Notice (8): Undefined index: CIL_0005RX_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_0005RX_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000069248' => 'nucleoporin 133kDa',
'ENSG00000135776' => 'ATP-binding cassette, sub-family B (MDR/TAP), member 10',
'ENSG00000199672' => 'RNA, U4 small nuclear 21, pseudogene',
'ENSG00000201492' => 'RNA, 5S ribosomal pseudogene 78',
'ENSG00000223635' => null,
'ENSG00000226920' => null,
'ENSMUSG00000031974' => 'ATP-binding cassette, sub-family B (MDR/TAP), member 10',
'ENSMUSG00000039509' => 'nucleoporin 133'
),
'gene_name_arr' => array(
'ENSG00000069248' => 'NUP133',
'ENSG00000135776' => 'ABCB10',
'ENSG00000199672' => 'RNU4-21P',
'ENSG00000201492' => 'RNA5SP78',
'ENSG00000223635' => 'RP4-613A2.1',
'ENSG00000226920' => 'RP5-1068B5.5',
'ENSMUSG00000031974' => 'Abcb10',
'ENSMUSG00000039509' => 'Nup133'
),
'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) 1 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 6 => 'Brain',
(int) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 17 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 22 => 'Ovary',
(int) 25 => 'Placenta',
(int) 28 => '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) 13,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000261396' => array(
'start' => '229440260',
'end' => '229508341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NUP133-001'
),
'ENST00000366678' => array(
'start' => '229499167',
'end' => '229508326',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-003'
),
'ENST00000485119' => array(
'start' => '229448772',
'end' => '229451070',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-004'
),
'ENST00000490352' => array(
'start' => '229441779',
'end' => '229450751',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-005'
),
'ENST00000344517' => array(
'start' => '229516582',
'end' => '229558695',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ABCB10-001'
),
'ENST00000486755' => array(
'start' => '229526062',
'end' => '229531902',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ABCB10-002'
),
'ENST00000498158' => array(
'start' => '229517797',
'end' => '229519103',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ABCB10-003'
),
'ENST00000362802' => array(
'start' => '229535064',
'end' => '229535189',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU4-21P-201'
),
'ENST00000364622' => array(
'start' => '229549905',
'end' => '229550022',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP78-201'
),
'ENST00000417605' => array(
'start' => '229508501',
'end' => '229514272',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP4-613A2.1-001'
),
'ENST00000434311' => array(
'start' => '229440284',
'end' => '229441020',
'transcript_biotype' => '3prime_overlapping_ncrna',
'transcript_name' => 'RP5-1068B5.5-001'
),
'ENSMUST00000075578' => array(
'start' => '123952459',
'end' => '123983122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Abcb10-001'
),
'ENSMUST00000044795' => array(
'start' => '123897123',
'end' => '123949265',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nup133-201'
)
),
'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_0005RX_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0005RX_0001' => array(
'genes_in_region' => array(
'ENSG00000069248' => array(
[maximum depth reached]
),
'ENSG00000135776' => array(
[maximum depth reached]
),
'ENSG00000199672' => array(
[maximum depth reached]
),
'ENSG00000201492' => array(
[maximum depth reached]
),
'ENSG00000223635' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Bladder',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Testis',
(int) 27 => 'Brain',
(int) 28 => 'Ovary',
(int) 29 => 'Testis',
(int) 30 => 'Adrenal',
(int) 31 => 'Placenta',
(int) 32 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000069248' => 'nucleoporin 133kDa',
'ENSG00000135776' => 'ATP-binding cassette, sub-family B (MDR/TAP), member 10',
'ENSG00000199672' => 'RNA, U4 small nuclear 21, pseudogene',
'ENSG00000201492' => 'RNA, 5S ribosomal pseudogene 78',
'ENSG00000223635' => null,
'ENSG00000226920' => null,
'ENSMUSG00000031974' => 'ATP-binding cassette, sub-family B (MDR/TAP), member 10',
'ENSMUSG00000039509' => 'nucleoporin 133'
)
$gene_name_arr = array(
'ENSG00000069248' => 'NUP133',
'ENSG00000135776' => 'ABCB10',
'ENSG00000199672' => 'RNU4-21P',
'ENSG00000201492' => 'RNA5SP78',
'ENSG00000223635' => 'RP4-613A2.1',
'ENSG00000226920' => 'RP5-1068B5.5',
'ENSMUSG00000031974' => 'Abcb10',
'ENSMUSG00000039509' => 'Nup133'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0005RX_0001',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '229440260',
'seq_end' => '229558695',
'region_length' => '118435',
'region_type' => 'CGP',
'el_id' => 'ENSG00000069248-ENSG00000135776'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0005RX_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123897123',
'seq_end' => '123983122',
'region_length' => '85999',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000039509-ENSMUSG00000031974'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 6 => 'Brain',
(int) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 17 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 22 => 'Ovary',
(int) 25 => 'Placenta',
(int) 28 => '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) 13
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000261396' => array(
'start' => '229440260',
'end' => '229508341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NUP133-001'
),
'ENST00000366678' => array(
'start' => '229499167',
'end' => '229508326',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-003'
