| Source ID |
Type |
Tax ID |
Position |
| ENSG00000198804-ENSG00000198712 |
CGP |
9606 |
MT:5904-8269  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00013F_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_00013F_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00013F_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000063905' => 'cytochrome c oxidase I, mitochondrial',
'ENSDARG00000063908' => 'cytochrome c oxidase II, mitochondrial',
'ENSDARG00000081369' => null,
'ENSDARG00000083519' => null,
'ENSG00000198712' => 'mitochondrially encoded cytochrome c oxidase II',
'ENSG00000198804' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSG00000210151' => 'mitochondrially encoded tRNA serine 1 (UCN)',
'ENSG00000210154' => 'mitochondrially encoded tRNA aspartic acid',
'ENSMUSG00000064351' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSMUSG00000064352' => 'mitochondrially encoded tRNA serine 1',
'ENSMUSG00000064353' => 'mitochondrially encoded tRNA aspartic acid',
'ENSMUSG00000064354' => 'mitochondrially encoded cytochrome c oxidase II'
),
'gene_name_arr' => array(
'ENSDARG00000063905' => 'mt-co1',
'ENSDARG00000063908' => 'mt-co2',
'ENSDARG00000081369' => 'AC024175.9',
'ENSDARG00000083519' => 'AC024175.24',
'ENSG00000198712' => 'MT-CO2',
'ENSG00000198804' => 'MT-CO1',
'ENSG00000210151' => 'MT-TS1',
'ENSG00000210154' => 'MT-TD',
'ENSMUSG00000064351' => 'mt-Co1',
'ENSMUSG00000064352' => 'mt-Ts1',
'ENSMUSG00000064353' => 'mt-Td',
'ENSMUSG00000064354' => 'mt-Co2'
),
'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) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 20 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 30 => 'Ovary',
(int) 33 => '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) 12,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000093606' => array(
'start' => '6425',
'end' => '7975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co1-201'
),
'ENSDART00000093609' => array(
'start' => '8130',
'end' => '8820',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co2-201'
),
'ENSDART00000117474' => array(
'start' => '7976',
'end' => '8046',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.9-201'
),
'ENSDART00000117438' => array(
'start' => '8049',
'end' => '8117',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.24-201'
),
'ENST00000361739' => array(
'start' => '7586',
'end' => '8269',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO2-201'
),
'ENST00000361624' => array(
'start' => '5904',
'end' => '7445',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO1-201'
),
'ENST00000387416' => array(
'start' => '7446',
'end' => '7514',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TS1-201'
),
'ENST00000387419' => array(
'start' => '7518',
'end' => '7585',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TD-201'
),
'ENSMUST00000082402' => array(
'start' => '5328',
'end' => '6872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co1-201'
),
'ENSMUST00000082403' => array(
'start' => '6870',
'end' => '6938',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ts1-201'
),
'ENSMUST00000082404' => array(
'start' => '6942',
'end' => '7011',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Td-201'
),
'ENSMUST00000082405' => array(
'start' => '7013',
'end' => '7696',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co2-201'
)
),
'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_00013F_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00013F_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00013F_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063905' => array(
[maximum depth reached]
),
'ENSDARG00000063908' => array(
[maximum depth reached]
),
'ENSDARG00000081369' => 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 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Muscle'
)
),
'CIL_00013F_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064351' => array(
[maximum depth reached]
),
'ENSMUSG00000064353' => array(
[maximum depth reached]
),
'ENSMUSG00000064354' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Ovary',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000063905' => 'cytochrome c oxidase I, mitochondrial',
'ENSDARG00000063908' => 'cytochrome c oxidase II, mitochondrial',
'ENSDARG00000081369' => null,
'ENSDARG00000083519' => null,
'ENSG00000198712' => 'mitochondrially encoded cytochrome c oxidase II',
'ENSG00000198804' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSG00000210151' => 'mitochondrially encoded tRNA serine 1 (UCN)',
'ENSG00000210154' => 'mitochondrially encoded tRNA aspartic acid',
'ENSMUSG00000064351' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSMUSG00000064352' => 'mitochondrially encoded tRNA serine 1',
'ENSMUSG00000064353' => 'mitochondrially encoded tRNA aspartic acid',
'ENSMUSG00000064354' => 'mitochondrially encoded cytochrome c oxidase II'
)
$gene_name_arr = array(
'ENSDARG00000063905' => 'mt-co1',
'ENSDARG00000063908' => 'mt-co2',
'ENSDARG00000081369' => 'AC024175.9',
'ENSDARG00000083519' => 'AC024175.24',
'ENSG00000198712' => 'MT-CO2',
'ENSG00000198804' => 'MT-CO1',
'ENSG00000210151' => 'MT-TS1',
'ENSG00000210154' => 'MT-TD',
'ENSMUSG00000064351' => 'mt-Co1',
'ENSMUSG00000064352' => 'mt-Ts1',
'ENSMUSG00000064353' => 'mt-Td',
'ENSMUSG00000064354' => 'mt-Co2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013F_0001',
'tax_id' => '7955',
'chromosome' => 'MT',
'seq_start' => '6425',
'seq_end' => '8820',
'region_length' => '2395',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000063905-ENSDARG00000063908'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013F_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '5904',
'seq_end' => '8269',
'region_length' => '2365',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198804-ENSG00000198712'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013F_0003',
'tax_id' => '10090',
'chromosome' => 'MT',
'seq_start' => '5328',
'seq_end' => '7696',
'region_length' => '2368',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000064351-ENSMUSG00000064354'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Brain',
(int) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 20 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 30 => 'Ovary',
