Notice (8): Undefined index: CIL_00066U_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_00066U_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000277117' => 'inducible T-cell co-stimulator ligand',
'ENSG00000279493' => null,
'ENSMUSG00000000730' => 'DNA (cytosine-5-)-methyltransferase 3-like',
'ENSMUSG00000000731' => 'autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)',
'ENSMUSG00000000732' => 'icos ligand'
),
'gene_name_arr' => array(
'ENSG00000277117' => 'ICOSLG',
'ENSG00000279493' => 'CH507-9B2.2',
'ENSMUSG00000000730' => 'Dnmt3l',
'ENSMUSG00000000731' => 'Aire',
'ENSMUSG00000000732' => 'Icosl'
),
'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) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 16 => 'Breast',
(int) 26 => 'Colon',
(int) 34 => 'Heart',
(int) 42 => 'Kidney',
(int) 53 => 'Liver',
(int) 59 => 'Lung',
(int) 68 => 'Muscle',
(int) 75 => 'Ovary',
(int) 85 => 'Placenta',
(int) 90 => '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) 31,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000612610' => array(
'start' => '5022493',
'end' => '5040661',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-003'
),
'ENST00000620481' => array(
'start' => '5022493',
'end' => '5040666',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-201'
),
'ENST00000623795' => array(
'start' => '5022533',
'end' => '5036125',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-004'
),
'ENST00000623903' => array(
'start' => '5022531',
'end' => '5034684',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ICOSLG-002'
),
'ENST00000623960' => array(
'start' => '5022494',
'end' => '5036771',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-001'
),
'ENST00000624081' => array(
'start' => '5011799',
'end' => '5017145',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CH507-9B2.2-001'
),
'ENSMUST00000000746' => array(
'start' => '78049842',
'end' => '78063622',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-003'
),
'ENSMUST00000123940' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-006'
),
'ENSMUST00000131825' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-004'
),
'ENSMUST00000135316' => array(
'start' => '78041947',
'end' => '78045903',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Dnmt3l-007'
),
'ENSMUST00000138785' => array(
'start' => '78042287',
'end' => '78063622',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-001'
),
'ENSMUST00000139539' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-005'
),
'ENSMUST00000144446' => array(
'start' => '78054835',
'end' => '78057368',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Dnmt3l-008'
),
'ENSMUST00000151242' => array(
'start' => '78049959',
'end' => '78063616',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-002'
),
'ENSMUST00000019257' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-008'
),
'ENSMUST00000105395' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-010'
),
'ENSMUST00000105396' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-012'
),
'ENSMUST00000128241' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-007'
),
'ENSMUST00000130972' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-002'
),
'ENSMUST00000131028' => array(
'start' => '78030023',
'end' => '78043610',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Aire-013'
),
'ENSMUST00000140636' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-004'
),
'ENSMUST00000141255' => array(
'start' => '78036264',
'end' => '78041717',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-014'
),
'ENSMUST00000143452' => array(
'start' => '78031855',
'end' => '78038260',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-016'
),
'ENSMUST00000143548' => array(
'start' => '78030023',
'end' => '78038258',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-015'
),
'ENSMUST00000143735' => array(
'start' => '78030071',
'end' => '78043572',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Aire-009'
),
'ENSMUST00000145975' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-001'
),
'ENSMUST00000148469' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-005'
),
'ENSMUST00000154374' => array(
'start' => '78030071',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-006'
),
'ENSMUST00000155021' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-003'
),
'ENSMUST00000156417' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-011'
),
'ENSMUST00000105393' => array(
'start' => '78069360',
'end' => '78079525',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Icosl-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_00066U_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00066U_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000000730' => array(
[maximum depth reached]
),
'ENSMUSG00000000732' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Ovary',
(int) 1 => 'Placenta',
(int) 2 => 'Testis',
(int) 3 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Muscle',
(int) 12 => 'Ovary',
