| Source ID |
Type |
Tax ID |
Position |
| ENSG00000183283-ENSG00000183283 |
CGP |
9606 |
12:51238292-51271362  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0003MV_0001 [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_0003MV_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000170545' => 'small cell adhesion glycoprotein',
'ENSG00000183283' => 'DAZ associated protein 2',
'ENSMUSG00000000346' => 'DAZ associated protein 2',
'ENSMUSG00000053559' => 'small cell adhesion glycoprotein'
),
'gene_name_arr' => array(
'ENSG00000170545' => 'SMAGP',
'ENSG00000183283' => 'DAZAP2',
'ENSMUSG00000000346' => 'Dazap2',
'ENSMUSG00000053559' => 'Smagp'
),
'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) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 20 => 'Breast',
(int) 26 => 'Colon',
(int) 31 => 'Heart',
(int) 37 => 'Kidney',
(int) 42 => 'Liver',
(int) 48 => 'Lung',
(int) 54 => 'Muscle',
(int) 59 => 'Ovary',
(int) 64 => 'Placenta',
(int) 71 => '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) 26,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000380103' => array(
'start' => '51245351',
'end' => '51269320',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMAGP-007'
),
'ENST00000398453' => array(
'start' => '51245351',
'end' => '51270198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-002'
),
'ENST00000603798' => array(
'start' => '51244558',
'end' => '51270890',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-001'
),
'ENST00000603838' => array(
'start' => '51246464',
'end' => '51269912',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-006'
),
'ENST00000603864' => array(
'start' => '51245388',
'end' => '51269949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-003'
),
'ENST00000604188' => array(
'start' => '51246597',
'end' => '51270184',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-005'
),
'ENST00000605426' => array(
'start' => '51246085',
'end' => '51269958',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-004'
),
'ENST00000605627' => array(
'start' => '51245745',
'end' => '51270284',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-008'
),
'ENST00000412716' => array(
'start' => '51238292',
'end' => '51243933',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-001'
),
'ENST00000425012' => array(
'start' => '51238826',
'end' => '51246717',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-003'
),
'ENST00000436900' => array(
'start' => '51238903',
'end' => '51243785',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DAZAP2-006'
),
'ENST00000439799' => array(
'start' => '51238826',
'end' => '51242816',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-013'
),
'ENST00000449723' => array(
'start' => '51238724',
'end' => '51243931',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-201'
),
'ENST00000549041' => array(
'start' => '51238837',
'end' => '51240856',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DAZAP2-007'
),
'ENST00000549497' => array(
'start' => '51238914',
'end' => '51242451',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-012'
),
'ENST00000549555' => array(
'start' => '51238824',
'end' => '51242816',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-002'
),
'ENST00000549732' => array(
'start' => '51238854',
'end' => '51242594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-010'
),
'ENST00000551313' => array(
'start' => '51239295',
'end' => '51242510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-014'
),
'ENST00000551534' => array(
'start' => '51238905',
'end' => '51242431',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-011'
),
'ENST00000551919' => array(
'start' => '51238827',
'end' => '51242474',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-009'
),
'ENST00000552173' => array(
'start' => '51238818',
'end' => '51241071',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-008'
),
'ENST00000552459' => array(
'start' => '51238908',
'end' => '51243784',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DAZAP2-005'
),
'ENST00000604900' => array(
'start' => '51238886',
'end' => '51271362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-015'
),
'ENSMUST00000000356' => array(
'start' => '100615628',
'end' => '100620731',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dazap2-201'
),
'ENSMUST00000066068' => array(
'start' => '100621342',
'end' => '100636855',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smagp-201'
),
'ENSMUST00000172334' => array(
'start' => '100621342',
'end' => '100636865',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smagp-202'
)
),
'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_0003MV_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0003MV_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000000346' => array(
[maximum depth reached]
),
'ENSMUSG00000053559' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000170545' => 'small cell adhesion glycoprotein',
'ENSG00000183283' => 'DAZ associated protein 2',
'ENSMUSG00000000346' => 'DAZ associated protein 2',
