENST00000332281' => array(
'start' => '88677682',
'end' => '88686493',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SNAI3-001'
),
'ENST00000563261' => array(
'start' => '88663298',
'end' => '88687186',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-001'
),
'ENST00000563475' => array(
'start' => '88663380',
'end' => '88675164',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-002'
),
'ENST00000565633' => array(
'start' => '88663335',
'end' => '88673647',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-005'
),
'ENST00000567997' => array(
'start' => '88685133',
'end' => '88687180',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-006'
),
'ENST00000568633' => array(
'start' => '88673396',
'end' => '88675491',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-007'
),
'ENST00000569786' => array(
'start' => '88663369',
'end' => '88672179',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-004'
),
'ENSMUST00000006692' => array(
'start' => '122433596',
'end' => '122443422',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mvd-201'
),
'ENSMUST00000006762' => array(
'start' => '122454206',
'end' => '122460692',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Snai3-201'
)
),
'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_00032X_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00032X_0001' => array(
'genes_in_region' => array(
'ENSG00000167508' => array(
[maximum depth reached]
),
'ENSG00000185669' => array(
[maximum depth reached]
),
'ENSG00000260630' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Lung',
(int) 5 => 'Muscle',
(int) 6 => 'Bladder',
(int) 7 => 'Colon',
(int) 8 => 'Colon',
(int) 9 => 'Liver',
(int) 10 => 'Adrenal',
(int) 11 => 'Brain',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Brain',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Kidney',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Adipose',
(int) 42 => 'Adrenal',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Lung',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Adipose',
(int) 54 => 'Brain',
(int) 55 => 'Bladder',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Ovary',
(int) 64 => 'Placenta',
(int) 65 => 'Testis',
(int) 66 => 'Bladder',
(int) 67 => 'Brain',
(int) 68 => 'Heart',
(int) 69 => 'Liver',
(int) 70 => 'Ovary',
(int) 71 => 'Testis',
(int) 72 => 'Adipose',
(int) 73 => 'Brain',
(int) 74 => 'Breast',
(int) 75 => 'Colon',
(int) 76 => 'Heart',
(int) 77 => 'Kidney',
(int) 78 => 'Liver',
(int) 79 => 'Lung',
(int) 80 => 'Muscle',
(int) 81 => 'Ovary',
(int) 82 => 'Placenta',
(int) 83 => 'Testis',
(int) 84 => 'Breast',
(int) 85 => 'Lung',
(int) 86 => 'Placenta'
)
)
)
$gene_desc_arr = array(
'ENSG00000167508' => 'mevalonate (diphospho) decarboxylase',
'ENSG00000185669' => 'snail family zinc finger 3',
'ENSG00000260630' => 'SNAI3 antisense RNA 1',
'ENSMUSG00000006517' => 'mevalonate (diphospho) decarboxylase',
'ENSMUSG00000006587' => 'snail family zinc finger 3'
)
$gene_name_arr = array(
'ENSG00000167508' => 'MVD',
'ENSG00000185669' => 'SNAI3',
'ENSG00000260630' => 'SNAI3-AS1',
'ENSMUSG00000006517' => 'Mvd',
'ENSMUSG00000006587' => 'Snai3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00032X_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '88651935',
'seq_end' => '88686493',
'region_length' => '34558',
'region_type' => 'CGP',
'el_id' => 'ENSG00000167508-ENSG00000185669'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00032X_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122433596',
'seq_end' => '122460692',
'region_length' => '27096',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006517-ENSMUSG00000006587'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 11 => 'Brain',
(int) 20 => 'Breast',
(int) 26 => 'Colon',
(int) 33 => 'Heart',
(int) 39 => 'Kidney',
(int) 46 => 'Liver',
(int) 53 => 'Lung',
(int) 61 => 'Muscle',
(int) 66 => 'Ovary',
(int) 74 => 'Placenta',
(int) 80 => '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) 27
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000301012' => array(
'start' => '88651935',
'end' => '88663110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-001'
),
'ENST00000561895' => array(
'start' => '88652510',
'end' => '88654985',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-004'
),
'ENST00000562651' => array(
'start' => '88657436',
'end' => '88660872',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-011'
),
'ENST00000562741' => array(
'start' => '88662102',
'end' => '88663161',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-014'
),
'ENST00000562981' => array(
'start' => '88652354',
'end' => '88653584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-003'
),
'ENST00000563170' => array(
'start' => '88656121',
'end' => '88663065',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-012'
),
'ENST00000563463' => array(
'start' => '88658973',
'end' => '88663079',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-016'
),
'ENST00000563785' => array(
'start' => '88655834',
'end' => '88663094',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-006'
),
'ENST00000565149' => array(
'start' => '88651935',
'end' => '88657266',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-002'
),
'ENST00000565610' => array(
'start' => '88657944',
'end' => '88663148',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-017'
),
'ENST00000565720' => array(
'start' => '88656261',