),
'ENST00000485119' => array(
'start' => '229448772',
'end' => '229451070',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-004'
),
'ENST00000490352' => array(
'start' => '229441779',
'end' => '229450751',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-005'
),
'ENST00000344517' => array(
'start' => '229516582',
'end' => '229558695',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ABCB10-001'
),
'ENST00000486755' => array(
'start' => '229526062',
'end' => '229531902',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ABCB10-002'
),
'ENST00000498158' => array(
'start' => '229517797',
'end' => '229519103',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ABCB10-003'
),
'ENST00000362802' => array(
'start' => '229535064',
'end' => '229535189',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU4-21P-201'
),
'ENST00000364622' => array(
'start' => '229549905',
'end' => '229550022',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP78-201'
),
'ENST00000417605' => array(
'start' => '229508501',
'end' => '229514272',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP4-613A2.1-001'
),
'ENST00000434311' => array(
'start' => '229440284',
'end' => '229441020',
'transcript_biotype' => '3prime_overlapping_ncrna',
'transcript_name' => 'RP5-1068B5.5-001'
),
'ENSMUST00000075578' => array(
'start' => '123952459',
'end' => '123983122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Abcb10-001'
),
'ENSMUST00000044795' => array(
'start' => '123897123',
'end' => '123949265',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nup133-201'
)
)
$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_0005RX_0001' => array(
'genes_in_region' => array(
'ENSG00000069248' => array(
[maximum depth reached]
),
'ENSG00000135776' => array(
[maximum depth reached]
),
'ENSG00000199672' => array(
[maximum depth reached]
),
'ENSG00000201492' => array(
[maximum depth reached]
),
'ENSG00000223635' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Bladder',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Testis',
(int) 27 => 'Brain',
(int) 28 => 'Ovary',
(int) 29 => 'Testis',
(int) 30 => 'Adrenal',
(int) 31 => 'Placenta',
(int) 32 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0005RX_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123897123',
'seq_end' => '123983122',
'region_length' => '85999',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000039509-ENSMUSG00000031974'
)
)
$gene_el = array(
'ENST00000417605' => array(
'Adrenal' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '5.559',
'stddev_FPKM' => '2.37'
)
)
)
$gene_key = 'ENSG00000223635'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '5.559',
'stddev_FPKM' => '2.37'
)
)
$tran_key = 'ENST00000417605'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0005RX_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000069248' => 'nucleoporin 133kDa',
'ENSG00000135776' => 'ATP-binding cassette, sub-family B (MDR/TAP), member 10',
'ENSG00000199672' => 'RNA, U4 small nuclear 21, pseudogene',
'ENSG00000201492' => 'RNA, 5S ribosomal pseudogene 78',
'ENSG00000223635' => null,
'ENSG00000226920' => null,
'ENSMUSG00000031974' => 'ATP-binding cassette, sub-family B (MDR/TAP), member 10',
'ENSMUSG00000039509' => 'nucleoporin 133'
),
'gene_name_arr' => array(
'ENSG00000069248' => 'NUP133',
'ENSG00000135776' => 'ABCB10',
'ENSG00000199672' => 'RNU4-21P',
'ENSG00000201492' => 'RNA5SP78',
'ENSG00000223635' => 'RP4-613A2.1',
'ENSG00000226920' => 'RP5-1068B5.5',
'ENSMUSG00000031974' => 'Abcb10',
'ENSMUSG00000039509' => 'Nup133'
),
'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) 1 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 6 => 'Brain',
(int) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 17 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 22 => 'Ovary',
(int) 25 => 'Placenta',
(int) 28 => '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) 13,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000261396' => array(
'start' => '229440260',
'end' => '229508341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NUP133-001'
),
'ENST00000366678' => array(
'start' => '229499167',
'end' => '229508326',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-003'
),
'ENST00000485119' => array(
'start' => '229448772',
'end' => '229451070',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-004'
),
'ENST00000490352' => array(
'start' => '229441779',
'end' => '229450751',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-005'
),
'ENST00000344517' => array(
'start' => '229516582',
'end' => '229558695',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ABCB10-001'
),
'ENST00000486755' => array(
'start' => '229526062',
'end' => '229531902',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ABCB10-002'
),
'ENST00000498158' => array(
'start' => '229517797',
'end' => '229519103',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ABCB10-003'
),
'ENST00000362802' => array(
'start' => '229535064',
'end' => '229535189',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU4-21P-201'
),
'ENST00000364622' => array(
'start' => '229549905',
'end' => '229550022',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP78-201'
),
'ENST00000417605' => array(
'start' => '229508501',
'end' => '229514272',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP4-613A2.1-001'
),
'ENST00000434311' => array(
'start' => '229440284',
'end' => '229441020',
'transcript_biotype' => '3prime_overlapping_ncrna',
'transcript_name' => 'RP5-1068B5.5-001'
),
'ENSMUST00000075578' => array(
'start' => '123952459',
'end' => '123983122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Abcb10-001'