(int) 13 => 'Ovary',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Lung',
(int) 17 => 'Testis',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Breast',
(int) 33 => 'Breast',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Ovary',
(int) 41 => 'Heart',
(int) 42 => 'Muscle',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Brain',
(int) 46 => 'Heart',
(int) 47 => 'Liver',
(int) 48 => 'Breast',
(int) 49 => 'Kidney',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Kidney',
(int) 54 => 'Colon',
(int) 55 => 'Colon',
(int) 56 => 'Lung',
(int) 57 => 'Muscle',
(int) 58 => 'Kidney',
(int) 59 => 'Lung',
(int) 60 => 'Ovary',
(int) 61 => 'Kidney',
(int) 62 => 'Ovary',
(int) 63 => 'Adipose',
(int) 64 => 'Adrenal',
(int) 65 => 'Bladder',
(int) 66 => 'Brain',
(int) 67 => 'Breast',
(int) 68 => 'Colon',
(int) 69 => 'Heart',
(int) 70 => 'Kidney',
(int) 71 => 'Liver',
(int) 72 => 'Lung',
(int) 73 => 'Muscle',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000277117' => 'inducible T-cell co-stimulator ligand',
'ENSG00000279493' => null,
'ENSMUSG00000000730' => 'DNA (cytosine-5-)-methyltransferase 3-like',
'ENSMUSG00000000731' => 'autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)',
'ENSMUSG00000000732' => 'icos ligand'
)
$gene_name_arr = array(
'ENSG00000277117' => 'ICOSLG',
'ENSG00000279493' => 'CH507-9B2.2',
'ENSMUSG00000000730' => 'Dnmt3l',
'ENSMUSG00000000731' => 'Aire',
'ENSMUSG00000000732' => 'Icosl'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00066U_0001',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '5011799',
'seq_end' => '5040666',
'region_length' => '28867',
'region_type' => 'CGP',
'el_id' => 'ENSG00000279493-ENSG00000277117'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00066U_0002',
'tax_id' => '10090',
'chromosome' => '10',
'seq_start' => '78041947',
'seq_end' => '78079525',
'region_length' => '37578',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000730-ENSMUSG00000000732'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 16 => 'Breast',
(int) 26 => 'Colon',
(int) 34 => 'Heart',
(int) 42 => 'Kidney',
(int) 53 => 'Liver',
(int) 59 => 'Lung',
(int) 68 => 'Muscle',
(int) 75 => 'Ovary',
(int) 85 => 'Placenta',
(int) 90 => '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) 31
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000612610' => array(
'start' => '5022493',
'end' => '5040661',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-003'
),
'ENST00000620481' => array(
'start' => '5022493',
'end' => '5040666',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-201'
),
'ENST00000623795' => array(
'start' => '5022533',
'end' => '5036125',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-004'
),
'ENST00000623903' => array(
'start' => '5022531',
'end' => '5034684',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ICOSLG-002'
),
'ENST00000623960' => array(
'start' => '5022494',
'end' => '5036771',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-001'
),
'ENST00000624081' => array(
'start' => '5011799',
'end' => '5017145',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CH507-9B2.2-001'
),
'ENSMUST00000000746' => array(
'start' => '78049842',
'end' => '78063622',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-003'
),
'ENSMUST00000123940' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-006'
),
'ENSMUST00000131825' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-004'
),
'ENSMUST00000135316' => array(
'start' => '78041947',
'end' => '78045903',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Dnmt3l-007'
),
'ENSMUST00000138785' => array(
'start' => '78042287',
'end' => '78063622',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-001'
),
'ENSMUST00000139539' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-005'
),
'ENSMUST00000144446' => array(
'start' => '78054835',
'end' => '78057368',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Dnmt3l-008'
),
'ENSMUST00000151242' => array(
'start' => '78049959',
'end' => '78063616',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-002'
),
'ENSMUST00000019257' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-008'
),
'ENSMUST00000105395' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-010'
),
'ENSMUST00000105396' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-012'
),
'ENSMUST00000128241' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-007'
),
'ENSMUST00000130972' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-002'
),
'ENSMUST00000131028' => array(
'start' => '78030023',
'end' => '78043610',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Aire-013'
),
'ENSMUST00000140636' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-004'
),
'ENSMUST00000141255' => array(
'start' => '78036264',
'end' => '78041717',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-014'
),
'ENSMUST00000143452' => array(
'start' => '78031855',
'end' => '78038260',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-016'
),
'ENSMUST00000143548' => array(
'start' => '78030023',
