| Source ID |
Type |
Tax ID |
Position |
| ENSG00000135390-ENSG00000012822 |
CGP |
9606 |
12:53632726-53727745  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00003I_0001 [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_00003I_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000012822' => 'calcium binding and coiled-coil domain 1',
'ENSG00000135390' => 'ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)',
'ENSG00000213470' => null,
'ENSMUSG00000023055' => 'calcium binding and coiled coil domain 1',
'ENSMUSG00000062683' => 'ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)',
'ENSMUSG00000076009' => 'microRNA 688'
),
'gene_name_arr' => array(
'ENSG00000012822' => 'CALCOCO1',
'ENSG00000135390' => 'ATP5G2',
'ENSG00000213470' => 'RP11-972K6.1',
'ENSMUSG00000023055' => 'Calcoco1',
'ENSMUSG00000062683' => 'Atp5g2',
'ENSMUSG00000076009' => 'Mir688'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 20 => 'Brain',
(int) 31 => 'Breast',
(int) 42 => 'Colon',
(int) 51 => 'Heart',
(int) 58 => 'Kidney',
(int) 67 => 'Liver',
(int) 75 => 'Lung',
(int) 83 => 'Muscle',
(int) 91 => 'Ovary',
(int) 104 => 'Placenta',
(int) 116 => '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) 41,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000262059' => array(
'start' => '53708517',
'end' => '53727745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-004'
),
'ENST00000430117' => array(
'start' => '53711119',
'end' => '53727439',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-006'
),
'ENST00000546443' => array(
'start' => '53711119',
'end' => '53714629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-011'
),
'ENST00000546619' => array(
'start' => '53722155',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-027'
),
'ENST00000546774' => array(
'start' => '53724583',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-018'
),
'ENST00000547885' => array(
'start' => '53724044',
'end' => '53727467',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CALCOCO1-019'
),
'ENST00000547949' => array(
'start' => '53722164',
'end' => '53725267',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CALCOCO1-021'
),
'ENST00000547988' => array(
'start' => '53719772',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-005'
),
'ENST00000548177' => array(
'start' => '53723640',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-016'
),
'ENST00000548263' => array(
'start' => '53711159',
'end' => '53727428',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-003'
),
'ENST00000548431' => array(
'start' => '53724404',
'end' => '53727491',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-020'
),
'ENST00000549173' => array(
'start' => '53723621',
'end' => '53727451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-030'
),
'ENST00000549349' => array(
'start' => '53723696',
'end' => '53727457',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-015'
),
'ENST00000549613' => array(
'start' => '53714137',
'end' => '53716349',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-013'
),
'ENST00000549688' => array(
'start' => '53723729',
'end' => '53726340',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-024'
),
'ENST00000549784' => array(
'start' => '53723594',
'end' => '53727606',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-017'
),
'ENST00000549935' => array(
'start' => '53713170',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-007'
),
'ENST00000550804' => array(
'start' => '53711790',
'end' => '53727440',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-001'
),
'ENST00000551900' => array(
'start' => '53722140',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-028'
),
'ENST00000552282' => array(
'start' => '53715675',
'end' => '53719778',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-022'
),
'ENST00000552623' => array(
'start' => '53723683',
'end' => '53726340',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-025'
),
'ENST00000553154' => array(
'start' => '53723550',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-026'
),
'ENST00000338662' => array(
'start' => '53665202',
'end' => '53677398',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-002'
),
'ENST00000394349' => array(
'start' => '53665166',
'end' => '53676325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-003'
),
'ENST00000495596' => array(
'start' => '53665171',
'end' => '53674021',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5G2-001'
),
'ENST00000549164' => array(
'start' => '53665183',
'end' => '53676398',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-006'
),
'ENST00000549748' => array(
'start' => '53665239',
'end' => '53676082',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-007'
),
'ENST00000550241' => array(
'start' => '53632726',
'end' => '53669212',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5G2-009'
),
'ENST00000552120' => array(
'start' => '53669222',
'end' => '53670261',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5G2-008'
