| Source ID |
Type |
Tax ID |
Position |
| ENSG00000198899-ENSG00000198840 |
CGP |
9606 |
MT:9207-10404  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_000138_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_000138_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_000138_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000063911' => 'ATP synthase 6, mitochondrial',
'ENSDARG00000063912' => 'cytochrome c oxidase III, mitochondrial',
'ENSDARG00000063914' => 'NADH dehydrogenase 3, mitochondrial',
'ENSDARG00000080329' => null,
'ENSDARG00000081758' => null,
'ENSG00000198840' => 'mitochondrially encoded NADH dehydrogenase 3',
'ENSG00000198899' => 'mitochondrially encoded ATP synthase 6',
'ENSG00000198938' => 'mitochondrially encoded cytochrome c oxidase III',
'ENSG00000210164' => 'mitochondrially encoded tRNA glycine',
'ENSMUSG00000064357' => 'mitochondrially encoded ATP synthase 6',
'ENSMUSG00000064358' => 'mitochondrially encoded cytochrome c oxidase III',
'ENSMUSG00000064359' => 'mitochondrially encoded tRNA glycine',
'ENSMUSG00000064360' => 'mitochondrially encoded NADH dehydrogenase 3'
),
'gene_name_arr' => array(
'ENSDARG00000063911' => 'mt-atp6',
'ENSDARG00000063912' => 'mt-co3',
'ENSDARG00000063914' => 'mt-nd3',
'ENSDARG00000080329' => 'AC024175.3',
'ENSDARG00000081758' => 'AC024175.12',
'ENSG00000198840' => 'MT-ND3',
'ENSG00000198899' => 'MT-ATP6',
'ENSG00000198938' => 'MT-CO3',
'ENSG00000210164' => 'MT-TG',
'ENSMUSG00000064357' => 'mt-Atp6',
'ENSMUSG00000064358' => 'mt-Co3',
'ENSMUSG00000064359' => 'mt-Tg',
'ENSMUSG00000064360' => 'mt-Nd3'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Brain',
(int) 8 => 'Breast',
(int) 10 => 'Colon',
(int) 12 => 'Heart',
(int) 15 => 'Kidney',
(int) 20 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 30 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => '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(
'ENSDART00000093612' => array(
'start' => '9052',
'end' => '9735',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-atp6-201'
),
'ENSDART00000093613' => array(
'start' => '9735',
'end' => '10520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co3-201'
),
'ENSDART00000093615' => array(
'start' => '10590',
'end' => '10940',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-nd3-201'
),
'ENSDART00000117281' => array(
'start' => '10939',
'end' => '11008',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.3-201'
),
'ENSDART00000116044' => array(
'start' => '10520',
'end' => '10589',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.12-201'
),
'ENST00000361227' => array(
'start' => '10059',
'end' => '10404',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ND3-201'
),
'ENST00000361899' => array(
'start' => '8527',
'end' => '9207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ATP6-201'
),
'ENST00000362079' => array(
'start' => '9207',
'end' => '9990',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO3-201'
),
'ENST00000387429' => array(
'start' => '9991',
'end' => '10058',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TG-201'
),
'ENSMUST00000082408' => array(
'start' => '7927',
'end' => '8607',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Atp6-201'
),
'ENSMUST00000082409' => array(
'start' => '8607',
'end' => '9390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co3-201'
),
'ENSMUST00000082410' => array(
'start' => '9391',
'end' => '9458',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tg-201'
),
'ENSMUST00000082411' => array(
'start' => '9459',
'end' => '9806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Nd3-201'
)
),
'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_000138_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_000138_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000138_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063911' => array(
[maximum depth reached]
),
'ENSDARG00000063912' => array(
[maximum depth reached]
),
'ENSDARG00000063914' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Muscle'
)
),
'CIL_000138_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064357' => array(
[maximum depth reached]
),
'ENSMUSG00000064358' => array(
[maximum depth reached]
),
'ENSMUSG00000064359' => array(
[maximum depth reached]
),
'ENSMUSG00000064360' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Ovary',
(int) 8 => 'Ovary',
(int) 9 => 'Ovary',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000063911' => 'ATP synthase 6, mitochondrial',
'ENSDARG00000063912' => 'cytochrome c oxidase III, mitochondrial',
'ENSDARG00000063914' => 'NADH dehydrogenase 3, mitochondrial',
'ENSDARG00000080329' => null,
'ENSDARG00000081758' => null,
'ENSG00000198840' => 'mitochondrially encoded NADH dehydrogenase 3',
'ENSG00000198899' => 'mitochondrially encoded ATP synthase 6',
'ENSG00000198938' => 'mitochondrially encoded cytochrome c oxidase III',
'ENSG00000210164' => 'mitochondrially encoded tRNA glycine',
'ENSMUSG00000064357' => 'mitochondrially encoded ATP synthase 6',
'ENSMUSG00000064358' => 'mitochondrially encoded cytochrome c oxidase III',