'end' => '78038258',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-015'
),
'ENSMUST00000143735' => array(
'start' => '78030071',
'end' => '78043572',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Aire-009'
),
'ENSMUST00000145975' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-001'
),
'ENSMUST00000148469' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-005'
),
'ENSMUST00000154374' => array(
'start' => '78030071',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-006'
),
'ENSMUST00000155021' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-003'
),
'ENSMUST00000156417' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-011'
),
'ENSMUST00000105393' => array(
'start' => '78069360',
'end' => '78079525',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Icosl-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_00066U_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000000730' => array(
[maximum depth reached]
),
'ENSMUSG00000000732' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Ovary',
(int) 1 => 'Placenta',
(int) 2 => 'Testis',
(int) 3 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Muscle',
(int) 12 => 'Ovary',
(int) 13 => 'Ovary',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Lung',
(int) 17 => 'Testis',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Breast',
(int) 33 => 'Breast',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Ovary',
(int) 41 => 'Heart',
(int) 42 => 'Muscle',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Brain',
(int) 46 => 'Heart',
(int) 47 => 'Liver',
(int) 48 => 'Breast',
(int) 49 => 'Kidney',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Kidney',
(int) 54 => 'Colon',
(int) 55 => 'Colon',
(int) 56 => 'Lung',
(int) 57 => 'Muscle',
(int) 58 => 'Kidney',
(int) 59 => 'Lung',
(int) 60 => 'Ovary',
(int) 61 => 'Kidney',
(int) 62 => 'Ovary',
(int) 63 => 'Adipose',
(int) 64 => 'Adrenal',
(int) 65 => 'Bladder',
(int) 66 => 'Brain',
(int) 67 => 'Breast',
(int) 68 => 'Colon',
(int) 69 => 'Heart',
(int) 70 => 'Kidney',
(int) 71 => 'Liver',
(int) 72 => 'Lung',
(int) 73 => 'Muscle',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00066U_0001',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '5011799',
'seq_end' => '5040666',
'region_length' => '28867',
'region_type' => 'CGP',
'el_id' => 'ENSG00000279493-ENSG00000277117'
)
)
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00066U_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000277117' => 'inducible T-cell co-stimulator ligand',
'ENSG00000279493' => null,
'ENSMUSG00000000730' => 'DNA (cytosine-5-)-methyltransferase 3-like',
'ENSMUSG00000000731' => 'autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)',
'ENSMUSG00000000732' => 'icos ligand'
),
'gene_name_arr' => array(
'ENSG00000277117' => 'ICOSLG',
'ENSG00000279493' => 'CH507-9B2.2',
'ENSMUSG00000000730' => 'Dnmt3l',
'ENSMUSG00000000731' => 'Aire',
'ENSMUSG00000000732' => 'Icosl'
),
'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) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 16 => 'Breast',
(int) 26 => 'Colon',
(int) 34 => 'Heart',
(int) 42 => 'Kidney',
(int) 53 => 'Liver',
(int) 59 => 'Lung',
(int) 68 => 'Muscle',
(int) 75 => 'Ovary',
(int) 85 => 'Placenta',
(int) 90 => '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) 31,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000612610' => array(
'start' => '5022493',
'end' => '5040661',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-003'
),
'ENST00000620481' => array(
'start' => '5022493',
'end' => '5040666',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-201'
),
'ENST00000623795' => array(
'start' => '5022533',
'end' => '5036125',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-004'
),
'ENST00000623903' => array(
'start' => '5022531',
'end' => '5034684',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ICOSLG-002'
),
'ENST00000623960' => array(
'start' => '5022494',
'end' => '5036771',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-001'
),
'ENST00000624081' => array(
'start' => '5011799',
'end' => '5017145',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CH507-9B2.2-001'
),
'ENSMUST00000000746' => array(
'start' => '78049842',
'end' => '78063622',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-003'
),
'ENSMUST00000123940' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-006'
),
'ENSMUST00000131825' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-004'
),
'ENSMUST00000135316' => array(
'start' => '78041947',
'end' => '78045903',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Dnmt3l-007'
),
'ENSMUST00000138785' => array(
'start' => '78042287',
'end' => '78063622',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-001'
),
'ENSMUST00000139539' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-005'
),
'ENSMUST00000144446' => array(
'start' => '78054835',
'end' => '78057368',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Dnmt3l-008'
),
'ENSMUST00000151242' => array(
'start' => '78049959',