),
'ENST00000552242' => array(
'start' => '53665171',
'end' => '53677408',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-004'
),
'ENST00000602871' => array(
'start' => '53665166',
'end' => '53676115',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-010'
),
'ENST00000462065' => array(
'start' => '53632788',
'end' => '53633151',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-972K6.1-001'
),
'ENSMUST00000023818' => array(
'start' => '102706779',
'end' => '102722178',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-001'
),
'ENSMUST00000166943' => array(
'start' => '102710225',
'end' => '102715796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Calcoco1-004'
),
'ENSMUST00000168112' => array(
'start' => '102706972',
'end' => '102709902',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-003'
),
'ENSMUST00000171838' => array(
'start' => '102707585',
'end' => '102722131',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-002'
),
'ENSMUST00000075630' => array(
'start' => '102663014',
'end' => '102667749',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-201'
),
'ENSMUST00000185641' => array(
'start' => '102662864',
'end' => '102671127',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-001'
),
'ENSMUST00000186952' => array(
'start' => '102665801',
'end' => '102672352',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-002'
),
'ENSMUST00000187160' => array(
'start' => '102664739',
'end' => '102667743',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-003'
),
'ENSMUST00000102055' => array(
'start' => '102671792',
'end' => '102671866',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir688-201'
)
),
'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_00003I_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00003I_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000023055' => array(
[maximum depth reached]
),
'ENSMUSG00000062683' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Ovary',
(int) 16 => 'Placenta',
(int) 17 => 'Testis',
(int) 18 => 'Breast',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Adrenal',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Brain',
(int) 33 => 'Muscle',
(int) 34 => 'Ovary',
(int) 35 => 'Placenta',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000012822' => 'calcium binding and coiled-coil domain 1',
'ENSG00000135390' => 'ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)',
'ENSG00000213470' => null,
'ENSMUSG00000023055' => 'calcium binding and coiled coil domain 1',
'ENSMUSG00000062683' => 'ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)',
'ENSMUSG00000076009' => 'microRNA 688'
)
$gene_name_arr = array(
'ENSG00000012822' => 'CALCOCO1',
'ENSG00000135390' => 'ATP5G2',
'ENSG00000213470' => 'RP11-972K6.1',
'ENSMUSG00000023055' => 'Calcoco1',
'ENSMUSG00000062683' => 'Atp5g2',
'ENSMUSG00000076009' => 'Mir688'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00003I_0001',
'tax_id' => '9606',
'chromosome' => '12',
'seq_start' => '53632726',
'seq_end' => '53727745',
'region_length' => '95019',
'region_type' => 'CGP',
'el_id' => 'ENSG00000135390-ENSG00000012822'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00003I_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '102662864',
'seq_end' => '102722178',
'region_length' => '59314',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000062683-ENSMUSG00000023055'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 20 => 'Brain',
(int) 31 => 'Breast',
(int) 42 => 'Colon',
(int) 51 => 'Heart',
(int) 58 => 'Kidney',
(int) 67 => 'Liver',
(int) 75 => 'Lung',
(int) 83 => 'Muscle',
(int) 91 => 'Ovary',
(int) 104 => 'Placenta',
(int) 116 => '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) 41
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000262059' => array(
'start' => '53708517',
'end' => '53727745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-004'
),
'ENST00000430117' => array(
'start' => '53711119',
'end' => '53727439',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-006'
),
'ENST00000546443' => array(
'start' => '53711119',
'end' => '53714629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-011'
),
'ENST00000546619' => array(
'start' => '53722155',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-027'
),
'ENST00000546774' => array(
'start' => '53724583',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-018'
),
'ENST00000547885' => array(
'start' => '53724044',
'end' => '53727467',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CALCOCO1-019'
),
'ENST00000547949' => array(
'start' => '53722164',
'end' => '53725267',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CALCOCO1-021'
),
'ENST00000547988' => array(
'start' => '53719772',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-005'
),
'ENST00000548177' => array(
'start' => '53723640',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-016'
),
'ENST00000548263' => array(
'start' => '53711159',