),
'ENSMUST00000044795' => array(
'start' => '123897123',
'end' => '123949265',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nup133-201'
)
),
'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_0005RX_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0005RX_0001' => array(
'genes_in_region' => array(
'ENSG00000069248' => array(
[maximum depth reached]
),
'ENSG00000135776' => array(
[maximum depth reached]
),
'ENSG00000199672' => array(
[maximum depth reached]
),
'ENSG00000201492' => array(
[maximum depth reached]
),
'ENSG00000223635' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Bladder',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Testis',
(int) 27 => 'Brain',
(int) 28 => 'Ovary',
(int) 29 => 'Testis',
(int) 30 => 'Adrenal',
(int) 31 => 'Placenta',
(int) 32 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000069248' => 'nucleoporin 133kDa',
'ENSG00000135776' => 'ATP-binding cassette, sub-family B (MDR/TAP), member 10',
'ENSG00000199672' => 'RNA, U4 small nuclear 21, pseudogene',
'ENSG00000201492' => 'RNA, 5S ribosomal pseudogene 78',
'ENSG00000223635' => null,
'ENSG00000226920' => null,
'ENSMUSG00000031974' => 'ATP-binding cassette, sub-family B (MDR/TAP), member 10',
'ENSMUSG00000039509' => 'nucleoporin 133'
)
$gene_name_arr = array(
'ENSG00000069248' => 'NUP133',
'ENSG00000135776' => 'ABCB10',
'ENSG00000199672' => 'RNU4-21P',
'ENSG00000201492' => 'RNA5SP78',
'ENSG00000223635' => 'RP4-613A2.1',
'ENSG00000226920' => 'RP5-1068B5.5',
'ENSMUSG00000031974' => 'Abcb10',
'ENSMUSG00000039509' => 'Nup133'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0005RX_0001',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '229440260',
'seq_end' => '229558695',
'region_length' => '118435',
'region_type' => 'CGP',
'el_id' => 'ENSG00000069248-ENSG00000135776'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0005RX_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123897123',
'seq_end' => '123983122',
'region_length' => '85999',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000039509-ENSMUSG00000031974'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 6 => 'Brain',
(int) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 17 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 22 => 'Ovary',
(int) 25 => 'Placenta',
(int) 28 => '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) 13
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000261396' => array(
'start' => '229440260',
'end' => '229508341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NUP133-001'
),
'ENST00000366678' => array(
'start' => '229499167',
'end' => '229508326',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-003'
),
'ENST00000485119' => array(
'start' => '229448772',
'end' => '229451070',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-004'
),
'ENST00000490352' => array(
'start' => '229441779',
'end' => '229450751',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NUP133-005'
),
'ENST00000344517' => array(
'start' => '229516582',
'end' => '229558695',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ABCB10-001'
),
'ENST00000486755' => array(
'start' => '229526062',
'end' => '229531902',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ABCB10-002'
),
'ENST00000498158' => array(
'start' => '229517797',
'end' => '229519103',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ABCB10-003'
),
'ENST00000362802' => array(
'start' => '229535064',
'end' => '229535189',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU4-21P-201'
),
'ENST00000364622' => array(
'start' => '229549905',
'end' => '229550022',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP78-201'
),
'ENST00000417605' => array(
'start' => '229508501',
'end' => '229514272',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP4-613A2.1-001'
),
'ENST00000434311' => array(
'start' => '229440284',
'end' => '229441020',
'transcript_biotype' => '3prime_overlapping_ncrna',
'transcript_name' => 'RP5-1068B5.5-001'
),
'ENSMUST00000075578' => array(
'start' => '123952459',
'end' => '123983122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Abcb10-001'
),
'ENSMUST00000044795' => array(
'start' => '123897123',
'end' => '123949265',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nup133-201'
)
)
$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_0005RX_0001' => array(
'genes_in_region' => array(
'ENSG00000069248' => array(
[maximum depth reached]
),
'ENSG00000135776' => array(
[maximum depth reached]
),
'ENSG00000199672' => array(
[maximum depth reached]
),
'ENSG00000201492' => array(
[maximum depth reached]
),
'ENSG00000223635' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Bladder',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Testis',
(int) 27 => 'Brain',
(int) 28 => 'Ovary',
(int) 29 => 'Testis',
(int) 30 => 'Adrenal',
(int) 31 => 'Placenta',
(int) 32 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0005RX_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123897123',
'seq_end' => '123983122',
'region_length' => '85999',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000039509-ENSMUSG00000031974'
)
)
$gene_el = array(
'ENST00000417605' => array(
'Adrenal' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '5.559',
'stddev_FPKM' => '2.37'
)
)
)
$gene_key = 'ENSG00000223635'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '5.559',
'stddev_FPKM' => '2.37'
)
)
$tran_key = 'ENST00000417605'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000039509-ENSMUSG00000031974 |
CGP |
10090 |
8:123897123-123983122  |
| Gene | Transcript | Position | Biotype |
|---|
(NUP133)