'end' => '88657507',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-005'
),
'ENST00000565842' => array(
'start' => '88662115',
'end' => '88663046',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-015'
),
'ENST00000566636' => array(
'start' => '88656170',
'end' => '88658783',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-010'
),
'ENST00000567064' => array(
'start' => '88655657',
'end' => '88663091',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-013'
),
'ENST00000568133' => array(
'start' => '88655663',
'end' => '88663082',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-009'
),
'ENST00000568709' => array(
'start' => '88656105',
'end' => '88663029',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-008'
),
'ENST00000569177' => array(
'start' => '88655385',
'end' => '88663137',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-007'
),
'ENST00000620002' => array(
'start' => '88651940',
'end' => '88663110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-201'
),
'ENST00000332281' => array(
'start' => '88677682',
'end' => '88686493',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SNAI3-001'
),
'ENST00000563261' => array(
'start' => '88663298',
'end' => '88687186',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-001'
),
'ENST00000563475' => array(
'start' => '88663380',
'end' => '88675164',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-002'
),
'ENST00000565633' => array(
'start' => '88663335',
'end' => '88673647',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-005'
),
'ENST00000567997' => array(
'start' => '88685133',
'end' => '88687180',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-006'
),
'ENST00000568633' => array(
'start' => '88673396',
'end' => '88675491',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-007'
),
'ENST00000569786' => array(
'start' => '88663369',
'end' => '88672179',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-004'
),
'ENSMUST00000006692' => array(
'start' => '122433596',
'end' => '122443422',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mvd-201'
),
'ENSMUST00000006762' => array(
'start' => '122454206',
'end' => '122460692',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Snai3-201'
)
)
$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_00032X_0001' => array(
'genes_in_region' => array(
'ENSG00000167508' => array(
[maximum depth reached]
),
'ENSG00000185669' => array(
[maximum depth reached]
),
'ENSG00000260630' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Lung',
(int) 5 => 'Muscle',
(int) 6 => 'Bladder',
(int) 7 => 'Colon',
(int) 8 => 'Colon',
(int) 9 => 'Liver',
(int) 10 => 'Adrenal',
(int) 11 => 'Brain',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Brain',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Kidney',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Adipose',
(int) 42 => 'Adrenal',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Lung',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Adipose',
(int) 54 => 'Brain',
(int) 55 => 'Bladder',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Ovary',
(int) 64 => 'Placenta',
(int) 65 => 'Testis',
(int) 66 => 'Bladder',
(int) 67 => 'Brain',
(int) 68 => 'Heart',
(int) 69 => 'Liver',
(int) 70 => 'Ovary',
(int) 71 => 'Testis',
(int) 72 => 'Adipose',
(int) 73 => 'Brain',
(int) 74 => 'Breast',
(int) 75 => 'Colon',
(int) 76 => 'Heart',
(int) 77 => 'Kidney',
(int) 78 => 'Liver',
(int) 79 => 'Lung',
(int) 80 => 'Muscle',
(int) 81 => 'Ovary',
(int) 82 => 'Placenta',
(int) 83 => 'Testis',
(int) 84 => 'Breast',
(int) 85 => 'Lung',
(int) 86 => 'Placenta'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00032X_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122433596',
'seq_end' => '122460692',
'region_length' => '27096',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006517-ENSMUSG00000006587'
)
)
$gene_el = array(
'ENST00000563261' => array(
'Adipose' => array(
'average_FPKM' => '0.310',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '2.158',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563475' => array(
'Bladder' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.961',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.178',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.205',
'stddev_FPKM' => '0.07'
),
'Heart' => array(
'average_FPKM' => '0.389',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.455',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.139',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '1.165',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.157',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.628',
'stddev_FPKM' => '0.18'
)
),
'ENST00000565633' => array(
'Bladder' => array(
'average_FPKM' => '0.644',
'stddev_FPKM' => '0.00'
)
),
'ENST00000567997' => array(
'Brain' => array(
'average_FPKM' => '1.392',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.882',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.247',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.224',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.908',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568633' => array(
'Adipose' => array(
'average_FPKM' => '0.158',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.935',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.233',
'stddev_FPKM' => '0.11'
),
'Colon' => array(