'ENSMUSG00000053559' => 'small cell adhesion glycoprotein'
)
$gene_name_arr = array(
'ENSG00000170545' => 'SMAGP',
'ENSG00000183283' => 'DAZAP2',
'ENSMUSG00000000346' => 'Dazap2',
'ENSMUSG00000053559' => 'Smagp'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0003MV_0001',
'tax_id' => '9606',
'chromosome' => '12',
'seq_start' => '51238292',
'seq_end' => '51271362',
'region_length' => '33070',
'region_type' => 'CGP',
'el_id' => 'ENSG00000183283-ENSG00000183283'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0003MV_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '100615628',
'seq_end' => '100636865',
'region_length' => '21237',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000346-ENSMUSG00000053559'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 20 => 'Breast',
(int) 26 => 'Colon',
(int) 31 => 'Heart',
(int) 37 => 'Kidney',
(int) 42 => 'Liver',
(int) 48 => 'Lung',
(int) 54 => 'Muscle',
(int) 59 => 'Ovary',
(int) 64 => 'Placenta',
(int) 71 => '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) 26
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000380103' => array(
'start' => '51245351',
'end' => '51269320',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMAGP-007'
),
'ENST00000398453' => array(
'start' => '51245351',
'end' => '51270198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-002'
),
'ENST00000603798' => array(
'start' => '51244558',
'end' => '51270890',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-001'
),
'ENST00000603838' => array(
'start' => '51246464',
'end' => '51269912',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-006'
),
'ENST00000603864' => array(
'start' => '51245388',
'end' => '51269949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-003'
),
'ENST00000604188' => array(
'start' => '51246597',
'end' => '51270184',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-005'
),
'ENST00000605426' => array(
'start' => '51246085',
'end' => '51269958',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-004'
),
'ENST00000605627' => array(
'start' => '51245745',
'end' => '51270284',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-008'
),
'ENST00000412716' => array(
'start' => '51238292',
'end' => '51243933',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-001'
),
'ENST00000425012' => array(
'start' => '51238826',
'end' => '51246717',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-003'
),
'ENST00000436900' => array(
'start' => '51238903',
'end' => '51243785',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DAZAP2-006'
),
'ENST00000439799' => array(
'start' => '51238826',
'end' => '51242816',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-013'
),
'ENST00000449723' => array(
'start' => '51238724',
'end' => '51243931',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-201'
),
'ENST00000549041' => array(
'start' => '51238837',
'end' => '51240856',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DAZAP2-007'
),
'ENST00000549497' => array(
'start' => '51238914',
'end' => '51242451',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-012'
),
'ENST00000549555' => array(
'start' => '51238824',
'end' => '51242816',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-002'
),
'ENST00000549732' => array(
'start' => '51238854',
'end' => '51242594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-010'
),
'ENST00000551313' => array(
'start' => '51239295',
'end' => '51242510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-014'
),
'ENST00000551534' => array(
'start' => '51238905',
'end' => '51242431',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-011'
),
'ENST00000551919' => array(
'start' => '51238827',
'end' => '51242474',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-009'
),
'ENST00000552173' => array(
'start' => '51238818',
'end' => '51241071',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-008'
),
'ENST00000552459' => array(
'start' => '51238908',
'end' => '51243784',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DAZAP2-005'
),
'ENST00000604900' => array(
'start' => '51238886',
'end' => '51271362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-015'
),
'ENSMUST00000000356' => array(
'start' => '100615628',
'end' => '100620731',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dazap2-201'
),
'ENSMUST00000066068' => array(
'start' => '100621342',
'end' => '100636855',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smagp-201'
),
'ENSMUST00000172334' => array(
'start' => '100621342',
'end' => '100636865',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smagp-202'
)
)
$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_0003MV_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000000346' => array(
[maximum depth reached]
),
'ENSMUSG00000053559' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0003MV_0001',
'tax_id' => '9606',
'chromosome' => '12',
'seq_start' => '51238292',
'seq_end' => '51271362',
'region_length' => '33070',
'region_type' => 'CGP',
'el_id' => 'ENSG00000183283-ENSG00000183283'
