| Source ID |
Type |
Tax ID |
Position |
| ENSG00000198763-ENSG00000198804 |
CGP |
9606 |
MT:4470-7445  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00013I_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_00013I_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00013I_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000063899' => 'NADH dehydrogenase 2, mitochondrial',
'ENSDARG00000063905' => 'cytochrome c oxidase I, mitochondrial',
'ENSDARG00000080128' => null,
'ENSDARG00000080401' => null,
'ENSDARG00000080718' => null,
'ENSDARG00000081938' => null,
'ENSDARG00000082789' => null,
'ENSG00000198763' => 'mitochondrially encoded NADH dehydrogenase 2',
'ENSG00000198804' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSG00000210117' => 'mitochondrially encoded tRNA tryptophan',
'ENSG00000210127' => 'mitochondrially encoded tRNA alanine',
'ENSG00000210135' => 'mitochondrially encoded tRNA asparagine',
'ENSG00000210140' => 'mitochondrially encoded tRNA cysteine',
'ENSG00000210144' => 'mitochondrially encoded tRNA tyrosine',
'ENSMUSG00000064345' => 'mitochondrially encoded NADH dehydrogenase 2',
'ENSMUSG00000064346' => 'mitochondrially encoded tRNA tryptophan',
'ENSMUSG00000064347' => 'mitochondrially encoded tRNA alanine',
'ENSMUSG00000064348' => 'mitochondrially encoded tRNA asparagine',
'ENSMUSG00000064349' => 'mitochondrially encoded tRNA cysteine',
'ENSMUSG00000064350' => 'mitochondrially encoded tRNA tyrosine',
'ENSMUSG00000064351' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSMUSG00000064352' => 'mitochondrially encoded tRNA serine 1'
),
'gene_name_arr' => array(
'ENSDARG00000063899' => 'mt-nd2',
'ENSDARG00000063905' => 'mt-co1',
'ENSDARG00000080128' => 'AC024175.1',
'ENSDARG00000080401' => 'AC024175.5',
'ENSDARG00000080718' => 'AC024175.7',
'ENSDARG00000081938' => 'AC024175.13',
'ENSDARG00000082789' => 'AC024175.18',
'ENSG00000198763' => 'MT-ND2',
'ENSG00000198804' => 'MT-CO1',
'ENSG00000210117' => 'MT-TW',
'ENSG00000210127' => 'MT-TA',
'ENSG00000210135' => 'MT-TN',
'ENSG00000210140' => 'MT-TC',
'ENSG00000210144' => 'MT-TY',
'ENSMUSG00000064345' => 'mt-Nd2',
'ENSMUSG00000064346' => 'mt-Tw',
'ENSMUSG00000064347' => 'mt-Ta',
'ENSMUSG00000064348' => 'mt-Tn',
'ENSMUSG00000064349' => 'mt-Tc',
'ENSMUSG00000064350' => 'mt-Ty',
'ENSMUSG00000064351' => 'mt-Co1',
'ENSMUSG00000064352' => 'mt-Ts1'
),
'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) 15 => 'Breast',
(int) 17 => 'Colon',
(int) 19 => 'Heart',
(int) 21 => 'Kidney',
(int) 27 => 'Liver',
(int) 34 => 'Lung',
(int) 36 => 'Muscle',
(int) 42 => 'Ovary',
(int) 47 => 'Placenta',
(int) 49 => '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) 22,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000093600' => array(
'start' => '4993',
'end' => '6039',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-nd2-201'
),
'ENSDART00000093606' => array(
'start' => '6425',
'end' => '7975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co1-201'
),
'ENSDART00000118615' => array(
'start' => '6353',
'end' => '6423',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.1-201'
),
'ENSDART00000118299' => array(
'start' => '6109',
'end' => '6176',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.5-201'
),
'ENSDART00000118316' => array(
'start' => '6038',
'end' => '6107',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.7-201'
),
'ENSDART00000116869' => array(
'start' => '6178',
'end' => '6250',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.13-201'
),
'ENSDART00000116146' => array(
'start' => '6283',
'end' => '6354',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.18-201'
),
'ENST00000361453' => array(
'start' => '4470',
'end' => '5511',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ND2-201'
),
'ENST00000361624' => array(
'start' => '5904',
'end' => '7445',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO1-201'
),
'ENST00000387382' => array(
'start' => '5512',
'end' => '5579',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TW-201'
),
'ENST00000387392' => array(
'start' => '5587',
