Notice (8): Undefined index: CIL_0007NG_0004 [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_0007NG_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007NG_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000112246' => 'single-minded family bHLH transcription factor 1',
'ENSG00000112249' => 'activating signal cointegrator 1 complex subunit 3',
'ENSG00000152034' => 'melanin-concentrating hormone receptor 2',
'ENSG00000213177' => 'peroxiredoxin 2 pseudogene 4',
'ENSG00000216378' => null,
'ENSG00000219257' => 'nucleophosmin 1 (nucleolar phosphoprotein B23, numatrin) pseudogene 38',
'ENSG00000220695' => null,
'ENSG00000228082' => null,
'ENSG00000229315' => 'MCHR2 antisense RNA 1',
'ENSG00000275020' => null,
'ENSG00000275716' => null,
'ENSMUSG00000019913' => 'single-minded homolog 1 (Drosophila)',
'ENSMUSG00000038774' => 'activating signal cointegrator 1 complex subunit 3',
'ENSMUSG00000084449' => 'predicted gene, 26257',
'ENSMUSG00000084635' => 'predicted gene, 23883'
),
'gene_name_arr' => array(
'ENSG00000112246' => 'SIM1',
'ENSG00000112249' => 'ASCC3',
'ENSG00000152034' => 'MCHR2',
'ENSG00000213177' => 'PRDX2P4',
'ENSG00000216378' => 'RP3-344J20.1',
'ENSG00000219257' => 'NPM1P38',
'ENSG00000220695' => 'RP1-121G13.3',
'ENSG00000228082' => 'RP1-121G13.2',
'ENSG00000229315' => 'MCHR2-AS1',
'ENSG00000275020' => 'AL080285.1',
'ENSG00000275716' => 'RP3-344J20.3',
'ENSMUSG00000019913' => 'Sim1',
'ENSMUSG00000038774' => 'Ascc3',
'ENSMUSG00000084449' => 'Gm26257',
'ENSMUSG00000084635' => 'Gm23883'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 31 => 'Colon',
(int) 38 => 'Heart',
(int) 42 => 'Kidney',
(int) 49 => 'Liver',
(int) 56 => 'Lung',
(int) 61 => 'Muscle',
(int) 70 => 'Ovary',
(int) 77 => 'Placenta',
(int) 84 => '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) 28,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000262901' => array(
'start' => '100388872',
'end' => '100463677',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SIM1-201'
),
'ENST00000369208' => array(
'start' => '100385015',
'end' => '100464929',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SIM1-001'
),
'ENST00000505753' => array(
'start' => '100391083',
'end' => '100394042',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SIM1-003'
),
'ENST00000511871' => array(
'start' => '100462603',
'end' => '100464889',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SIM1-002'
),
'ENST00000324696' => array(
'start' => '100647288',
'end' => '100881372',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ASCC3-003'
),
'ENST00000324723' => array(
'start' => '100848420',
'end' => '100881348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-006'
),
'ENST00000369143' => array(
'start' => '100856303',
'end' => '100881311',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-002'
),
'ENST00000369162' => array(
'start' => '100508194',
'end' => '100881364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-001'
),
'ENST00000468245' => array(
'start' => '100848004',
'end' => '100881301',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ASCC3-005'
),
'ENST00000518006' => array(
'start' => '100509218',
'end' => '100510308',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ASCC3-007'
),
'ENST00000522650' => array(
'start' => '100715130',
'end' => '100881364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-004'
),
'ENST00000281806' => array(
'start' => '99919910',
'end' => '99994223',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MCHR2-201'
),
'ENST00000369212' => array(
'start' => '99920752',
'end' => '99994247',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MCHR2-001'
),
'ENST00000447134' => array(
'start' => '100136064',
'end' => '100136663',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PRDX2P4-001'
),
'ENST00000404225' => array(
'start' => '100177209',
'end' => '100178192',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP3-344J20.1-001'
),
'ENST00000403835' => array(
'start' => '100050372',
'end' => '100051236',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'NPM1P38-001'
),
'ENST00000406773' => array(
'start' => '100530276',
'end' => '100531052',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP1-121G13.3-001'
),
'ENST00000411442' => array(
'start' => '100427118',
'end' => '100437484',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP1-121G13.2-001'
),
'ENST00000430122' => array(
'start' => '99994056',
'end' => '100076413',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-002'
),
'ENST00000443234' => array(
'start' => '99993944',
'end' => '100076411',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-003'
),
'ENST00000451220' => array(
'start' => '100000940',