)
)
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0003MV_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000170545' => 'small cell adhesion glycoprotein',
'ENSG00000183283' => 'DAZ associated protein 2',
'ENSMUSG00000000346' => 'DAZ associated protein 2',
'ENSMUSG00000053559' => 'small cell adhesion glycoprotein'
),
'gene_name_arr' => array(
'ENSG00000170545' => 'SMAGP',
'ENSG00000183283' => 'DAZAP2',
'ENSMUSG00000000346' => 'Dazap2',
'ENSMUSG00000053559' => 'Smagp'
),
'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) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 20 => 'Breast',
(int) 26 => 'Colon',
(int) 31 => 'Heart',
(int) 37 => 'Kidney',
(int) 42 => 'Liver',
(int) 48 => 'Lung',
(int) 54 => 'Muscle',
(int) 59 => 'Ovary',
(int) 64 => 'Placenta',
(int) 71 => '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) 26,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000380103' => array(
'start' => '51245351',
'end' => '51269320',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMAGP-007'
),
'ENST00000398453' => array(
'start' => '51245351',
'end' => '51270198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-002'
),
'ENST00000603798' => array(
'start' => '51244558',
'end' => '51270890',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-001'
),
'ENST00000603838' => array(
'start' => '51246464',
'end' => '51269912',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-006'
),
'ENST00000603864' => array(
'start' => '51245388',
'end' => '51269949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-003'
),
'ENST00000604188' => array(
'start' => '51246597',
'end' => '51270184',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-005'
),
'ENST00000605426' => array(
'start' => '51246085',
'end' => '51269958',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-004'
),
'ENST00000605627' => array(
'start' => '51245745',
'end' => '51270284',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-008'
),
'ENST00000412716' => array(
'start' => '51238292',
'end' => '51243933',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-001'
),
'ENST00000425012' => array(
'start' => '51238826',
'end' => '51246717',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-003'
),
'ENST00000436900' => array(
'start' => '51238903',
'end' => '51243785',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DAZAP2-006'
),
'ENST00000439799' => array(
'start' => '51238826',
'end' => '51242816',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-013'
),
'ENST00000449723' => array(
'start' => '51238724',
'end' => '51243931',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-201'
),
'ENST00000549041' => array(
'start' => '51238837',
'end' => '51240856',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DAZAP2-007'
),
'ENST00000549497' => array(
'start' => '51238914',
'end' => '51242451',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-012'
),
'ENST00000549555' => array(
'start' => '51238824',
'end' => '51242816',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-002'
),
'ENST00000549732' => array(
'start' => '51238854',
'end' => '51242594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-010'
),
'ENST00000551313' => array(
'start' => '51239295',
'end' => '51242510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-014'
),
'ENST00000551534' => array(
'start' => '51238905',
'end' => '51242431',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-011'
),
'ENST00000551919' => array(
'start' => '51238827',
'end' => '51242474',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-009'
),
'ENST00000552173' => array(
'start' => '51238818',
'end' => '51241071',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-008'
),
'ENST00000552459' => array(
'start' => '51238908',
'end' => '51243784',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DAZAP2-005'
),
'ENST00000604900' => array(
'start' => '51238886',
'end' => '51271362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-015'
),
'ENSMUST00000000356' => array(
'start' => '100615628',
'end' => '100620731',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dazap2-201'
),
'ENSMUST00000066068' => array(
'start' => '100621342',
'end' => '100636855',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smagp-201'
),
'ENSMUST00000172334' => array(
'start' => '100621342',
'end' => '100636865',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smagp-202'
)
),
'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_0003MV_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0003MV_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000000346' => array(
[maximum depth reached]
),
'ENSMUSG00000053559' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000170545' => 'small cell adhesion glycoprotein',
'ENSG00000183283' => 'DAZ associated protein 2',
'ENSMUSG00000000346' => 'DAZ associated protein 2',
'ENSMUSG00000053559' => 'small cell adhesion glycoprotein'
)
$gene_name_arr = array(
'ENSG00000170545' => 'SMAGP',
'ENSG00000183283' => 'DAZAP2',
