Notice (8): Undefined index: CIL_0002HW_0009 [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_0002HW_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0006' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0007' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0008' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_000A' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000197849' => 'olfactory receptor, family 8, subfamily G, member 1 (gene/pseudogene)',
'ENSG00000255298' => 'olfactory receptor, family 8, subfamily G, member 5',
'ENSMUSG00000049708' => 'olfactory receptor 27',
'ENSMUSG00000094970' => 'olfactory receptor 943',
'ENSMUSG00000057349' => 'olfactory receptor 948',
'ENSMUSG00000094269' => 'olfactory receptor 951',
'ENSMUSG00000058820' => 'olfactory receptor 146',
'ENSMUSG00000095194' => 'olfactory receptor 936',
'ENSMUSG00000059595' => 'olfactory receptor 935',
'ENSMUSG00000063380' => 'olfactory receptor 945',
'ENSMUSG00000096555' => 'olfactory receptor 944',
'ENSMUSG00000093935' => 'predicted gene, 25529',
'ENSMUSG00000094182' => 'olfactory receptor 937',
'ENSMUSG00000096109' => 'olfactory receptor 1537'
),
'gene_name_arr' => array(
'ENSG00000197849' => 'OR8G1',
'ENSG00000255298' => 'OR8G5',
'ENSMUSG00000049708' => 'Olfr27',
'ENSMUSG00000094970' => 'Olfr943',
'ENSMUSG00000057349' => 'Olfr948',
'ENSMUSG00000094269' => 'Olfr951',
'ENSMUSG00000058820' => 'Olfr146',
'ENSMUSG00000095194' => 'Olfr936',
'ENSMUSG00000059595' => 'Olfr935',
'ENSMUSG00000063380' => 'Olfr945',
'ENSMUSG00000096555' => 'Olfr944',
'ENSMUSG00000093935' => 'Gm25529',
'ENSMUSG00000094182' => 'Olfr937',
'ENSMUSG00000096109' => 'Olfr1537'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Heart',
(int) 2 => 'Lung',
(int) 3 => 'Placenta',
(int) 4 => '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) 21,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000341493' => array(
'start' => '124249676',
'end' => '124250611',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OR8G1-001'
),
'ENST00000524943' => array(
'start' => '124264827',
'end' => '124265867',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OR8G5-001'
),
'ENSMUST00000057811' => array(
'start' => '39128167',
'end' => '39145072',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr27-201'
),
'ENSMUST00000071617' => array(
'start' => '39166310',
'end' => '39185124',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr943-201'
),
'ENSMUST00000076516' => array(
'start' => '39318647',
'end' => '39319612',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr948-201'
),
'ENSMUST00000078531' => array(
'start' => '39393793',
'end' => '39394737',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr951-201'
),
'ENSMUST00000073671' => array(
'start' => '39018559',
'end' => '39019619',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr146-201'
),
'ENSMUST00000178303' => array(
'start' => '39046614',
'end' => '39047549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr936-201'
),
'ENSMUST00000080748' => array(
'start' => '38994507',
'end' => '38995433',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr935-201'
),
'ENSMUST00000076903' => array(
'start' => '39257720',
'end' => '39258682',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr945-201'
),
'ENSMUST00000079650' => array(
'start' => '39217359',
'end' => '39218294',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr944-201'
),
'ENSMUST00000104850' => array(
'start' => '39048558',
'end' => '39048649',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25529-201'
),
'ENSMUST00000055567' => array(
'start' => '39059729',
'end' => '39060664',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr937-201'
),
'ENSMUST00000073248' => array(
'start' => '39237487',
'end' => '39238431',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr1537-201'
)
),
'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_0002HW_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0006' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0007' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0008' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_000A' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0002HW_0001' => array(
'genes_in_region' => array(
'ENSG00000255298' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Heart',
(int) 2 => 'Lung',
(int) 3 => 'Placenta',
(int) 4 => 'Testis'
)
),
'CIL_0002HW_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000049708' => array(
[maximum depth reached]
),
'ENSMUSG00000094970' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000057349' => array(
[maximum depth reached]
),
'ENSMUSG00000094269' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000058820' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0005' => array(
'genes_in_region' => array(
'ENSMUSG00000058820' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0006' => array(
'genes_in_region' => array(
'ENSMUSG00000057349' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0007' => array(
'genes_in_region' => array(
'ENSMUSG00000094970' => array(
[maximum depth reached]
),
'ENSMUSG00000096555' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0008' => array(
'genes_in_region' => array(
'ENSMUSG00000094182' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_000A' => array(
'genes_in_region' => array(