'end' => '100076406',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-001'
),
'ENST00000452482' => array(
'start' => '99994066',
'end' => '100026384',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-004'
),
'ENST00000617868' => array(
'start' => '100229545',
'end' => '100229649',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL080285.1-201'
),
'ENST00000612765' => array(
'start' => '100093311',
'end' => '100093768',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP3-344J20.3-001'
),
'ENSMUST00000020071' => array(
'start' => '50895651',
'end' => '50989152',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sim1-201'
),
'ENSMUST00000035606' => array(
'start' => '50592669',
'end' => '50851202',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ascc3-201'
),
'ENSMUST00000122500' => array(
'start' => '51182299',
'end' => '51182405',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm26257-201'
),
'ENSMUST00000122686' => array(
'start' => '50866075',
'end' => '50866364',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm23883-201'
)
),
'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_0007NG_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007NG_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007NG_0001' => array(
'genes_in_region' => array(
'ENSG00000112246' => array(
[maximum depth reached]
),
'ENSG00000112249' => array(
[maximum depth reached]
),
'ENSG00000152034' => array(
[maximum depth reached]
),
'ENSG00000213177' => array(
[maximum depth reached]
),
'ENSG00000219257' => array(
[maximum depth reached]
),
'ENSG00000220695' => array(
[maximum depth reached]
),
'ENSG00000228082' => array(
[maximum depth reached]
),
'ENSG00000229315' => array(
[maximum depth reached]
),
'ENSG00000275716' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Colon',
(int) 1 => 'Kidney',
(int) 2 => 'Muscle',
(int) 3 => 'Placenta',
(int) 4 => 'Testis',
(int) 5 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 8 => 'Breast',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Lung',
(int) 13 => 'Muscle',
(int) 14 => 'Placenta',
(int) 15 => 'Bladder',
(int) 16 => 'Muscle',
(int) 17 => 'Liver',
(int) 18 => 'Adipose',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Liver',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Muscle',
(int) 42 => 'Adrenal',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Kidney',
(int) 47 => 'Ovary',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Liver',
(int) 51 => 'Brain',
(int) 52 => 'Colon',
(int) 53 => 'Muscle',
(int) 54 => 'Ovary',
(int) 55 => 'Adrenal',
(int) 56 => 'Colon',
(int) 57 => 'Lung',
(int) 58 => 'Muscle',
(int) 59 => 'Testis',
(int) 60 => 'Bladder',
(int) 61 => 'Kidney',
(int) 62 => 'Ovary',
(int) 63 => 'Testis',
(int) 64 => 'Testis',
(int) 65 => 'Testis',
(int) 66 => 'Heart',
(int) 67 => 'Testis',
(int) 68 => 'Placenta',
(int) 69 => 'Testis'
)
),
'CIL_0007NG_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000019913' => array(
[maximum depth reached]
),
'ENSMUSG00000038774' => array(
[maximum depth reached]
),
'ENSMUSG00000084635' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Liver',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000112246' => 'single-minded family bHLH transcription factor 1',
'ENSG00000112249' => 'activating signal cointegrator 1 complex subunit 3',
'ENSG00000152034' => 'melanin-concentrating hormone receptor 2',
'ENSG00000213177' => 'peroxiredoxin 2 pseudogene 4',
'ENSG00000216378' => null,
'ENSG00000219257' => 'nucleophosmin 1 (nucleolar phosphoprotein B23, numatrin) pseudogene 38',
'ENSG00000220695' => null,
'ENSG00000228082' => null,
'ENSG00000229315' => 'MCHR2 antisense RNA 1',
'ENSG00000275020' => null,
'ENSG00000275716' => null,
'ENSMUSG00000019913' => 'single-minded homolog 1 (Drosophila)',
'ENSMUSG00000038774' => 'activating signal cointegrator 1 complex subunit 3',
'ENSMUSG00000084449' => 'predicted gene, 26257',
'ENSMUSG00000084635' => 'predicted gene, 23883'
)
$gene_name_arr = array(
'ENSG00000112246' => 'SIM1',
'ENSG00000112249' => 'ASCC3',
'ENSG00000152034' => 'MCHR2',
'ENSG00000213177' => 'PRDX2P4',
'ENSG00000216378' => 'RP3-344J20.1',
'ENSG00000219257' => 'NPM1P38',
'ENSG00000220695' => 'RP1-121G13.3',
'ENSG00000228082' => 'RP1-121G13.2',
'ENSG00000229315' => 'MCHR2-AS1',
'ENSG00000275020' => 'AL080285.1',
'ENSG00000275716' => 'RP3-344J20.3',
'ENSMUSG00000019913' => 'Sim1',
'ENSMUSG00000038774' => 'Ascc3',
'ENSMUSG00000084449' => 'Gm26257',
'ENSMUSG00000084635' => 'Gm23883'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0001',
'tax_id' => '9606',
'chromosome' => '6',
'seq_start' => '99749802',
'seq_end' => '100612540',
'region_length' => '862738',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0002',