'end' => '5655',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TA-201'
),
'ENST00000387400' => array(
'start' => '5657',
'end' => '5729',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TN-201'
),
'ENST00000387405' => array(
'start' => '5761',
'end' => '5826',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TC-201'
),
'ENST00000387409' => array(
'start' => '5826',
'end' => '5891',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TY-201'
),
'ENSMUST00000082396' => array(
'start' => '3914',
'end' => '4951',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Nd2-201'
),
'ENSMUST00000082397' => array(
'start' => '4950',
'end' => '5016',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tw-201'
),
'ENSMUST00000082398' => array(
'start' => '5018',
'end' => '5086',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ta-201'
),
'ENSMUST00000082399' => array(
'start' => '5089',
'end' => '5159',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tn-201'
),
'ENSMUST00000082400' => array(
'start' => '5192',
'end' => '5257',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tc-201'
),
'ENSMUST00000082401' => array(
'start' => '5260',
'end' => '5326',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ty-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'
)
),
'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_00013I_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00013I_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00013I_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063899' => array(
[maximum depth reached]
),
'ENSDARG00000063905' => array(
[maximum depth reached]
),
'ENSDARG00000080128' => array(
[maximum depth reached]
),
'ENSDARG00000080401' => array(
[maximum depth reached]
),
'ENSDARG00000081938' => array(
[maximum depth reached]
),
'ENSDARG00000082789' => 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',
(int) 14 => 'Brain',
(int) 15 => 'Muscle',
(int) 16 => 'Brain',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Muscle',
(int) 20 => 'Brain',
(int) 21 => 'Liver',
(int) 22 => 'Muscle'
)
),
'CIL_00013I_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064345' => array(
[maximum depth reached]
),
'ENSMUSG00000064347' => array(
[maximum depth reached]
),
'ENSMUSG00000064348' => array(
[maximum depth reached]
),
'ENSMUSG00000064350' => array(
[maximum depth reached]
),
'ENSMUSG00000064351' => 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 => 'Brain',
(int) 12 => 'Ovary',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Ovary',
(int) 16 => 'Brain',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000063899' => 'NADH dehydrogenase 2, mitochondrial',
'ENSDARG00000063905' => 'cytochrome c oxidase I, mitochondrial',
'ENSDARG00000080128' => null,
'ENSDARG00000080401' => null,
'ENSDARG00000080718' => null,
'ENSDARG00000081938' => null,
'ENSDARG00000082789' => null,
'ENSG00000198763' => 'mitochondrially encoded NADH dehydrogenase 2',
'ENSG00000198804' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSG00000210117' => 'mitochondrially encoded tRNA tryptophan',
'ENSG00000210127' => 'mitochondrially encoded tRNA alanine',
'ENSG00000210135' => 'mitochondrially encoded tRNA asparagine',
'ENSG00000210140' => 'mitochondrially encoded tRNA cysteine',
'ENSG00000210144' => 'mitochondrially encoded tRNA tyrosine',
'ENSMUSG00000064345' => 'mitochondrially encoded NADH dehydrogenase 2',
'ENSMUSG00000064346' => 'mitochondrially encoded tRNA tryptophan',
'ENSMUSG00000064347' => 'mitochondrially encoded tRNA alanine',
'ENSMUSG00000064348' => 'mitochondrially encoded tRNA asparagine',
'ENSMUSG00000064349' => 'mitochondrially encoded tRNA cysteine',
'ENSMUSG00000064350' => 'mitochondrially encoded tRNA tyrosine',
'ENSMUSG00000064351' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSMUSG00000064352' => 'mitochondrially encoded tRNA serine 1'
)
$gene_name_arr = array(
'ENSDARG00000063899' => 'mt-nd2',
'ENSDARG00000063905' => 'mt-co1',
'ENSDARG00000080128' => 'AC024175.1',
'ENSDARG00000080401' => 'AC024175.5',
'ENSDARG00000080718' => 'AC024175.7',
'ENSDARG00000081938' => 'AC024175.13',
'ENSDARG00000082789' => 'AC024175.18',