'end' => '53727428',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-003'
),
'ENST00000548431' => array(
'start' => '53724404',
'end' => '53727491',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-020'
),
'ENST00000549173' => array(
'start' => '53723621',
'end' => '53727451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-030'
),
'ENST00000549349' => array(
'start' => '53723696',
'end' => '53727457',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-015'
),
'ENST00000549613' => array(
'start' => '53714137',
'end' => '53716349',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-013'
),
'ENST00000549688' => array(
'start' => '53723729',
'end' => '53726340',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-024'
),
'ENST00000549784' => array(
'start' => '53723594',
'end' => '53727606',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-017'
),
'ENST00000549935' => array(
'start' => '53713170',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-007'
),
'ENST00000550804' => array(
'start' => '53711790',
'end' => '53727440',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-001'
),
'ENST00000551900' => array(
'start' => '53722140',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-028'
),
'ENST00000552282' => array(
'start' => '53715675',
'end' => '53719778',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-022'
),
'ENST00000552623' => array(
'start' => '53723683',
'end' => '53726340',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-025'
),
'ENST00000553154' => array(
'start' => '53723550',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-026'
),
'ENST00000338662' => array(
'start' => '53665202',
'end' => '53677398',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-002'
),
'ENST00000394349' => array(
'start' => '53665166',
'end' => '53676325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-003'
),
'ENST00000495596' => array(
'start' => '53665171',
'end' => '53674021',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5G2-001'
),
'ENST00000549164' => array(
'start' => '53665183',
'end' => '53676398',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-006'
),
'ENST00000549748' => array(
'start' => '53665239',
'end' => '53676082',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-007'
),
'ENST00000550241' => array(
'start' => '53632726',
'end' => '53669212',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5G2-009'
),
'ENST00000552120' => array(
'start' => '53669222',
'end' => '53670261',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5G2-008'
),
'ENST00000552242' => array(
'start' => '53665171',
'end' => '53677408',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-004'
),
'ENST00000602871' => array(
'start' => '53665166',
'end' => '53676115',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-010'
),
'ENST00000462065' => array(
'start' => '53632788',
'end' => '53633151',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-972K6.1-001'
),
'ENSMUST00000023818' => array(
'start' => '102706779',
'end' => '102722178',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-001'
),
'ENSMUST00000166943' => array(
'start' => '102710225',
'end' => '102715796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Calcoco1-004'
),
'ENSMUST00000168112' => array(
'start' => '102706972',
'end' => '102709902',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-003'
),
'ENSMUST00000171838' => array(
'start' => '102707585',
'end' => '102722131',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-002'
),
'ENSMUST00000075630' => array(
'start' => '102663014',
'end' => '102667749',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-201'
),
'ENSMUST00000185641' => array(
'start' => '102662864',
'end' => '102671127',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-001'
),
'ENSMUST00000186952' => array(
'start' => '102665801',
'end' => '102672352',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-002'
),
'ENSMUST00000187160' => array(
'start' => '102664739',
'end' => '102667743',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-003'
),
'ENSMUST00000102055' => array(
'start' => '102671792',
'end' => '102671866',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir688-201'
)
)
$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_00003I_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000023055' => array(
[maximum depth reached]
),
'ENSMUSG00000062683' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Ovary',
(int) 16 => 'Placenta',
(int) 17 => 'Testis',
(int) 18 => 'Breast',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Adrenal',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Brain',
(int) 33 => 'Muscle',
(int) 34 => 'Ovary',
(int) 35 => 'Placenta',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00003I_0001',
'tax_id' => '9606',
'chromosome' => '12',
'seq_start' => '53632726',
'seq_end' => '53727745',
'region_length' => '95019',
'region_type' => 'CGP',
'el_id' => 'ENSG00000135390-ENSG00000012822'