'end' => '78063616',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-002'
),
'ENSMUST00000019257' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-008'
),
'ENSMUST00000105395' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-010'
),
'ENSMUST00000105396' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-012'
),
'ENSMUST00000128241' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-007'
),
'ENSMUST00000130972' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-002'
),
'ENSMUST00000131028' => array(
'start' => '78030023',
'end' => '78043610',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Aire-013'
),
'ENSMUST00000140636' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-004'
),
'ENSMUST00000141255' => array(
'start' => '78036264',
'end' => '78041717',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-014'
),
'ENSMUST00000143452' => array(
'start' => '78031855',
'end' => '78038260',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-016'
),
'ENSMUST00000143548' => array(
'start' => '78030023',
'end' => '78038258',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-015'
),
'ENSMUST00000143735' => array(
'start' => '78030071',
'end' => '78043572',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Aire-009'
),
'ENSMUST00000145975' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-001'
),
'ENSMUST00000148469' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-005'
),
'ENSMUST00000154374' => array(
'start' => '78030071',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-006'
),
'ENSMUST00000155021' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-003'
),
'ENSMUST00000156417' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-011'
),
'ENSMUST00000105393' => array(
'start' => '78069360',
'end' => '78079525',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Icosl-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_00066U_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00066U_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000000730' => array(
[maximum depth reached]
),
'ENSMUSG00000000732' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Ovary',
(int) 1 => 'Placenta',
(int) 2 => 'Testis',
(int) 3 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Muscle',
(int) 12 => 'Ovary',
(int) 13 => 'Ovary',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Lung',
(int) 17 => 'Testis',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Breast',
(int) 33 => 'Breast',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Ovary',
(int) 41 => 'Heart',
(int) 42 => 'Muscle',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Brain',
(int) 46 => 'Heart',
(int) 47 => 'Liver',
(int) 48 => 'Breast',
(int) 49 => 'Kidney',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Kidney',
(int) 54 => 'Colon',
(int) 55 => 'Colon',
(int) 56 => 'Lung',
(int) 57 => 'Muscle',
(int) 58 => 'Kidney',
(int) 59 => 'Lung',
(int) 60 => 'Ovary',
(int) 61 => 'Kidney',
(int) 62 => 'Ovary',
(int) 63 => 'Adipose',
(int) 64 => 'Adrenal',
(int) 65 => 'Bladder',
(int) 66 => 'Brain',
(int) 67 => 'Breast',
(int) 68 => 'Colon',
(int) 69 => 'Heart',
(int) 70 => 'Kidney',
(int) 71 => 'Liver',
(int) 72 => 'Lung',
(int) 73 => 'Muscle',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000277117' => 'inducible T-cell co-stimulator ligand',
'ENSG00000279493' => null,
'ENSMUSG00000000730' => 'DNA (cytosine-5-)-methyltransferase 3-like',
'ENSMUSG00000000731' => 'autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)',
'ENSMUSG00000000732' => 'icos ligand'
)
$gene_name_arr = array(
'ENSG00000277117' => 'ICOSLG',
'ENSG00000279493' => 'CH507-9B2.2',
'ENSMUSG00000000730' => 'Dnmt3l',
'ENSMUSG00000000731' => 'Aire',
'ENSMUSG00000000732' => 'Icosl'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00066U_0001',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '5011799',
'seq_end' => '5040666',
'region_length' => '28867',
'region_type' => 'CGP',
'el_id' => 'ENSG00000279493-ENSG00000277117'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00066U_0002',
'tax_id' => '10090',
'chromosome' => '10',
'seq_start' => '78041947',
'seq_end' => '78079525',
'region_length' => '37578',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000730-ENSMUSG00000000732'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 16 => 'Breast',
(int) 26 => 'Colon',
(int) 34 => 'Heart',
(int) 42 => 'Kidney',
(int) 53 => 'Liver',
(int) 59 => 'Lung',
(int) 68 => 'Muscle',
(int) 75 => 'Ovary',
(int) 85 => 'Placenta',
(int) 90 => '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) 31
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000612610' => array(
'start' => '5022493',
'end' => '5040661',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-003'
),
'ENST00000620481' => array(
'start' => '5022493',
'end' => '5040666',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-201'
),
'ENST00000623795' => array(
'start' => '5022533',
'end' => '5036125',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-004'
),
'ENST00000623903' => array(