(int) 33 => '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) 12
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000093606' => array(
'start' => '6425',
'end' => '7975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co1-201'
),
'ENSDART00000093609' => array(
'start' => '8130',
'end' => '8820',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co2-201'
),
'ENSDART00000117474' => array(
'start' => '7976',
'end' => '8046',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.9-201'
),
'ENSDART00000117438' => array(
'start' => '8049',
'end' => '8117',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.24-201'
),
'ENST00000361739' => array(
'start' => '7586',
'end' => '8269',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO2-201'
),
'ENST00000361624' => array(
'start' => '5904',
'end' => '7445',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO1-201'
),
'ENST00000387416' => array(
'start' => '7446',
'end' => '7514',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TS1-201'
),
'ENST00000387419' => array(
'start' => '7518',
'end' => '7585',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TD-201'
),
'ENSMUST00000082402' => array(
'start' => '5328',
'end' => '6872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co1-201'
),
'ENSMUST00000082403' => array(
'start' => '6870',
'end' => '6938',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ts1-201'
),
'ENSMUST00000082404' => array(
'start' => '6942',
'end' => '7011',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Td-201'
),
'ENSMUST00000082405' => array(
'start' => '7013',
'end' => '7696',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co2-201'
)
)
$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_00013F_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063905' => array(
[maximum depth reached]
),
'ENSDARG00000063908' => array(
[maximum depth reached]
),
'ENSDARG00000081369' => 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 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Muscle'
)
),
'CIL_00013F_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064351' => array(
[maximum depth reached]
),
'ENSMUSG00000064353' => array(
[maximum depth reached]
),
'ENSMUSG00000064354' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Ovary',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00013F_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '5904',
'seq_end' => '8269',
'region_length' => '2365',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198804-ENSG00000198712'
)
)
$gene_el = array(
'ENSDART00000117474' => array(
'Brain' => array(
'average_FPKM' => '18495.699',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '7995.950',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1070.030',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '20760.199',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000081369'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '18495.699',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '7995.950',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1070.030',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '20760.199',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000117474'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00013F_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00013F_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000063905' => 'cytochrome c oxidase I, mitochondrial',
'ENSDARG00000063908' => 'cytochrome c oxidase II, mitochondrial',
'ENSDARG00000081369' => null,
'ENSDARG00000083519' => null,
'ENSG00000198712' => 'mitochondrially encoded cytochrome c oxidase II',
'ENSG00000198804' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSG00000210151' => 'mitochondrially encoded tRNA serine 1 (UCN)',
'ENSG00000210154' => 'mitochondrially encoded tRNA aspartic acid',
'ENSMUSG00000064351' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSMUSG00000064352' => 'mitochondrially encoded tRNA serine 1',
'ENSMUSG00000064353' => 'mitochondrially encoded tRNA aspartic acid',
'ENSMUSG00000064354' => 'mitochondrially encoded cytochrome c oxidase II'
),
'gene_name_arr' => array(
'ENSDARG00000063905' => 'mt-co1',
'ENSDARG00000063908' => 'mt-co2',
'ENSDARG00000081369' => 'AC024175.9',
'ENSDARG00000083519' => 'AC024175.24',
'ENSG00000198712' => 'MT-CO2',
'ENSG00000198804' => 'MT-CO1',
'ENSG00000210151' => 'MT-TS1',
'ENSG00000210154' => 'MT-TD',
'ENSMUSG00000064351' => 'mt-Co1',
'ENSMUSG00000064352' => 'mt-Ts1',
'ENSMUSG00000064353' => 'mt-Td',
'ENSMUSG00000064354' => 'mt-Co2'
),
'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) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 20 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 30 => 'Ovary',
(int) 33 => '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) 12,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000093606' => array(
'start' => '6425',
'end' => '7975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co1-201'
),
'ENSDART00000093609' => array(
'start' => '8130',
'end' => '8820',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co2-201'
),
'ENSDART00000117474' => array(
'start' => '7976',
'end' => '8046',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.9-201'
),
'ENSDART00000117438' => array(
'start' => '8049',
'end' => '8117',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.24-201'
),
'ENST00000361739' => array(
'start' => '7586',
'end' => '8269',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO2-201'
),
'ENST00000361624' => array(
'start' => '5904',
'end' => '7445',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO1-201'
),
'ENST00000387416' => array(
'start' => '7446',
'end' => '7514',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TS1-201'
),
'ENST00000387419' => array(
'start' => '7518',
'end' => '7585',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TD-201'
),
'ENSMUST00000082402' => array(
'start' => '5328',
'end' => '6872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co1-201'
),
'ENSMUST00000082403' => array(
'start' => '6870',
'end' => '6938',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ts1-201'
),
'ENSMUST00000082404' => array(
'start' => '6942',
'end' => '7011',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Td-201'
),
'ENSMUST00000082405' => array(