)
)
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00003I_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000012822' => 'calcium binding and coiled-coil domain 1',
'ENSG00000135390' => 'ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)',
'ENSG00000213470' => null,
'ENSMUSG00000023055' => 'calcium binding and coiled coil domain 1',
'ENSMUSG00000062683' => 'ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)',
'ENSMUSG00000076009' => 'microRNA 688'
),
'gene_name_arr' => array(
'ENSG00000012822' => 'CALCOCO1',
'ENSG00000135390' => 'ATP5G2',
'ENSG00000213470' => 'RP11-972K6.1',
'ENSMUSG00000023055' => 'Calcoco1',
'ENSMUSG00000062683' => 'Atp5g2',
'ENSMUSG00000076009' => 'Mir688'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 20 => 'Brain',
(int) 31 => 'Breast',
(int) 42 => 'Colon',
(int) 51 => 'Heart',
(int) 58 => 'Kidney',
(int) 67 => 'Liver',
(int) 75 => 'Lung',
(int) 83 => 'Muscle',
(int) 91 => 'Ovary',
(int) 104 => 'Placenta',
(int) 116 => '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) 41,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000262059' => array(
'start' => '53708517',
'end' => '53727745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-004'
),
'ENST00000430117' => array(
'start' => '53711119',
'end' => '53727439',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-006'
),
'ENST00000546443' => array(
'start' => '53711119',
'end' => '53714629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-011'
),
'ENST00000546619' => array(
'start' => '53722155',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-027'
),
'ENST00000546774' => array(
'start' => '53724583',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-018'
),
'ENST00000547885' => array(
'start' => '53724044',
'end' => '53727467',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CALCOCO1-019'
),
'ENST00000547949' => array(
'start' => '53722164',
'end' => '53725267',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CALCOCO1-021'
),
'ENST00000547988' => array(
'start' => '53719772',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-005'
),
'ENST00000548177' => array(
'start' => '53723640',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-016'
),
'ENST00000548263' => array(
'start' => '53711159',
'end' => '53727428',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-003'
),
'ENST00000548431' => array(
'start' => '53724404',
'end' => '53727491',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-020'
),
'ENST00000549173' => array(
'start' => '53723621',
'end' => '53727451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-030'
),
'ENST00000549349' => array(
'start' => '53723696',
'end' => '53727457',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-015'
),
'ENST00000549613' => array(
'start' => '53714137',
'end' => '53716349',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-013'
),
'ENST00000549688' => array(
'start' => '53723729',
'end' => '53726340',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-024'
),
'ENST00000549784' => array(
'start' => '53723594',
'end' => '53727606',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-017'
),
'ENST00000549935' => array(
'start' => '53713170',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-007'
),
'ENST00000550804' => array(
'start' => '53711790',
'end' => '53727440',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-001'
),
'ENST00000551900' => array(
'start' => '53722140',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-028'
),
'ENST00000552282' => array(
'start' => '53715675',
'end' => '53719778',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-022'
),
'ENST00000552623' => array(
'start' => '53723683',
'end' => '53726340',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-025'
),
'ENST00000553154' => array(
'start' => '53723550',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-026'
),
'ENST00000338662' => array(
'start' => '53665202',
'end' => '53677398',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-002'
),
'ENST00000394349' => array(
'start' => '53665166',
'end' => '53676325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-003'
),
'ENST00000495596' => array(
'start' => '53665171',
'end' => '53674021',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5G2-001'
),
'ENST00000549164' => array(
'start' => '53665183',
'end' => '53676398',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-006'
),
'ENST00000549748' => array(
'start' => '53665239',
'end' => '53676082',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-007'
),
'ENST00000550241' => array(
'start' => '53632726',
'end' => '53669212',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5G2-009'
),
'ENST00000552120' => array(
'start' => '53669222',
'end' => '53670261',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5G2-008'
),
'ENST00000552242' => array(
'start' => '53665171',
'end' => '53677408',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-004'
),
'ENST00000602871' => array(