'average_FPKM' => '0.066',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.618',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.816',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.346',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.306',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.355',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.07'
),
'Placenta' => array(
'average_FPKM' => '0.283',
'stddev_FPKM' => '0.10'
),
'Testis' => array(
'average_FPKM' => '0.492',
'stddev_FPKM' => '0.08'
)
),
'ENST00000569786' => array(
'Breast' => array(
'average_FPKM' => '0.890',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.333',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.13'
)
)
)
$gene_key = 'ENSG00000260630'
$is_first = false
$tran_el = array(
'Breast' => array(
'average_FPKM' => '0.890',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.333',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.13'
)
)
$tran_key = 'ENST00000569786'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00032X_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000167508' => 'mevalonate (diphospho) decarboxylase',
'ENSG00000185669' => 'snail family zinc finger 3',
'ENSG00000260630' => 'SNAI3 antisense RNA 1',
'ENSMUSG00000006517' => 'mevalonate (diphospho) decarboxylase',
'ENSMUSG00000006587' => 'snail family zinc finger 3'
),
'gene_name_arr' => array(
'ENSG00000167508' => 'MVD',
'ENSG00000185669' => 'SNAI3',
'ENSG00000260630' => 'SNAI3-AS1',
'ENSMUSG00000006517' => 'Mvd',
'ENSMUSG00000006587' => 'Snai3'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 11 => 'Brain',
(int) 20 => 'Breast',
(int) 26 => 'Colon',
(int) 33 => 'Heart',
(int) 39 => 'Kidney',
(int) 46 => 'Liver',
(int) 53 => 'Lung',
(int) 61 => 'Muscle',
(int) 66 => 'Ovary',
(int) 74 => 'Placenta',
(int) 80 => '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) 27,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000301012' => array(
'start' => '88651935',
'end' => '88663110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-001'
),
'ENST00000561895' => array(
'start' => '88652510',
'end' => '88654985',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-004'
),
'ENST00000562651' => array(
'start' => '88657436',
'end' => '88660872',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-011'
),
'ENST00000562741' => array(
'start' => '88662102',
'end' => '88663161',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-014'
),
'ENST00000562981' => array(
'start' => '88652354',
'end' => '88653584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-003'
),
'ENST00000563170' => array(
'start' => '88656121',
'end' => '88663065',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-012'
),
'ENST00000563463' => array(
'start' => '88658973',
'end' => '88663079',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-016'
),
'ENST00000563785' => array(
'start' => '88655834',
'end' => '88663094',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-006'
),
'ENST00000565149' => array(
'start' => '88651935',
'end' => '88657266',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-002'
),
'ENST00000565610' => array(
'start' => '88657944',
'end' => '88663148',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-017'
),
'ENST00000565720' => array(
'start' => '88656261',
'end' => '88657507',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-005'
),
'ENST00000565842' => array(
'start' => '88662115',
'end' => '88663046',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-015'
),
'ENST00000566636' => array(
'start' => '88656170',
'end' => '88658783',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-010'
),
'ENST00000567064' => array(
'start' => '88655657',
'end' => '88663091',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-013'
),
'ENST00000568133' => array(
'start' => '88655663',
'end' => '88663082',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-009'
),
'ENST00000568709' => array(
'start' => '88656105',
'end' => '88663029',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-008'
),
'ENST00000569177' => array(
'start' => '88655385',
'end' => '88663137',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-007'
),
'ENST00000620002' => array(
'start' => '88651940',
'end' => '88663110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-201'
),
'ENST00000332281' => array(
'start' => '88677682',
'end' => '88686493',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SNAI3-001'
),
'ENST00000563261' => array(
'start' => '88663298',
'end' => '88687186',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-001'
),
'ENST00000563475' => array(
'start' => '88663380',
'end' => '88675164',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-002'
),
'ENST00000565633' => array(
'start' => '88663335',
'end' => '88673647',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-005'
),
'ENST00000567997' => array(
'start' => '88685133',
'end' => '88687180',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-006'
),
'ENST00000568633' => array(
'start' => '88673396',
'end' => '88675491',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-007'
),
'ENST00000569786' => array(
'start' => '88663369',
'end' => '88672179',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-004'
),
'ENSMUST00000006692' => array(
'start' => '122433596',
'end' => '122443422',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mvd-201'