'ENSG00000198763' => 'MT-ND2',
'ENSG00000198804' => 'MT-CO1',
'ENSG00000210117' => 'MT-TW',
'ENSG00000210127' => 'MT-TA',
'ENSG00000210135' => 'MT-TN',
'ENSG00000210140' => 'MT-TC',
'ENSG00000210144' => 'MT-TY',
'ENSMUSG00000064345' => 'mt-Nd2',
'ENSMUSG00000064346' => 'mt-Tw',
'ENSMUSG00000064347' => 'mt-Ta',
'ENSMUSG00000064348' => 'mt-Tn',
'ENSMUSG00000064349' => 'mt-Tc',
'ENSMUSG00000064350' => 'mt-Ty',
'ENSMUSG00000064351' => 'mt-Co1',
'ENSMUSG00000064352' => 'mt-Ts1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013I_0001',
'tax_id' => '7955',
'chromosome' => 'MT',
'seq_start' => '4993',
'seq_end' => '7975',
'region_length' => '2982',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000063899-ENSDARG00000063905'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013I_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '4470',
'seq_end' => '7445',
'region_length' => '2975',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198763-ENSG00000198804'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013I_0003',
'tax_id' => '10090',
'chromosome' => 'MT',
'seq_start' => '3914',
'seq_end' => '6872',
'region_length' => '2958',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000064345-ENSMUSG00000064351'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Brain',
(int) 15 => 'Breast',
(int) 17 => 'Colon',
(int) 19 => 'Heart',
(int) 21 => 'Kidney',
(int) 27 => 'Liver',
(int) 34 => 'Lung',
(int) 36 => 'Muscle',
(int) 42 => 'Ovary',
(int) 47 => 'Placenta',
(int) 49 => '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) 22
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000093600' => array(
'start' => '4993',
'end' => '6039',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-nd2-201'
),
'ENSDART00000093606' => array(
'start' => '6425',
'end' => '7975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co1-201'
),
'ENSDART00000118615' => array(
'start' => '6353',
'end' => '6423',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.1-201'
),
'ENSDART00000118299' => array(
'start' => '6109',
'end' => '6176',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.5-201'
),
'ENSDART00000118316' => array(
'start' => '6038',
'end' => '6107',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.7-201'
),
'ENSDART00000116869' => array(
'start' => '6178',
'end' => '6250',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.13-201'
),
'ENSDART00000116146' => array(
'start' => '6283',
'end' => '6354',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.18-201'
),
'ENST00000361453' => array(
'start' => '4470',
'end' => '5511',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ND2-201'
),
'ENST00000361624' => array(
'start' => '5904',
'end' => '7445',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO1-201'
),
'ENST00000387382' => array(
'start' => '5512',
'end' => '5579',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TW-201'
),
'ENST00000387392' => array(
'start' => '5587',
'end' => '5655',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TA-201'
),
'ENST00000387400' => array(
'start' => '5657',
'end' => '5729',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TN-201'
),
'ENST00000387405' => array(
'start' => '5761',
'end' => '5826',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TC-201'
),
'ENST00000387409' => array(
'start' => '5826',
'end' => '5891',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TY-201'
),
'ENSMUST00000082396' => array(
'start' => '3914',
'end' => '4951',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Nd2-201'
),
'ENSMUST00000082397' => array(
'start' => '4950',
'end' => '5016',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tw-201'
),
'ENSMUST00000082398' => array(
'start' => '5018',
'end' => '5086',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ta-201'
),
'ENSMUST00000082399' => array(
'start' => '5089',
'end' => '5159',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tn-201'
),
'ENSMUST00000082400' => array(
'start' => '5192',
'end' => '5257',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tc-201'
),
'ENSMUST00000082401' => array(