'ENSMUSG00000064359' => 'mitochondrially encoded tRNA glycine',
'ENSMUSG00000064360' => 'mitochondrially encoded NADH dehydrogenase 3'
)
$gene_name_arr = array(
'ENSDARG00000063911' => 'mt-atp6',
'ENSDARG00000063912' => 'mt-co3',
'ENSDARG00000063914' => 'mt-nd3',
'ENSDARG00000080329' => 'AC024175.3',
'ENSDARG00000081758' => 'AC024175.12',
'ENSG00000198840' => 'MT-ND3',
'ENSG00000198899' => 'MT-ATP6',
'ENSG00000198938' => 'MT-CO3',
'ENSG00000210164' => 'MT-TG',
'ENSMUSG00000064357' => 'mt-Atp6',
'ENSMUSG00000064358' => 'mt-Co3',
'ENSMUSG00000064359' => 'mt-Tg',
'ENSMUSG00000064360' => 'mt-Nd3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000138_0001',
'tax_id' => '7955',
'chromosome' => 'MT',
'seq_start' => '9735',
'seq_end' => '10940',
'region_length' => '1205',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000063911-ENSDARG00000063914'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000138_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '9207',
'seq_end' => '10404',
'region_length' => '1197',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198899-ENSG00000198840'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000138_0003',
'tax_id' => '10090',
'chromosome' => 'MT',
'seq_start' => '8607',
'seq_end' => '9806',
'region_length' => '1199',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000064357-ENSMUSG00000064360'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Brain',
(int) 8 => 'Breast',
(int) 10 => 'Colon',
(int) 12 => 'Heart',
(int) 15 => 'Kidney',
(int) 20 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 30 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => '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(
'ENSDART00000093612' => array(
'start' => '9052',
'end' => '9735',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-atp6-201'
),
'ENSDART00000093613' => array(
'start' => '9735',
'end' => '10520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co3-201'
),
'ENSDART00000093615' => array(
'start' => '10590',
'end' => '10940',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-nd3-201'
),
'ENSDART00000117281' => array(
'start' => '10939',
'end' => '11008',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.3-201'
),
'ENSDART00000116044' => array(
'start' => '10520',
'end' => '10589',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.12-201'
),
'ENST00000361227' => array(
'start' => '10059',
'end' => '10404',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ND3-201'
),
'ENST00000361899' => array(
'start' => '8527',
'end' => '9207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ATP6-201'
),
'ENST00000362079' => array(
'start' => '9207',
'end' => '9990',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO3-201'
),
'ENST00000387429' => array(
'start' => '9991',
'end' => '10058',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TG-201'
),
'ENSMUST00000082408' => array(
'start' => '7927',
'end' => '8607',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Atp6-201'
),
'ENSMUST00000082409' => array(
'start' => '8607',
'end' => '9390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co3-201'
),
'ENSMUST00000082410' => array(
'start' => '9391',
'end' => '9458',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tg-201'
),
'ENSMUST00000082411' => array(
'start' => '9459',
'end' => '9806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Nd3-201'
)
)
$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_000138_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063911' => array(
[maximum depth reached]
),
'ENSDARG00000063912' => array(
[maximum depth reached]
),
'ENSDARG00000063914' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Muscle'
)
),
'CIL_000138_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064357' => array(
[maximum depth reached]
),
'ENSMUSG00000064358' => array(
[maximum depth reached]
),
'ENSMUSG00000064359' => array(
[maximum depth reached]
),
'ENSMUSG00000064360' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Ovary',
(int) 8 => 'Ovary',
(int) 9 => 'Ovary',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000138_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '9207',
'seq_end' => '10404',
'region_length' => '1197',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198899-ENSG00000198840'
)
)
$gene_el = array(
'ENSDART00000093615' => array(
'Brain' => array(
'average_FPKM' => '1890.810',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3997.550',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1293.230',
'stddev_FPKM' => '12.43'
),
'Liver' => array(
'average_FPKM' => '53.385',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '1953.330',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000063914'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '1890.810',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3997.550',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1293.230',
'stddev_FPKM' => '12.43'
),
'Liver' => array(