),
'ENSMUST00000006762' => array(
'start' => '122454206',
'end' => '122460692',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Snai3-201'
)
),
'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_00032X_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00032X_0001' => array(
'genes_in_region' => array(
'ENSG00000167508' => array(
[maximum depth reached]
),
'ENSG00000185669' => array(
[maximum depth reached]
),
'ENSG00000260630' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Lung',
(int) 5 => 'Muscle',
(int) 6 => 'Bladder',
(int) 7 => 'Colon',
(int) 8 => 'Colon',
(int) 9 => 'Liver',
(int) 10 => 'Adrenal',
(int) 11 => 'Brain',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Brain',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Kidney',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Adipose',
(int) 42 => 'Adrenal',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Lung',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Adipose',
(int) 54 => 'Brain',
(int) 55 => 'Bladder',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Ovary',
(int) 64 => 'Placenta',
(int) 65 => 'Testis',
(int) 66 => 'Bladder',
(int) 67 => 'Brain',
(int) 68 => 'Heart',
(int) 69 => 'Liver',
(int) 70 => 'Ovary',
(int) 71 => 'Testis',
(int) 72 => 'Adipose',
(int) 73 => 'Brain',
(int) 74 => 'Breast',
(int) 75 => 'Colon',
(int) 76 => 'Heart',
(int) 77 => 'Kidney',
(int) 78 => 'Liver',
(int) 79 => 'Lung',
(int) 80 => 'Muscle',
(int) 81 => 'Ovary',
(int) 82 => 'Placenta',
(int) 83 => 'Testis',
(int) 84 => 'Breast',
(int) 85 => 'Lung',
(int) 86 => 'Placenta'
)
)
)
$gene_desc_arr = array(
'ENSG00000167508' => 'mevalonate (diphospho) decarboxylase',
'ENSG00000185669' => 'snail family zinc finger 3',
'ENSG00000260630' => 'SNAI3 antisense RNA 1',
'ENSMUSG00000006517' => 'mevalonate (diphospho) decarboxylase',
'ENSMUSG00000006587' => 'snail family zinc finger 3'
)
$gene_name_arr = array(
'ENSG00000167508' => 'MVD',
'ENSG00000185669' => 'SNAI3',
'ENSG00000260630' => 'SNAI3-AS1',
'ENSMUSG00000006517' => 'Mvd',
'ENSMUSG00000006587' => 'Snai3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00032X_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '88651935',
'seq_end' => '88686493',
'region_length' => '34558',
'region_type' => 'CGP',
'el_id' => 'ENSG00000167508-ENSG00000185669'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00032X_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122433596',
'seq_end' => '122460692',
'region_length' => '27096',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006517-ENSMUSG00000006587'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 11 => 'Brain',
(int) 20 => 'Breast',
(int) 26 => 'Colon',
(int) 33 => 'Heart',
(int) 39 => 'Kidney',
(int) 46 => 'Liver',
(int) 53 => 'Lung',
(int) 61 => 'Muscle',
(int) 66 => 'Ovary',
(int) 74 => 'Placenta',
(int) 80 => '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) 27
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000301012' => array(
'start' => '88651935',
'end' => '88663110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-001'
),
'ENST00000561895' => array(
'start' => '88652510',
'end' => '88654985',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-004'
),
'ENST00000562651' => array(
'start' => '88657436',
'end' => '88660872',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-011'
),
'ENST00000562741' => array(
'start' => '88662102',
'end' => '88663161',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-014'
),
'ENST00000562981' => array(
'start' => '88652354',
'end' => '88653584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-003'
),
'ENST00000563170' => array(
'start' => '88656121',
'end' => '88663065',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-012'
),
'ENST00000563463' => array(
'start' => '88658973',
'end' => '88663079',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-016'
),
'ENST00000563785' => array(
'start' => '88655834',
'end' => '88663094',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-006'
),
'ENST00000565149' => array(
'start' => '88651935',
'end' => '88657266',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-002'
),
'ENST00000565610' => array(
'start' => '88657944',
'end' => '88663148',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-017'
),
'ENST00000565720' => array(
'start' => '88656261',
'end' => '88657507',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-005'
),
'ENST00000565842' => array(
'start' => '88662115',
'end' => '88663046',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-015'
),
'ENST00000566636' => array(
'start' => '88656170',
'end' => '88658783',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MVD-010'
),
'ENST00000567064' => array(
'start' => '88655657',
'end' => '88663091',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-013'
),
'ENST00000568133' => array(
'start' => '88655663',
'end' => '88663082',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MVD-009'
),
'ENST00000568709' => array(
'start' => '88656105',
'end' => '88663029',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MVD-008'
),
'ENST00000569177' => array(
'start' => '88655385',
'end' => '88663137',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-007'
),
'ENST00000620002' => array(
'start' => '88651940',
'end' => '88663110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MVD-201'
),
'ENST00000332281' => array(