'start' => '5260',
'end' => '5326',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ty-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'
)
)
$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_00013I_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063899' => array(
[maximum depth reached]
),
'ENSDARG00000063905' => array(
[maximum depth reached]
),
'ENSDARG00000080128' => array(
[maximum depth reached]
),
'ENSDARG00000080401' => array(
[maximum depth reached]
),
'ENSDARG00000081938' => array(
[maximum depth reached]
),
'ENSDARG00000082789' => 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',
(int) 14 => 'Brain',
(int) 15 => 'Muscle',
(int) 16 => 'Brain',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Muscle',
(int) 20 => 'Brain',
(int) 21 => 'Liver',
(int) 22 => 'Muscle'
)
),
'CIL_00013I_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064345' => array(
[maximum depth reached]
),
'ENSMUSG00000064347' => array(
[maximum depth reached]
),
'ENSMUSG00000064348' => array(
[maximum depth reached]
),
'ENSMUSG00000064350' => array(
[maximum depth reached]
),
'ENSMUSG00000064351' => 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 => 'Brain',
(int) 12 => 'Ovary',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Ovary',
(int) 16 => 'Brain',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00013I_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '4470',
'seq_end' => '7445',
'region_length' => '2975',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198763-ENSG00000198804'
)
)
$gene_el = array(
'ENSDART00000116146' => array(
'Brain' => array(
'average_FPKM' => '580.720',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '4.798',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '790.389',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000082789'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '580.720',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '4.798',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '790.389',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000116146'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00013I_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00013I_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000063899' => 'NADH dehydrogenase 2, mitochondrial',
'ENSDARG00000063905' => 'cytochrome c oxidase I, mitochondrial',
'ENSDARG00000080128' => null,
'ENSDARG00000080401' => null,
'ENSDARG00000080718' => null,
'ENSDARG00000081938' => null,
'ENSDARG00000082789' => null,
'ENSG00000198763' => 'mitochondrially encoded NADH dehydrogenase 2',
'ENSG00000198804' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSG00000210117' => 'mitochondrially encoded tRNA tryptophan',
'ENSG00000210127' => 'mitochondrially encoded tRNA alanine',
'ENSG00000210135' => 'mitochondrially encoded tRNA asparagine',
'ENSG00000210140' => 'mitochondrially encoded tRNA cysteine',
'ENSG00000210144' => 'mitochondrially encoded tRNA tyrosine',
'ENSMUSG00000064345' => 'mitochondrially encoded NADH dehydrogenase 2',
'ENSMUSG00000064346' => 'mitochondrially encoded tRNA tryptophan',
'ENSMUSG00000064347' => 'mitochondrially encoded tRNA alanine',
'ENSMUSG00000064348' => 'mitochondrially encoded tRNA asparagine',
'ENSMUSG00000064349' => 'mitochondrially encoded tRNA cysteine',
'ENSMUSG00000064350' => 'mitochondrially encoded tRNA tyrosine',
'ENSMUSG00000064351' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSMUSG00000064352' => 'mitochondrially encoded tRNA serine 1'
),
'gene_name_arr' => array(
'ENSDARG00000063899' => 'mt-nd2',
'ENSDARG00000063905' => 'mt-co1',
'ENSDARG00000080128' => 'AC024175.1',
'ENSDARG00000080401' => 'AC024175.5',
'ENSDARG00000080718' => 'AC024175.7',
'ENSDARG00000081938' => 'AC024175.13',
'ENSDARG00000082789' => 'AC024175.18',
'ENSG00000198763' => 'MT-ND2',
'ENSG00000198804' => 'MT-CO1',
'ENSG00000210117' => 'MT-TW',
'ENSG00000210127' => 'MT-TA',
'ENSG00000210135' => 'MT-TN',
'ENSG00000210140' => 'MT-TC',
'ENSG00000210144' => 'MT-TY',
'ENSMUSG00000064345' => 'mt-Nd2',
'ENSMUSG00000064346' => 'mt-Tw',
'ENSMUSG00000064347' => 'mt-Ta',