'ENSMUSG00000096555' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000197849' => 'olfactory receptor, family 8, subfamily G, member 1 (gene/pseudogene)',
'ENSG00000255298' => 'olfactory receptor, family 8, subfamily G, member 5',
'ENSMUSG00000049708' => 'olfactory receptor 27',
'ENSMUSG00000094970' => 'olfactory receptor 943',
'ENSMUSG00000057349' => 'olfactory receptor 948',
'ENSMUSG00000094269' => 'olfactory receptor 951',
'ENSMUSG00000058820' => 'olfactory receptor 146',
'ENSMUSG00000095194' => 'olfactory receptor 936',
'ENSMUSG00000059595' => 'olfactory receptor 935',
'ENSMUSG00000063380' => 'olfactory receptor 945',
'ENSMUSG00000096555' => 'olfactory receptor 944',
'ENSMUSG00000093935' => 'predicted gene, 25529',
'ENSMUSG00000094182' => 'olfactory receptor 937',
'ENSMUSG00000096109' => 'olfactory receptor 1537'
)
$gene_name_arr = array(
'ENSG00000197849' => 'OR8G1',
'ENSG00000255298' => 'OR8G5',
'ENSMUSG00000049708' => 'Olfr27',
'ENSMUSG00000094970' => 'Olfr943',
'ENSMUSG00000057349' => 'Olfr948',
'ENSMUSG00000094269' => 'Olfr951',
'ENSMUSG00000058820' => 'Olfr146',
'ENSMUSG00000095194' => 'Olfr936',
'ENSMUSG00000059595' => 'Olfr935',
'ENSMUSG00000063380' => 'Olfr945',
'ENSMUSG00000096555' => 'Olfr944',
'ENSMUSG00000093935' => 'Gm25529',
'ENSMUSG00000094182' => 'Olfr937',
'ENSMUSG00000096109' => 'Olfr1537'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0001',
'tax_id' => '9606',
'chromosome' => '11',
'seq_start' => '124249676',
'seq_end' => '124265867',
'region_length' => '16191',
'region_type' => 'CGP',
'el_id' => 'ENSG00000197849-ENSG00000255298'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0002',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39128167',
'seq_end' => '39185124',
'region_length' => '56957',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000049708-ENSMUSG00000094970'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0003',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39318647',
'seq_end' => '39394737',
'region_length' => '76090',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000057349-ENSMUSG00000094269'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0004',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39018559',
'seq_end' => '39047549',
'region_length' => '28990',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000058820-ENSMUSG00000095194'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0005',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '38994507',
'seq_end' => '39019619',
'region_length' => '25112',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000059595-ENSMUSG00000058820'
)
),
(int) 5 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0006',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39257720',
'seq_end' => '39319612',
'region_length' => '61892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000063380-ENSMUSG00000057349'
)
),
(int) 6 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0007',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39166310',
'seq_end' => '39218294',
'region_length' => '51984',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000094970-ENSMUSG00000096555'
)
),
(int) 7 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0008',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39046614',
'seq_end' => '39060664',
'region_length' => '14050',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000095194-ENSMUSG00000094182'
)
),
(int) 8 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0009',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39237487',
'seq_end' => '39258682',
'region_length' => '21195',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000096109-ENSMUSG00000063380'
)
),
(int) 9 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_000A',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39217359',
'seq_end' => '39238431',
'region_length' => '21072',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000096555-ENSMUSG00000096109'
)
)
)
$all_tissues = array(
(int) 0 => 'Adrenal',
(int) 1 => 'Heart',
(int) 2 => 'Lung',
(int) 3 => 'Placenta',
(int) 4 => '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) 21
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000341493' => array(
'start' => '124249676',
'end' => '124250611',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OR8G1-001'
),
'ENST00000524943' => array(
'start' => '124264827',
'end' => '124265867',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OR8G5-001'
),
'ENSMUST00000057811' => array(
'start' => '39128167',
'end' => '39145072',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr27-201'
),
'ENSMUST00000071617' => array(
'start' => '39166310',
'end' => '39185124',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr943-201'
),
'ENSMUST00000076516' => array(
'start' => '39318647',
'end' => '39319612',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr948-201'
),
'ENSMUST00000078531' => array(
'start' => '39393793',
'end' => '39394737',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr951-201'
),
'ENSMUST00000073671' => array(
'start' => '39018559',
'end' => '39019619',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr146-201'
),
'ENSMUST00000178303' => array(
'start' => '39046614',
'end' => '39047549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr936-201'
),
'ENSMUST00000080748' => array(