'average_FPKM' => '53.385',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '1953.330',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000093615'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_000138_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_000138_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000063911' => 'ATP synthase 6, mitochondrial',
'ENSDARG00000063912' => 'cytochrome c oxidase III, mitochondrial',
'ENSDARG00000063914' => 'NADH dehydrogenase 3, mitochondrial',
'ENSDARG00000080329' => null,
'ENSDARG00000081758' => null,
'ENSG00000198840' => 'mitochondrially encoded NADH dehydrogenase 3',
'ENSG00000198899' => 'mitochondrially encoded ATP synthase 6',
'ENSG00000198938' => 'mitochondrially encoded cytochrome c oxidase III',
'ENSG00000210164' => 'mitochondrially encoded tRNA glycine',
'ENSMUSG00000064357' => 'mitochondrially encoded ATP synthase 6',
'ENSMUSG00000064358' => 'mitochondrially encoded cytochrome c oxidase III',
'ENSMUSG00000064359' => 'mitochondrially encoded tRNA glycine',
'ENSMUSG00000064360' => 'mitochondrially encoded NADH dehydrogenase 3'
),
'gene_name_arr' => array(
'ENSDARG00000063911' => 'mt-atp6',
'ENSDARG00000063912' => 'mt-co3',
'ENSDARG00000063914' => 'mt-nd3',
'ENSDARG00000080329' => 'AC024175.3',
'ENSDARG00000081758' => 'AC024175.12',
'ENSG00000198840' => 'MT-ND3',
'ENSG00000198899' => 'MT-ATP6',
'ENSG00000198938' => 'MT-CO3',
'ENSG00000210164' => 'MT-TG',
'ENSMUSG00000064357' => 'mt-Atp6',
'ENSMUSG00000064358' => 'mt-Co3',
'ENSMUSG00000064359' => 'mt-Tg',
'ENSMUSG00000064360' => 'mt-Nd3'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Brain',
(int) 8 => 'Breast',
(int) 10 => 'Colon',
(int) 12 => 'Heart',
(int) 15 => 'Kidney',
(int) 20 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 30 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => '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(
'ENSDART00000093612' => array(
'start' => '9052',
'end' => '9735',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-atp6-201'
),
'ENSDART00000093613' => array(
'start' => '9735',
'end' => '10520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co3-201'
),
'ENSDART00000093615' => array(
'start' => '10590',
'end' => '10940',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-nd3-201'
),
'ENSDART00000117281' => array(
'start' => '10939',
'end' => '11008',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.3-201'
),
'ENSDART00000116044' => array(
'start' => '10520',
'end' => '10589',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.12-201'
),
'ENST00000361227' => array(
'start' => '10059',
'end' => '10404',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ND3-201'
),
'ENST00000361899' => array(
'start' => '8527',
'end' => '9207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ATP6-201'
),
'ENST00000362079' => array(
'start' => '9207',
'end' => '9990',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO3-201'
),
'ENST00000387429' => array(
'start' => '9991',
'end' => '10058',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TG-201'
),
'ENSMUST00000082408' => array(
'start' => '7927',
'end' => '8607',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Atp6-201'
),
'ENSMUST00000082409' => array(
'start' => '8607',
'end' => '9390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co3-201'
),
'ENSMUST00000082410' => array(
'start' => '9391',
'end' => '9458',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tg-201'
),
'ENSMUST00000082411' => array(
'start' => '9459',
'end' => '9806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Nd3-201'
)
),
'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_000138_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_000138_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000138_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063911' => array(
[maximum depth reached]
),
'ENSDARG00000063912' => array(
[maximum depth reached]
),
'ENSDARG00000063914' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Muscle'
)
),
'CIL_000138_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064357' => array(
[maximum depth reached]
),
'ENSMUSG00000064358' => array(
[maximum depth reached]
),
'ENSMUSG00000064359' => array(
[maximum depth reached]
),
'ENSMUSG00000064360' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Ovary',
(int) 8 => 'Ovary',
(int) 9 => 'Ovary',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000063911' => 'ATP synthase 6, mitochondrial',
'ENSDARG00000063912' => 'cytochrome c oxidase III, mitochondrial',
'ENSDARG00000063914' => 'NADH dehydrogenase 3, mitochondrial',
'ENSDARG00000080329' => null,
'ENSDARG00000081758' => null,
'ENSG00000198840' => 'mitochondrially encoded NADH dehydrogenase 3',
'ENSG00000198899' => 'mitochondrially encoded ATP synthase 6',
'ENSG00000198938' => 'mitochondrially encoded cytochrome c oxidase III',
'ENSG00000210164' => 'mitochondrially encoded tRNA glycine',
'ENSMUSG00000064357' => 'mitochondrially encoded ATP synthase 6',
'ENSMUSG00000064358' => 'mitochondrially encoded cytochrome c oxidase III',
'ENSMUSG00000064359' => 'mitochondrially encoded tRNA glycine',
'ENSMUSG00000064360' => 'mitochondrially encoded NADH dehydrogenase 3'
)
$gene_name_arr = array(