'ENSMUSG00000064348' => 'mt-Tn',
'ENSMUSG00000064349' => 'mt-Tc',
'ENSMUSG00000064350' => 'mt-Ty',
'ENSMUSG00000064351' => 'mt-Co1',
'ENSMUSG00000064352' => 'mt-Ts1'
),
'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) 15 => 'Breast',
(int) 17 => 'Colon',
(int) 19 => 'Heart',
(int) 21 => 'Kidney',
(int) 27 => 'Liver',
(int) 34 => 'Lung',
(int) 36 => 'Muscle',
(int) 42 => 'Ovary',
(int) 47 => 'Placenta',
(int) 49 => '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) 22,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000093600' => array(
'start' => '4993',
'end' => '6039',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-nd2-201'
),
'ENSDART00000093606' => array(
'start' => '6425',
'end' => '7975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co1-201'
),
'ENSDART00000118615' => array(
'start' => '6353',
'end' => '6423',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.1-201'
),
'ENSDART00000118299' => array(
'start' => '6109',
'end' => '6176',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.5-201'
),
'ENSDART00000118316' => array(
'start' => '6038',
'end' => '6107',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.7-201'
),
'ENSDART00000116869' => array(
'start' => '6178',
'end' => '6250',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.13-201'
),
'ENSDART00000116146' => array(
'start' => '6283',
'end' => '6354',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.18-201'
),
'ENST00000361453' => array(
'start' => '4470',
'end' => '5511',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ND2-201'
),
'ENST00000361624' => array(
'start' => '5904',
'end' => '7445',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO1-201'
),
'ENST00000387382' => array(
'start' => '5512',
'end' => '5579',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TW-201'
),
'ENST00000387392' => array(
'start' => '5587',
'end' => '5655',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TA-201'
),
'ENST00000387400' => array(
'start' => '5657',
'end' => '5729',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TN-201'
),
'ENST00000387405' => array(
'start' => '5761',
'end' => '5826',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TC-201'
),
'ENST00000387409' => array(
'start' => '5826',
'end' => '5891',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TY-201'
),
'ENSMUST00000082396' => array(
'start' => '3914',
'end' => '4951',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Nd2-201'
),
'ENSMUST00000082397' => array(
'start' => '4950',
'end' => '5016',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tw-201'
),
'ENSMUST00000082398' => array(
'start' => '5018',
'end' => '5086',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ta-201'
),
'ENSMUST00000082399' => array(
'start' => '5089',
'end' => '5159',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tn-201'
),
'ENSMUST00000082400' => array(
'start' => '5192',
'end' => '5257',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tc-201'
),
'ENSMUST00000082401' => array(
'start' => '5260',
'end' => '5326',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ty-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'
)
),
'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_00013I_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00013I_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00013I_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063899' => array(
[maximum depth reached]
),
'ENSDARG00000063905' => array(
[maximum depth reached]
),
'ENSDARG00000080128' => array(
[maximum depth reached]
),
'ENSDARG00000080401' => array(
[maximum depth reached]
),
'ENSDARG00000081938' => array(
[maximum depth reached]
),
'ENSDARG00000082789' => 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',
(int) 14 => 'Brain',
(int) 15 => 'Muscle',
(int) 16 => 'Brain',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Muscle',
(int) 20 => 'Brain',
(int) 21 => 'Liver',
(int) 22 => 'Muscle'
)
),
'CIL_00013I_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064345' => array(
[maximum depth reached]
),
'ENSMUSG00000064347' => array(