'start' => '53665166',
'end' => '53676115',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-010'
),
'ENST00000462065' => array(
'start' => '53632788',
'end' => '53633151',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-972K6.1-001'
),
'ENSMUST00000023818' => array(
'start' => '102706779',
'end' => '102722178',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-001'
),
'ENSMUST00000166943' => array(
'start' => '102710225',
'end' => '102715796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Calcoco1-004'
),
'ENSMUST00000168112' => array(
'start' => '102706972',
'end' => '102709902',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-003'
),
'ENSMUST00000171838' => array(
'start' => '102707585',
'end' => '102722131',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-002'
),
'ENSMUST00000075630' => array(
'start' => '102663014',
'end' => '102667749',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-201'
),
'ENSMUST00000185641' => array(
'start' => '102662864',
'end' => '102671127',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-001'
),
'ENSMUST00000186952' => array(
'start' => '102665801',
'end' => '102672352',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-002'
),
'ENSMUST00000187160' => array(
'start' => '102664739',
'end' => '102667743',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-003'
),
'ENSMUST00000102055' => array(
'start' => '102671792',
'end' => '102671866',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir688-201'
)
),
'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_00003I_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00003I_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000023055' => array(
[maximum depth reached]
),
'ENSMUSG00000062683' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Ovary',
(int) 16 => 'Placenta',
(int) 17 => 'Testis',
(int) 18 => 'Breast',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Adrenal',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Brain',
(int) 33 => 'Muscle',
(int) 34 => 'Ovary',
(int) 35 => 'Placenta',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000012822' => 'calcium binding and coiled-coil domain 1',
'ENSG00000135390' => 'ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)',
'ENSG00000213470' => null,
'ENSMUSG00000023055' => 'calcium binding and coiled coil domain 1',
'ENSMUSG00000062683' => 'ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)',
'ENSMUSG00000076009' => 'microRNA 688'
)
$gene_name_arr = array(
'ENSG00000012822' => 'CALCOCO1',
'ENSG00000135390' => 'ATP5G2',
'ENSG00000213470' => 'RP11-972K6.1',
'ENSMUSG00000023055' => 'Calcoco1',
'ENSMUSG00000062683' => 'Atp5g2',
'ENSMUSG00000076009' => 'Mir688'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00003I_0001',
'tax_id' => '9606',
'chromosome' => '12',
'seq_start' => '53632726',
'seq_end' => '53727745',
'region_length' => '95019',
'region_type' => 'CGP',
'el_id' => 'ENSG00000135390-ENSG00000012822'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00003I_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '102662864',
'seq_end' => '102722178',
'region_length' => '59314',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000062683-ENSMUSG00000023055'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 20 => 'Brain',
(int) 31 => 'Breast',
(int) 42 => 'Colon',
(int) 51 => 'Heart',
(int) 58 => 'Kidney',
(int) 67 => 'Liver',
(int) 75 => 'Lung',
(int) 83 => 'Muscle',
(int) 91 => 'Ovary',
(int) 104 => 'Placenta',
(int) 116 => '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) 41
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000262059' => array(
'start' => '53708517',
'end' => '53727745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-004'
),
'ENST00000430117' => array(
'start' => '53711119',
'end' => '53727439',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-006'
),
'ENST00000546443' => array(
'start' => '53711119',
'end' => '53714629',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-011'
),
'ENST00000546619' => array(
'start' => '53722155',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-027'
),
'ENST00000546774' => array(
'start' => '53724583',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-018'
),
'ENST00000547885' => array(
'start' => '53724044',
'end' => '53727467',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CALCOCO1-019'
),
'ENST00000547949' => array(
'start' => '53722164',
'end' => '53725267',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CALCOCO1-021'
),
'ENST00000547988' => array(
'start' => '53719772',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-005'
),
'ENST00000548177' => array(
'start' => '53723640',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-016'
),
'ENST00000548263' => array(
'start' => '53711159',
'end' => '53727428',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-003'
),
'ENST00000548431' => array(
'start' => '53724404',
'end' => '53727491',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-020'