'tax_id' => '10090',
'chromosome' => '10',
'seq_start' => '50743535',
'seq_end' => '51257731',
'region_length' => '514196',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0003',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '1453092',
'seq_end' => '1453346',
'region_length' => '254',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0004',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '21532354',
'seq_end' => '21532586',
'region_length' => '232',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0005',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '2540150',
'seq_end' => '2548274',
'region_length' => '8124',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 5 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0006',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '35109233',
'seq_end' => '35109442',
'region_length' => '209',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 31 => 'Colon',
(int) 38 => 'Heart',
(int) 42 => 'Kidney',
(int) 49 => 'Liver',
(int) 56 => 'Lung',
(int) 61 => 'Muscle',
(int) 70 => 'Ovary',
(int) 77 => 'Placenta',
(int) 84 => '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) 28
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000262901' => array(
'start' => '100388872',
'end' => '100463677',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SIM1-201'
),
'ENST00000369208' => array(
'start' => '100385015',
'end' => '100464929',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SIM1-001'
),
'ENST00000505753' => array(
'start' => '100391083',
'end' => '100394042',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SIM1-003'
),
'ENST00000511871' => array(
'start' => '100462603',
'end' => '100464889',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SIM1-002'
),
'ENST00000324696' => array(
'start' => '100647288',
'end' => '100881372',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ASCC3-003'
),
'ENST00000324723' => array(
'start' => '100848420',
'end' => '100881348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-006'
),
'ENST00000369143' => array(
'start' => '100856303',
'end' => '100881311',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-002'
),
'ENST00000369162' => array(
'start' => '100508194',
'end' => '100881364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-001'
),
'ENST00000468245' => array(
'start' => '100848004',
'end' => '100881301',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ASCC3-005'
),
'ENST00000518006' => array(
'start' => '100509218',
'end' => '100510308',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ASCC3-007'
),
'ENST00000522650' => array(
'start' => '100715130',
'end' => '100881364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-004'
),
'ENST00000281806' => array(
'start' => '99919910',
'end' => '99994223',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MCHR2-201'
),
'ENST00000369212' => array(
'start' => '99920752',
'end' => '99994247',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MCHR2-001'
),
'ENST00000447134' => array(
'start' => '100136064',
'end' => '100136663',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PRDX2P4-001'
),
'ENST00000404225' => array(
'start' => '100177209',
'end' => '100178192',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP3-344J20.1-001'
),
'ENST00000403835' => array(
'start' => '100050372',
'end' => '100051236',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'NPM1P38-001'
),
'ENST00000406773' => array(
'start' => '100530276',
'end' => '100531052',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP1-121G13.3-001'
),
'ENST00000411442' => array(
'start' => '100427118',
'end' => '100437484',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP1-121G13.2-001'
),
'ENST00000430122' => array(
'start' => '99994056',
'end' => '100076413',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-002'
),
'ENST00000443234' => array(
'start' => '99993944',
'end' => '100076411',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-003'
),
'ENST00000451220' => array(
'start' => '100000940',
'end' => '100076406',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-001'
),
'ENST00000452482' => array(
'start' => '99994066',
'end' => '100026384',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-004'
),
'ENST00000617868' => array(
'start' => '100229545',
'end' => '100229649',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL080285.1-201'
),
'ENST00000612765' => array(
'start' => '100093311',
'end' => '100093768',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP3-344J20.3-001'
),
'ENSMUST00000020071' => array(
'start' => '50895651',
'end' => '50989152',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sim1-201'
),
'ENSMUST00000035606' => array(