'ENSMUSG00000000346' => 'Dazap2',
'ENSMUSG00000053559' => 'Smagp'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0003MV_0001',
'tax_id' => '9606',
'chromosome' => '12',
'seq_start' => '51238292',
'seq_end' => '51271362',
'region_length' => '33070',
'region_type' => 'CGP',
'el_id' => 'ENSG00000183283-ENSG00000183283'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0003MV_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '100615628',
'seq_end' => '100636865',
'region_length' => '21237',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000346-ENSMUSG00000053559'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 20 => 'Breast',
(int) 26 => 'Colon',
(int) 31 => 'Heart',
(int) 37 => 'Kidney',
(int) 42 => 'Liver',
(int) 48 => 'Lung',
(int) 54 => 'Muscle',
(int) 59 => 'Ovary',
(int) 64 => 'Placenta',
(int) 71 => '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) 26
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000380103' => array(
'start' => '51245351',
'end' => '51269320',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMAGP-007'
),
'ENST00000398453' => array(
'start' => '51245351',
'end' => '51270198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-002'
),
'ENST00000603798' => array(
'start' => '51244558',
'end' => '51270890',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-001'
),
'ENST00000603838' => array(
'start' => '51246464',
'end' => '51269912',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-006'
),
'ENST00000603864' => array(
'start' => '51245388',
'end' => '51269949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-003'
),
'ENST00000604188' => array(
'start' => '51246597',
'end' => '51270184',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-005'
),
'ENST00000605426' => array(
'start' => '51246085',
'end' => '51269958',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-004'
),
'ENST00000605627' => array(
'start' => '51245745',
'end' => '51270284',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMAGP-008'
),
'ENST00000412716' => array(
'start' => '51238292',
'end' => '51243933',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-001'
),
'ENST00000425012' => array(
'start' => '51238826',
'end' => '51246717',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-003'
),
'ENST00000436900' => array(
'start' => '51238903',
'end' => '51243785',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DAZAP2-006'
),
'ENST00000439799' => array(
'start' => '51238826',
'end' => '51242816',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-013'
),
'ENST00000449723' => array(
'start' => '51238724',
'end' => '51243931',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-201'
),
'ENST00000549041' => array(
'start' => '51238837',
'end' => '51240856',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DAZAP2-007'
),
'ENST00000549497' => array(
'start' => '51238914',
'end' => '51242451',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-012'
),
'ENST00000549555' => array(
'start' => '51238824',
'end' => '51242816',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-002'
),
'ENST00000549732' => array(
'start' => '51238854',
'end' => '51242594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-010'
),
'ENST00000551313' => array(
'start' => '51239295',
'end' => '51242510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-014'
),
'ENST00000551534' => array(
'start' => '51238905',
'end' => '51242431',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-011'
),
'ENST00000551919' => array(
'start' => '51238827',
'end' => '51242474',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-009'
),
'ENST00000552173' => array(
'start' => '51238818',
'end' => '51241071',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'DAZAP2-008'
),
'ENST00000552459' => array(
'start' => '51238908',
'end' => '51243784',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DAZAP2-005'
),
'ENST00000604900' => array(
'start' => '51238886',
'end' => '51271362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DAZAP2-015'
),
'ENSMUST00000000356' => array(
'start' => '100615628',
'end' => '100620731',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dazap2-201'
),
'ENSMUST00000066068' => array(
'start' => '100621342',
'end' => '100636855',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smagp-201'
),
'ENSMUST00000172334' => array(
'start' => '100621342',
'end' => '100636865',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smagp-202'
)
)
$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_0003MV_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000000346' => array(
[maximum depth reached]
),
'ENSMUSG00000053559' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Bladder',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0003MV_0001',
'tax_id' => '9606',
'chromosome' => '12',
'seq_start' => '51238292',
'seq_end' => '51271362',
'region_length' => '33070',
'region_type' => 'CGP',
'el_id' => 'ENSG00000183283-ENSG00000183283'
)
)
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
(Dazap2)