'start' => '88677682',
'end' => '88686493',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SNAI3-001'
),
'ENST00000563261' => array(
'start' => '88663298',
'end' => '88687186',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-001'
),
'ENST00000563475' => array(
'start' => '88663380',
'end' => '88675164',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-002'
),
'ENST00000565633' => array(
'start' => '88663335',
'end' => '88673647',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-005'
),
'ENST00000567997' => array(
'start' => '88685133',
'end' => '88687180',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-006'
),
'ENST00000568633' => array(
'start' => '88673396',
'end' => '88675491',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-007'
),
'ENST00000569786' => array(
'start' => '88663369',
'end' => '88672179',
'transcript_biotype' => 'antisense',
'transcript_name' => 'SNAI3-AS1-004'
),
'ENSMUST00000006692' => array(
'start' => '122433596',
'end' => '122443422',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mvd-201'
),
'ENSMUST00000006762' => array(
'start' => '122454206',
'end' => '122460692',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Snai3-201'
)
)
$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_00032X_0001' => array(
'genes_in_region' => array(
'ENSG00000167508' => array(
[maximum depth reached]
),
'ENSG00000185669' => array(
[maximum depth reached]
),
'ENSG00000260630' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Lung',
(int) 5 => 'Muscle',
(int) 6 => 'Bladder',
(int) 7 => 'Colon',
(int) 8 => 'Colon',
(int) 9 => 'Liver',
(int) 10 => 'Adrenal',
(int) 11 => 'Brain',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Brain',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Kidney',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Adipose',
(int) 42 => 'Adrenal',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Lung',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Adipose',
(int) 54 => 'Brain',
(int) 55 => 'Bladder',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Ovary',
(int) 64 => 'Placenta',
(int) 65 => 'Testis',
(int) 66 => 'Bladder',
(int) 67 => 'Brain',
(int) 68 => 'Heart',
(int) 69 => 'Liver',
(int) 70 => 'Ovary',
(int) 71 => 'Testis',
(int) 72 => 'Adipose',
(int) 73 => 'Brain',
(int) 74 => 'Breast',
(int) 75 => 'Colon',
(int) 76 => 'Heart',
(int) 77 => 'Kidney',
(int) 78 => 'Liver',
(int) 79 => 'Lung',
(int) 80 => 'Muscle',
(int) 81 => 'Ovary',
(int) 82 => 'Placenta',
(int) 83 => 'Testis',
(int) 84 => 'Breast',
(int) 85 => 'Lung',
(int) 86 => 'Placenta'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00032X_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122433596',
'seq_end' => '122460692',
'region_length' => '27096',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006517-ENSMUSG00000006587'
)
)
$gene_el = array(
'ENST00000563261' => array(
'Adipose' => array(
'average_FPKM' => '0.310',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '2.158',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563475' => array(
'Bladder' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.961',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.178',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.205',
'stddev_FPKM' => '0.07'
),
'Heart' => array(
'average_FPKM' => '0.389',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.455',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.139',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '1.165',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.157',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.628',
'stddev_FPKM' => '0.18'
)
),
'ENST00000565633' => array(
'Bladder' => array(
'average_FPKM' => '0.644',
'stddev_FPKM' => '0.00'
)
),
'ENST00000567997' => array(
'Brain' => array(
'average_FPKM' => '1.392',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.882',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.247',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.224',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.908',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568633' => array(
'Adipose' => array(
'average_FPKM' => '0.158',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.935',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.233',
'stddev_FPKM' => '0.11'
),
'Colon' => array(
'average_FPKM' => '0.066',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.618',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.816',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.346',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.306',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.355',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.07'
),
'Placenta' => array(
'average_FPKM' => '0.283',
'stddev_FPKM' => '0.10'
),
'Testis' => array(
'average_FPKM' => '0.492',
'stddev_FPKM' => '0.08'
)
),
'ENST00000569786' => array(
'Breast' => array(
'average_FPKM' => '0.890',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.333',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.13'
)
)
)
$gene_key = 'ENSG00000260630'
$is_first = false
$tran_el = array(
'Breast' => array(
'average_FPKM' => '0.890',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.333',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.13'
)
)
$tran_key = 'ENST00000569786'
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
(MVD)