[maximum depth reached]
),
'ENSMUSG00000064348' => array(
[maximum depth reached]
),
'ENSMUSG00000064350' => array(
[maximum depth reached]
),
'ENSMUSG00000064351' => 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 => 'Brain',
(int) 12 => 'Ovary',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Ovary',
(int) 16 => 'Brain',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000063899' => 'NADH dehydrogenase 2, mitochondrial',
'ENSDARG00000063905' => 'cytochrome c oxidase I, mitochondrial',
'ENSDARG00000080128' => null,
'ENSDARG00000080401' => null,
'ENSDARG00000080718' => null,
'ENSDARG00000081938' => null,
'ENSDARG00000082789' => null,
'ENSG00000198763' => 'mitochondrially encoded NADH dehydrogenase 2',
'ENSG00000198804' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSG00000210117' => 'mitochondrially encoded tRNA tryptophan',
'ENSG00000210127' => 'mitochondrially encoded tRNA alanine',
'ENSG00000210135' => 'mitochondrially encoded tRNA asparagine',
'ENSG00000210140' => 'mitochondrially encoded tRNA cysteine',
'ENSG00000210144' => 'mitochondrially encoded tRNA tyrosine',
'ENSMUSG00000064345' => 'mitochondrially encoded NADH dehydrogenase 2',
'ENSMUSG00000064346' => 'mitochondrially encoded tRNA tryptophan',
'ENSMUSG00000064347' => 'mitochondrially encoded tRNA alanine',
'ENSMUSG00000064348' => 'mitochondrially encoded tRNA asparagine',
'ENSMUSG00000064349' => 'mitochondrially encoded tRNA cysteine',
'ENSMUSG00000064350' => 'mitochondrially encoded tRNA tyrosine',
'ENSMUSG00000064351' => 'mitochondrially encoded cytochrome c oxidase I',
'ENSMUSG00000064352' => 'mitochondrially encoded tRNA serine 1'
)
$gene_name_arr = array(
'ENSDARG00000063899' => 'mt-nd2',
'ENSDARG00000063905' => 'mt-co1',
'ENSDARG00000080128' => 'AC024175.1',
'ENSDARG00000080401' => 'AC024175.5',
'ENSDARG00000080718' => 'AC024175.7',
'ENSDARG00000081938' => 'AC024175.13',
'ENSDARG00000082789' => 'AC024175.18',
'ENSG00000198763' => 'MT-ND2',
'ENSG00000198804' => 'MT-CO1',
'ENSG00000210117' => 'MT-TW',
'ENSG00000210127' => 'MT-TA',
'ENSG00000210135' => 'MT-TN',
'ENSG00000210140' => 'MT-TC',
'ENSG00000210144' => 'MT-TY',
'ENSMUSG00000064345' => 'mt-Nd2',
'ENSMUSG00000064346' => 'mt-Tw',
'ENSMUSG00000064347' => 'mt-Ta',
'ENSMUSG00000064348' => 'mt-Tn',
'ENSMUSG00000064349' => 'mt-Tc',
'ENSMUSG00000064350' => 'mt-Ty',
'ENSMUSG00000064351' => 'mt-Co1',
'ENSMUSG00000064352' => 'mt-Ts1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013I_0001',
'tax_id' => '7955',
'chromosome' => 'MT',
'seq_start' => '4993',
'seq_end' => '7975',
'region_length' => '2982',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000063899-ENSDARG00000063905'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013I_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '4470',
'seq_end' => '7445',
'region_length' => '2975',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198763-ENSG00000198804'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00013I_0003',
'tax_id' => '10090',
'chromosome' => 'MT',
'seq_start' => '3914',
'seq_end' => '6872',
'region_length' => '2958',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000064345-ENSMUSG00000064351'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Brain',
(int) 15 => 'Breast',
(int) 17 => 'Colon',
(int) 19 => 'Heart',
(int) 21 => 'Kidney',
(int) 27 => 'Liver',
(int) 34 => 'Lung',
(int) 36 => 'Muscle',
(int) 42 => 'Ovary',
(int) 47 => 'Placenta',
(int) 49 => '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) 22
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000093600' => array(
'start' => '4993',
'end' => '6039',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-nd2-201'
),
'ENSDART00000093606' => array(
'start' => '6425',
'end' => '7975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-co1-201'
),
'ENSDART00000118615' => array(
'start' => '6353',
'end' => '6423',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.1-201'
),
'ENSDART00000118299' => array(
'start' => '6109',
'end' => '6176',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.5-201'
),
'ENSDART00000118316' => array(