),
'ENST00000549173' => array(
'start' => '53723621',
'end' => '53727451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-030'
),
'ENST00000549349' => array(
'start' => '53723696',
'end' => '53727457',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-015'
),
'ENST00000549613' => array(
'start' => '53714137',
'end' => '53716349',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-013'
),
'ENST00000549688' => array(
'start' => '53723729',
'end' => '53726340',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-024'
),
'ENST00000549784' => array(
'start' => '53723594',
'end' => '53727606',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-017'
),
'ENST00000549935' => array(
'start' => '53713170',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-007'
),
'ENST00000550804' => array(
'start' => '53711790',
'end' => '53727440',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-001'
),
'ENST00000551900' => array(
'start' => '53722140',
'end' => '53727452',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-028'
),
'ENST00000552282' => array(
'start' => '53715675',
'end' => '53719778',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-022'
),
'ENST00000552623' => array(
'start' => '53723683',
'end' => '53726340',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CALCOCO1-025'
),
'ENST00000553154' => array(
'start' => '53723550',
'end' => '53727452',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CALCOCO1-026'
),
'ENST00000338662' => array(
'start' => '53665202',
'end' => '53677398',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-002'
),
'ENST00000394349' => array(
'start' => '53665166',
'end' => '53676325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-003'
),
'ENST00000495596' => array(
'start' => '53665171',
'end' => '53674021',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5G2-001'
),
'ENST00000549164' => array(
'start' => '53665183',
'end' => '53676398',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-006'
),
'ENST00000549748' => array(
'start' => '53665239',
'end' => '53676082',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-007'
),
'ENST00000550241' => array(
'start' => '53632726',
'end' => '53669212',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP5G2-009'
),
'ENST00000552120' => array(
'start' => '53669222',
'end' => '53670261',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP5G2-008'
),
'ENST00000552242' => array(
'start' => '53665171',
'end' => '53677408',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-004'
),
'ENST00000602871' => array(
'start' => '53665166',
'end' => '53676115',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP5G2-010'
),
'ENST00000462065' => array(
'start' => '53632788',
'end' => '53633151',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-972K6.1-001'
),
'ENSMUST00000023818' => array(
'start' => '102706779',
'end' => '102722178',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-001'
),
'ENSMUST00000166943' => array(
'start' => '102710225',
'end' => '102715796',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Calcoco1-004'
),
'ENSMUST00000168112' => array(
'start' => '102706972',
'end' => '102709902',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-003'
),
'ENSMUST00000171838' => array(
'start' => '102707585',
'end' => '102722131',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Calcoco1-002'
),
'ENSMUST00000075630' => array(
'start' => '102663014',
'end' => '102667749',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-201'
),
'ENSMUST00000185641' => array(
'start' => '102662864',
'end' => '102671127',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-001'
),
'ENSMUST00000186952' => array(
'start' => '102665801',
'end' => '102672352',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-002'
),
'ENSMUST00000187160' => array(
'start' => '102664739',
'end' => '102667743',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Atp5g2-003'
),
'ENSMUST00000102055' => array(
'start' => '102671792',
'end' => '102671866',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir688-201'
)
)
$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_00003I_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000023055' => array(
[maximum depth reached]
),
'ENSMUSG00000062683' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Brain',
(int) 15 => 'Ovary',
(int) 16 => 'Placenta',
(int) 17 => 'Testis',
(int) 18 => 'Breast',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Adrenal',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Brain',
(int) 33 => 'Muscle',
(int) 34 => 'Ovary',
(int) 35 => 'Placenta',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00003I_0001',
'tax_id' => '9606',
'chromosome' => '12',
'seq_start' => '53632726',
'seq_end' => '53727745',
'region_length' => '95019',
'region_type' => 'CGP',
'el_id' => 'ENSG00000135390-ENSG00000012822'
)
)
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
(Calcoco1)