'start' => '38994507',
'end' => '38995433',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr935-201'
),
'ENSMUST00000076903' => array(
'start' => '39257720',
'end' => '39258682',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr945-201'
),
'ENSMUST00000079650' => array(
'start' => '39217359',
'end' => '39218294',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr944-201'
),
'ENSMUST00000104850' => array(
'start' => '39048558',
'end' => '39048649',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25529-201'
),
'ENSMUST00000055567' => array(
'start' => '39059729',
'end' => '39060664',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr937-201'
),
'ENSMUST00000073248' => array(
'start' => '39237487',
'end' => '39238431',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr1537-201'
)
)
$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_0002HW_0001' => array(
'genes_in_region' => array(
'ENSG00000255298' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Heart',
(int) 2 => 'Lung',
(int) 3 => 'Placenta',
(int) 4 => 'Testis'
)
),
'CIL_0002HW_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000049708' => array(
[maximum depth reached]
),
'ENSMUSG00000094970' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000057349' => array(
[maximum depth reached]
),
'ENSMUSG00000094269' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000058820' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0005' => array(
'genes_in_region' => array(
'ENSMUSG00000058820' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0006' => array(
'genes_in_region' => array(
'ENSMUSG00000057349' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0007' => array(
'genes_in_region' => array(
'ENSMUSG00000094970' => array(
[maximum depth reached]
),
'ENSMUSG00000096555' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0008' => array(
'genes_in_region' => array(
'ENSMUSG00000094182' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_000A' => array(
'genes_in_region' => array(
'ENSMUSG00000096555' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0009',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39237487',
'seq_end' => '39258682',
'region_length' => '21195',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000096109-ENSMUSG00000063380'
)
)
$gene_el = array(
'ENSMUST00000055567' => array(
'Testis' => array(
'average_FPKM' => '0.015',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000094182'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '0.015',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000055567'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0002HW_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0006' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0007' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0008' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_000A' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000197849' => 'olfactory receptor, family 8, subfamily G, member 1 (gene/pseudogene)',
'ENSG00000255298' => 'olfactory receptor, family 8, subfamily G, member 5',
'ENSMUSG00000049708' => 'olfactory receptor 27',
'ENSMUSG00000094970' => 'olfactory receptor 943',
'ENSMUSG00000057349' => 'olfactory receptor 948',
'ENSMUSG00000094269' => 'olfactory receptor 951',
'ENSMUSG00000058820' => 'olfactory receptor 146',
'ENSMUSG00000095194' => 'olfactory receptor 936',
'ENSMUSG00000059595' => 'olfactory receptor 935',
'ENSMUSG00000063380' => 'olfactory receptor 945',
'ENSMUSG00000096555' => 'olfactory receptor 944',
'ENSMUSG00000093935' => 'predicted gene, 25529',
'ENSMUSG00000094182' => 'olfactory receptor 937',
'ENSMUSG00000096109' => 'olfactory receptor 1537'
),
'gene_name_arr' => array(
'ENSG00000197849' => 'OR8G1',
'ENSG00000255298' => 'OR8G5',
'ENSMUSG00000049708' => 'Olfr27',
'ENSMUSG00000094970' => 'Olfr943',
'ENSMUSG00000057349' => 'Olfr948',
'ENSMUSG00000094269' => 'Olfr951',
'ENSMUSG00000058820' => 'Olfr146',
'ENSMUSG00000095194' => 'Olfr936',
'ENSMUSG00000059595' => 'Olfr935',
'ENSMUSG00000063380' => 'Olfr945',
'ENSMUSG00000096555' => 'Olfr944',
'ENSMUSG00000093935' => 'Gm25529',
'ENSMUSG00000094182' => 'Olfr937',
'ENSMUSG00000096109' => 'Olfr1537'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Heart',
(int) 2 => 'Lung',
(int) 3 => 'Placenta',
(int) 4 => '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) 21,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000341493' => array(
'start' => '124249676',
'end' => '124250611',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OR8G1-001'
),
'ENST00000524943' => array(
'start' => '124264827',
'end' => '124265867',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OR8G5-001'
),
'ENSMUST00000057811' => array(
'start' => '39128167',
'end' => '39145072',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr27-201'
),
'ENSMUST00000071617' => array(
'start' => '39166310',
'end' => '39185124',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr943-201'
),
'ENSMUST00000076516' => array(
'start' => '39318647',
'end' => '39319612',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr948-201'
),
'ENSMUST00000078531' => array(
'start' => '39393793',
'end' => '39394737',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr951-201'
),
'ENSMUST00000073671' => array(
'start' => '39018559',
'end' => '39019619',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr146-201'