'start' => '6038',
'end' => '6107',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.7-201'
),
'ENSDART00000116869' => array(
'start' => '6178',
'end' => '6250',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.13-201'
),
'ENSDART00000116146' => array(
'start' => '6283',
'end' => '6354',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'AC024175.18-201'
),
'ENST00000361453' => array(
'start' => '4470',
'end' => '5511',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-ND2-201'
),
'ENST00000361624' => array(
'start' => '5904',
'end' => '7445',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MT-CO1-201'
),
'ENST00000387382' => array(
'start' => '5512',
'end' => '5579',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TW-201'
),
'ENST00000387392' => array(
'start' => '5587',
'end' => '5655',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TA-201'
),
'ENST00000387400' => array(
'start' => '5657',
'end' => '5729',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TN-201'
),
'ENST00000387405' => array(
'start' => '5761',
'end' => '5826',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TC-201'
),
'ENST00000387409' => array(
'start' => '5826',
'end' => '5891',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'MT-TY-201'
),
'ENSMUST00000082396' => array(
'start' => '3914',
'end' => '4951',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'mt-Nd2-201'
),
'ENSMUST00000082397' => array(
'start' => '4950',
'end' => '5016',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tw-201'
),
'ENSMUST00000082398' => array(
'start' => '5018',
'end' => '5086',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ta-201'
),
'ENSMUST00000082399' => array(
'start' => '5089',
'end' => '5159',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tn-201'
),
'ENSMUST00000082400' => array(
'start' => '5192',
'end' => '5257',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Tc-201'
),
'ENSMUST00000082401' => array(
'start' => '5260',
'end' => '5326',
'transcript_biotype' => 'Mt_tRNA',
'transcript_name' => 'mt-Ty-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'
)
)
$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_00013I_0001' => array(
'genes_in_region' => array(
'ENSDARG00000063899' => array(
[maximum depth reached]
),
'ENSDARG00000063905' => array(
[maximum depth reached]
),
'ENSDARG00000080128' => array(
[maximum depth reached]
),
'ENSDARG00000080401' => array(
[maximum depth reached]
),
'ENSDARG00000081938' => array(
[maximum depth reached]
),
'ENSDARG00000082789' => 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',
(int) 14 => 'Brain',
(int) 15 => 'Muscle',
(int) 16 => 'Brain',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Muscle',
(int) 20 => 'Brain',
(int) 21 => 'Liver',
(int) 22 => 'Muscle'
)
),
'CIL_00013I_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000064345' => array(
[maximum depth reached]
),
'ENSMUSG00000064347' => array(
[maximum depth reached]
),
'ENSMUSG00000064348' => array(
[maximum depth reached]
),
'ENSMUSG00000064350' => array(
[maximum depth reached]
),
'ENSMUSG00000064351' => 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 => 'Brain',
(int) 12 => 'Ovary',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Ovary',
(int) 16 => 'Brain',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00013I_0002',
'tax_id' => '9606',
'chromosome' => 'MT',
'seq_start' => '4470',
'seq_end' => '7445',
'region_length' => '2975',
'region_type' => 'CGP',
'el_id' => 'ENSG00000198763-ENSG00000198804'
)
)
$gene_el = array(
'ENSDART00000116146' => array(
'Brain' => array(
'average_FPKM' => '580.720',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '4.798',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '790.389',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000082789'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '580.720',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '4.798',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '790.389',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000116146'
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-nd2)