'ENSDARG00000063911' => 'mt-atp6',
'ENSDARG00000063912' => 'mt-co3',
'ENSDARG00000063914' => 'mt-nd3',
'ENSDARG00000080329' => 'AC024175.3',
'ENSDARG00000081758' => 'AC024175.12',
'ENSG00000198840' => 'MT-ND3',
'ENSG00000198899' => 'MT-ATP6',
'ENSG00000198938' => 'MT-CO3',
'ENSG00000210164' => 'MT-TG',
'ENSMUSG00000064357' => 'mt-Atp6',
'ENSMUSG00000064358' => 'mt-Co3',
'ENSMUSG00000064359' => 'mt-Tg',
'ENSMUSG00000064360' => 'mt-Nd3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000138_0001',
'tax_id' => '7955',
'chromosome' => 'MT',
'seq_start' => '9735',
'seq_end' => '10940',
'region_length' => '1205',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000063911-ENSDARG00000063914'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000138_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '9207',
'seq_end' => '10404',
'region_length' => '1197',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198899-ENSG00000198840'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000138_0003',
'tax_id' => '10090',
'chromosome' => 'MT',
'seq_start' => '8607',
'seq_end' => '9806',
'region_length' => '1199',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000064357-ENSMUSG00000064360'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Brain',
(int) 8 => 'Breast',
(int) 10 => 'Colon',
(int) 12 => 'Heart',
(int) 15 => 'Kidney',
(int) 20 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 30 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => '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(
'ENSDART00000093612' => array(
'start' => '9052',
'end' => '9735',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-atp6-201'
),
'ENSDART00000093613' => array(
'start' => '9735',
'end' => '10520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co3-201'
),
'ENSDART00000093615' => array(
'start' => '10590',
'end' => '10940',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-nd3-201'
),
'ENSDART00000117281' => array(
'start' => '10939',
'end' => '11008',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.3-201'
),
'ENSDART00000116044' => array(
'start' => '10520',
'end' => '10589',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.12-201'
),
'ENST00000361227' => array(
'start' => '10059',
'end' => '10404',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ND3-201'
),
'ENST00000361899' => array(
'start' => '8527',
'end' => '9207',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ATP6-201'
),
'ENST00000362079' => array(
'start' => '9207',
'end' => '9990',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO3-201'
),
'ENST00000387429' => array(
'start' => '9991',
'end' => '10058',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TG-201'
),
'ENSMUST00000082408' => array(
'start' => '7927',
'end' => '8607',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Atp6-201'
),
'ENSMUST00000082409' => array(
'start' => '8607',
'end' => '9390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co3-201'
),
'ENSMUST00000082410' => array(
'start' => '9391',
'end' => '9458',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tg-201'
),
'ENSMUST00000082411' => array(
'start' => '9459',
'end' => '9806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Nd3-201'
)
)
$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_000138_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063911' => array(
[maximum depth reached]
),
'ENSDARG00000063912' => array(
[maximum depth reached]
),
'ENSDARG00000063914' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle',
(int) 10 => 'Brain',
(int) 11 => 'Heart',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Muscle'
)
),
'CIL_000138_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064357' => array(
[maximum depth reached]
),
'ENSMUSG00000064358' => array(
[maximum depth reached]
),
'ENSMUSG00000064359' => array(
[maximum depth reached]
),
'ENSMUSG00000064360' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Ovary',
(int) 8 => 'Ovary',
(int) 9 => 'Ovary',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000138_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '9207',
'seq_end' => '10404',
'region_length' => '1197',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198899-ENSG00000198840'
)
)
$gene_el = array(
'ENSDART00000093615' => array(
'Brain' => array(
'average_FPKM' => '1890.810',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3997.550',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1293.230',
'stddev_FPKM' => '12.43'
),
'Liver' => array(
'average_FPKM' => '53.385',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '1953.330',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000063914'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '1890.810',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3997.550',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1293.230',
'stddev_FPKM' => '12.43'
),
'Liver' => array(
'average_FPKM' => '53.385',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '1953.330',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000093615'
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
(mt-atp6)