),
'ENSMUST00000178303' => array(
'start' => '39046614',
'end' => '39047549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr936-201'
),
'ENSMUST00000080748' => array(
'start' => '38994507',
'end' => '38995433',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr935-201'
),
'ENSMUST00000076903' => array(
'start' => '39257720',
'end' => '39258682',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr945-201'
),
'ENSMUST00000079650' => array(
'start' => '39217359',
'end' => '39218294',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr944-201'
),
'ENSMUST00000104850' => array(
'start' => '39048558',
'end' => '39048649',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25529-201'
),
'ENSMUST00000055567' => array(
'start' => '39059729',
'end' => '39060664',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr937-201'
),
'ENSMUST00000073248' => array(
'start' => '39237487',
'end' => '39238431',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr1537-201'
)
),
'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_0002HW_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0006' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0007' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_0008' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0002HW_000A' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0002HW_0001' => array(
'genes_in_region' => array(
'ENSG00000255298' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Heart',
(int) 2 => 'Lung',
(int) 3 => 'Placenta',
(int) 4 => 'Testis'
)
),
'CIL_0002HW_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000049708' => array(
[maximum depth reached]
),
'ENSMUSG00000094970' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000057349' => array(
[maximum depth reached]
),
'ENSMUSG00000094269' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000058820' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0005' => array(
'genes_in_region' => array(
'ENSMUSG00000058820' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0006' => array(
'genes_in_region' => array(
'ENSMUSG00000057349' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0007' => array(
'genes_in_region' => array(
'ENSMUSG00000094970' => array(
[maximum depth reached]
),
'ENSMUSG00000096555' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0008' => array(
'genes_in_region' => array(
'ENSMUSG00000094182' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_000A' => array(
'genes_in_region' => array(
'ENSMUSG00000096555' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000197849' => 'olfactory receptor, family 8, subfamily G, member 1 (gene/pseudogene)',
'ENSG00000255298' => 'olfactory receptor, family 8, subfamily G, member 5',
'ENSMUSG00000049708' => 'olfactory receptor 27',
'ENSMUSG00000094970' => 'olfactory receptor 943',
'ENSMUSG00000057349' => 'olfactory receptor 948',
'ENSMUSG00000094269' => 'olfactory receptor 951',
'ENSMUSG00000058820' => 'olfactory receptor 146',
'ENSMUSG00000095194' => 'olfactory receptor 936',
'ENSMUSG00000059595' => 'olfactory receptor 935',
'ENSMUSG00000063380' => 'olfactory receptor 945',
'ENSMUSG00000096555' => 'olfactory receptor 944',
'ENSMUSG00000093935' => 'predicted gene, 25529',
'ENSMUSG00000094182' => 'olfactory receptor 937',
'ENSMUSG00000096109' => 'olfactory receptor 1537'
)
$gene_name_arr = array(
'ENSG00000197849' => 'OR8G1',
'ENSG00000255298' => 'OR8G5',
'ENSMUSG00000049708' => 'Olfr27',
'ENSMUSG00000094970' => 'Olfr943',
'ENSMUSG00000057349' => 'Olfr948',
'ENSMUSG00000094269' => 'Olfr951',
'ENSMUSG00000058820' => 'Olfr146',
'ENSMUSG00000095194' => 'Olfr936',
'ENSMUSG00000059595' => 'Olfr935',
'ENSMUSG00000063380' => 'Olfr945',
'ENSMUSG00000096555' => 'Olfr944',
'ENSMUSG00000093935' => 'Gm25529',
'ENSMUSG00000094182' => 'Olfr937',
'ENSMUSG00000096109' => 'Olfr1537'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0001',
'tax_id' => '9606',
'chromosome' => '11',
'seq_start' => '124249676',
'seq_end' => '124265867',
'region_length' => '16191',
'region_type' => 'CGP',
'el_id' => 'ENSG00000197849-ENSG00000255298'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0002',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39128167',
'seq_end' => '39185124',
'region_length' => '56957',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000049708-ENSMUSG00000094970'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0003',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39318647',
'seq_end' => '39394737',
'region_length' => '76090',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000057349-ENSMUSG00000094269'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0004',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39018559',
'seq_end' => '39047549',
'region_length' => '28990',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000058820-ENSMUSG00000095194'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0005',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '38994507',
'seq_end' => '39019619',
'region_length' => '25112',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000059595-ENSMUSG00000058820'
)
),
(int) 5 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0006',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39257720',
'seq_end' => '39319612',
'region_length' => '61892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000063380-ENSMUSG00000057349'