'start' => '5022531',
'end' => '5034684',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ICOSLG-002'
),
'ENST00000623960' => array(
'start' => '5022494',
'end' => '5036771',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ICOSLG-001'
),
'ENST00000624081' => array(
'start' => '5011799',
'end' => '5017145',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CH507-9B2.2-001'
),
'ENSMUST00000000746' => array(
'start' => '78049842',
'end' => '78063622',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-003'
),
'ENSMUST00000123940' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-006'
),
'ENSMUST00000131825' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-004'
),
'ENSMUST00000135316' => array(
'start' => '78041947',
'end' => '78045903',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Dnmt3l-007'
),
'ENSMUST00000138785' => array(
'start' => '78042287',
'end' => '78063622',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-001'
),
'ENSMUST00000139539' => array(
'start' => '78055335',
'end' => '78063615',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-005'
),
'ENSMUST00000144446' => array(
'start' => '78054835',
'end' => '78057368',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Dnmt3l-008'
),
'ENSMUST00000151242' => array(
'start' => '78049959',
'end' => '78063616',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dnmt3l-002'
),
'ENSMUST00000019257' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-008'
),
'ENSMUST00000105395' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-010'
),
'ENSMUST00000105396' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-012'
),
'ENSMUST00000128241' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-007'
),
'ENSMUST00000130972' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-002'
),
'ENSMUST00000131028' => array(
'start' => '78030023',
'end' => '78043610',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Aire-013'
),
'ENSMUST00000140636' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-004'
),
'ENSMUST00000141255' => array(
'start' => '78036264',
'end' => '78041717',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-014'
),
'ENSMUST00000143452' => array(
'start' => '78031855',
'end' => '78038260',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-016'
),
'ENSMUST00000143548' => array(
'start' => '78030023',
'end' => '78038258',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Aire-015'
),
'ENSMUST00000143735' => array(
'start' => '78030071',
'end' => '78043572',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Aire-009'
),
'ENSMUST00000145975' => array(
'start' => '78030022',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-001'
),
'ENSMUST00000148469' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-005'
),
'ENSMUST00000154374' => array(
'start' => '78030071',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-006'
),
'ENSMUST00000155021' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-003'
),
'ENSMUST00000156417' => array(
'start' => '78030031',
'end' => '78043580',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aire-011'
),
'ENSMUST00000105393' => array(
'start' => '78069360',
'end' => '78079525',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Icosl-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_00066U_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000000730' => array(
[maximum depth reached]
),
'ENSMUSG00000000732' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Ovary',
(int) 1 => 'Placenta',
(int) 2 => 'Testis',
(int) 3 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Muscle',
(int) 12 => 'Ovary',
(int) 13 => 'Ovary',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Lung',
(int) 17 => 'Testis',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Breast',
(int) 33 => 'Breast',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Ovary',
(int) 41 => 'Heart',
(int) 42 => 'Muscle',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Brain',
(int) 46 => 'Heart',
(int) 47 => 'Liver',
(int) 48 => 'Breast',
(int) 49 => 'Kidney',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Kidney',
(int) 54 => 'Colon',
(int) 55 => 'Colon',
(int) 56 => 'Lung',
(int) 57 => 'Muscle',
(int) 58 => 'Kidney',
(int) 59 => 'Lung',
(int) 60 => 'Ovary',
(int) 61 => 'Kidney',
(int) 62 => 'Ovary',
(int) 63 => 'Adipose',
(int) 64 => 'Adrenal',
(int) 65 => 'Bladder',
(int) 66 => 'Brain',
(int) 67 => 'Breast',
(int) 68 => 'Colon',
(int) 69 => 'Heart',
(int) 70 => 'Kidney',
(int) 71 => 'Liver',
(int) 72 => 'Lung',
(int) 73 => 'Muscle',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00066U_0001',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '5011799',
'seq_end' => '5040666',
'region_length' => '28867',
'region_type' => 'CGP',
'el_id' => 'ENSG00000279493-ENSG00000277117'
)
)
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
| Source ID |
Type |
Tax ID |
Position |
| ENSG00000279493-ENSG00000277117 |
CGP |
9606 |
21:5011799-5040666  |
| Gene | Transcript | Position | Biotype |
|---|
(Dnmt3l)