'start' => '7013',
'end' => '7696',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co2-201'
)
),
'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_00013F_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00013F_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00013F_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063905' => array(
[maximum depth reached]
),
'ENSDARG00000063908' => array(
[maximum depth reached]
),
'ENSDARG00000081369' => 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 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Muscle'
)
),
'CIL_00013F_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064351' => array(
[maximum depth reached]
),
'ENSMUSG00000064353' => array(
[maximum depth reached]
),
'ENSMUSG00000064354' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Ovary',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000063905' => 'cytochrome c oxidase I, mitochondrial',
'ENSDARG00000063908' => 'cytochrome c oxidase II, mitochondrial',
'ENSDARG00000081369' => null,
'ENSDARG00000083519' => null,
'ENSG00000198712' => 'mitochondrially encoded cytochrome c oxidase II',
'ENSG00000198804' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSG00000210151' => 'mitochondrially encoded tRNA serine 1 (UCN)',
'ENSG00000210154' => 'mitochondrially encoded tRNA aspartic acid',
'ENSMUSG00000064351' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSMUSG00000064352' => 'mitochondrially encoded tRNA serine 1',
'ENSMUSG00000064353' => 'mitochondrially encoded tRNA aspartic acid',
'ENSMUSG00000064354' => 'mitochondrially encoded cytochrome c oxidase II'
)
$gene_name_arr = array(
'ENSDARG00000063905' => 'mt-co1',
'ENSDARG00000063908' => 'mt-co2',
'ENSDARG00000081369' => 'AC024175.9',
'ENSDARG00000083519' => 'AC024175.24',
'ENSG00000198712' => 'MT-CO2',
'ENSG00000198804' => 'MT-CO1',
'ENSG00000210151' => 'MT-TS1',
'ENSG00000210154' => 'MT-TD',
'ENSMUSG00000064351' => 'mt-Co1',
'ENSMUSG00000064352' => 'mt-Ts1',
'ENSMUSG00000064353' => 'mt-Td',
'ENSMUSG00000064354' => 'mt-Co2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013F_0001',
'tax_id' => '7955',
'chromosome' => 'MT',
'seq_start' => '6425',
'seq_end' => '8820',
'region_length' => '2395',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000063905-ENSDARG00000063908'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013F_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '5904',
'seq_end' => '8269',
'region_length' => '2365',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198804-ENSG00000198712'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013F_0003',
'tax_id' => '10090',
'chromosome' => 'MT',
'seq_start' => '5328',
'seq_end' => '7696',
'region_length' => '2368',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000064351-ENSMUSG00000064354'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Brain',
(int) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 20 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 30 => 'Ovary',
(int) 33 => '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) 12
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000093606' => array(
'start' => '6425',
'end' => '7975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co1-201'
),
'ENSDART00000093609' => array(
'start' => '8130',
'end' => '8820',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co2-201'
),
'ENSDART00000117474' => array(
'start' => '7976',
'end' => '8046',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.9-201'
),
'ENSDART00000117438' => array(
'start' => '8049',
'end' => '8117',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.24-201'
),
'ENST00000361739' => array(
'start' => '7586',
'end' => '8269',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO2-201'
),
'ENST00000361624' => array(
'start' => '5904',
'end' => '7445',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO1-201'
),
'ENST00000387416' => array(
'start' => '7446',
'end' => '7514',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TS1-201'
),
'ENST00000387419' => array(
'start' => '7518',
'end' => '7585',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TD-201'
),
'ENSMUST00000082402' => array(
'start' => '5328',
'end' => '6872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co1-201'
),
'ENSMUST00000082403' => array(
'start' => '6870',
'end' => '6938',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ts1-201'
),
'ENSMUST00000082404' => array(
'start' => '6942',
'end' => '7011',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Td-201'
),
'ENSMUST00000082405' => array(
'start' => '7013',
'end' => '7696',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Co2-201'
)
)
$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_00013F_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063905' => array(
[maximum depth reached]
),
'ENSDARG00000063908' => array(
[maximum depth reached]
),
'ENSDARG00000081369' => 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 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Muscle'
)
),
'CIL_00013F_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064351' => array(
[maximum depth reached]
),
'ENSMUSG00000064353' => array(
[maximum depth reached]
),
'ENSMUSG00000064354' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Ovary',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00013F_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '5904',
'seq_end' => '8269',
'region_length' => '2365',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198804-ENSG00000198712'
)
)
$gene_el = array(
'ENSDART00000117474' => array(
'Brain' => array(
'average_FPKM' => '18495.699',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '7995.950',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1070.030',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '20760.199',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000081369'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '18495.699',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '7995.950',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1070.030',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '20760.199',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000117474'
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-co1)