)
),
(int) 6 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0007',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39166310',
'seq_end' => '39218294',
'region_length' => '51984',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000094970-ENSMUSG00000096555'
)
),
(int) 7 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0008',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39046614',
'seq_end' => '39060664',
'region_length' => '14050',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000095194-ENSMUSG00000094182'
)
),
(int) 8 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0009',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39237487',
'seq_end' => '39258682',
'region_length' => '21195',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000096109-ENSMUSG00000063380'
)
),
(int) 9 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_000A',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39217359',
'seq_end' => '39238431',
'region_length' => '21072',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000096555-ENSMUSG00000096109'
)
)
)
$all_tissues = array(
(int) 0 => 'Adrenal',
(int) 1 => 'Heart',
(int) 2 => 'Lung',
(int) 3 => 'Placenta',
(int) 4 => '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) 21
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000341493' => array(
'start' => '124249676',
'end' => '124250611',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OR8G1-001'
),
'ENST00000524943' => array(
'start' => '124264827',
'end' => '124265867',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'OR8G5-001'
),
'ENSMUST00000057811' => array(
'start' => '39128167',
'end' => '39145072',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr27-201'
),
'ENSMUST00000071617' => array(
'start' => '39166310',
'end' => '39185124',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr943-201'
),
'ENSMUST00000076516' => array(
'start' => '39318647',
'end' => '39319612',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr948-201'
),
'ENSMUST00000078531' => array(
'start' => '39393793',
'end' => '39394737',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr951-201'
),
'ENSMUST00000073671' => array(
'start' => '39018559',
'end' => '39019619',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr146-201'
),
'ENSMUST00000178303' => array(
'start' => '39046614',
'end' => '39047549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr936-201'
),
'ENSMUST00000080748' => array(
'start' => '38994507',
'end' => '38995433',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr935-201'
),
'ENSMUST00000076903' => array(
'start' => '39257720',
'end' => '39258682',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr945-201'
),
'ENSMUST00000079650' => array(
'start' => '39217359',
'end' => '39218294',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr944-201'
),
'ENSMUST00000104850' => array(
'start' => '39048558',
'end' => '39048649',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25529-201'
),
'ENSMUST00000055567' => array(
'start' => '39059729',
'end' => '39060664',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr937-201'
),
'ENSMUST00000073248' => array(
'start' => '39237487',
'end' => '39238431',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Olfr1537-201'
)
)
$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_0002HW_0001' => array(
'genes_in_region' => array(
'ENSG00000255298' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Heart',
(int) 2 => 'Lung',
(int) 3 => 'Placenta',
(int) 4 => 'Testis'
)
),
'CIL_0002HW_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000049708' => array(
[maximum depth reached]
),
'ENSMUSG00000094970' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000057349' => array(
[maximum depth reached]
),
'ENSMUSG00000094269' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000058820' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0005' => array(
'genes_in_region' => array(
'ENSMUSG00000058820' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0006' => array(
'genes_in_region' => array(
'ENSMUSG00000057349' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_0007' => array(
'genes_in_region' => array(
'ENSMUSG00000094970' => array(
[maximum depth reached]
),
'ENSMUSG00000096555' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis',
(int) 1 => 'Testis'
)
),
'CIL_0002HW_0008' => array(
'genes_in_region' => array(
'ENSMUSG00000094182' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
),
'CIL_0002HW_000A' => array(
'genes_in_region' => array(
'ENSMUSG00000096555' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0002HW_0009',
'tax_id' => '10090',
'chromosome' => '9',
'seq_start' => '39237487',
'seq_end' => '39258682',
'region_length' => '21195',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000096109-ENSMUSG00000063380'
)
)
$gene_el = array(
'ENSMUST00000055567' => array(
'Testis' => array(
'average_FPKM' => '0.015',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000094182'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '0.015',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000055567'
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 |
| ENSMUSG00000096109-ENSMUSG00000063380 |
CGP |
10090 |
9:39237487-39258682  |
| Gene | Transcript | Position | Biotype |
|---|
(OR8G5)