'start' => '50592669',
'end' => '50851202',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ascc3-201'
),
'ENSMUST00000122500' => array(
'start' => '51182299',
'end' => '51182405',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm26257-201'
),
'ENSMUST00000122686' => array(
'start' => '50866075',
'end' => '50866364',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm23883-201'
)
)
$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_0007NG_0001' => array(
'genes_in_region' => array(
'ENSG00000112246' => array(
[maximum depth reached]
),
'ENSG00000112249' => array(
[maximum depth reached]
),
'ENSG00000152034' => array(
[maximum depth reached]
),
'ENSG00000213177' => array(
[maximum depth reached]
),
'ENSG00000219257' => array(
[maximum depth reached]
),
'ENSG00000220695' => array(
[maximum depth reached]
),
'ENSG00000228082' => array(
[maximum depth reached]
),
'ENSG00000229315' => array(
[maximum depth reached]
),
'ENSG00000275716' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Colon',
(int) 1 => 'Kidney',
(int) 2 => 'Muscle',
(int) 3 => 'Placenta',
(int) 4 => 'Testis',
(int) 5 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 8 => 'Breast',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Lung',
(int) 13 => 'Muscle',
(int) 14 => 'Placenta',
(int) 15 => 'Bladder',
(int) 16 => 'Muscle',
(int) 17 => 'Liver',
(int) 18 => 'Adipose',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Liver',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Muscle',
(int) 42 => 'Adrenal',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Kidney',
(int) 47 => 'Ovary',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Liver',
(int) 51 => 'Brain',
(int) 52 => 'Colon',
(int) 53 => 'Muscle',
(int) 54 => 'Ovary',
(int) 55 => 'Adrenal',
(int) 56 => 'Colon',
(int) 57 => 'Lung',
(int) 58 => 'Muscle',
(int) 59 => 'Testis',
(int) 60 => 'Bladder',
(int) 61 => 'Kidney',
(int) 62 => 'Ovary',
(int) 63 => 'Testis',
(int) 64 => 'Testis',
(int) 65 => 'Testis',
(int) 66 => 'Heart',
(int) 67 => 'Testis',
(int) 68 => 'Placenta',
(int) 69 => 'Testis'
)
),
'CIL_0007NG_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000019913' => array(
[maximum depth reached]
),
'ENSMUSG00000038774' => array(
[maximum depth reached]
),
'ENSMUSG00000084635' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Liver',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0004',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '21532354',
'seq_end' => '21532586',
'region_length' => '232',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
)
$gene_el = array(
'ENSMUST00000122686' => array(
'Testis' => array(
'average_FPKM' => '0.228',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000084635'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '0.228',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000122686'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007NG_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007NG_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000112246' => 'single-minded family bHLH transcription factor 1',
'ENSG00000112249' => 'activating signal cointegrator 1 complex subunit 3',
'ENSG00000152034' => 'melanin-concentrating hormone receptor 2',
'ENSG00000213177' => 'peroxiredoxin 2 pseudogene 4',
'ENSG00000216378' => null,
'ENSG00000219257' => 'nucleophosmin 1 (nucleolar phosphoprotein B23, numatrin) pseudogene 38',
'ENSG00000220695' => null,
'ENSG00000228082' => null,
'ENSG00000229315' => 'MCHR2 antisense RNA 1',
'ENSG00000275020' => null,
'ENSG00000275716' => null,
'ENSMUSG00000019913' => 'single-minded homolog 1 (Drosophila)',
'ENSMUSG00000038774' => 'activating signal cointegrator 1 complex subunit 3',
'ENSMUSG00000084449' => 'predicted gene, 26257',
'ENSMUSG00000084635' => 'predicted gene, 23883'
),
'gene_name_arr' => array(
'ENSG00000112246' => 'SIM1',
'ENSG00000112249' => 'ASCC3',
'ENSG00000152034' => 'MCHR2',
'ENSG00000213177' => 'PRDX2P4',
'ENSG00000216378' => 'RP3-344J20.1',
'ENSG00000219257' => 'NPM1P38',
'ENSG00000220695' => 'RP1-121G13.3',
'ENSG00000228082' => 'RP1-121G13.2',
'ENSG00000229315' => 'MCHR2-AS1',
'ENSG00000275020' => 'AL080285.1',
'ENSG00000275716' => 'RP3-344J20.3',
'ENSMUSG00000019913' => 'Sim1',
'ENSMUSG00000038774' => 'Ascc3',
'ENSMUSG00000084449' => 'Gm26257',
'ENSMUSG00000084635' => 'Gm23883'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 31 => 'Colon',
(int) 38 => 'Heart',
(int) 42 => 'Kidney',
(int) 49 => 'Liver',
(int) 56 => 'Lung',
(int) 61 => 'Muscle',
(int) 70 => 'Ovary',
(int) 77 => 'Placenta',
(int) 84 => '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) 28,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000262901' => array(
'start' => '100388872',
'end' => '100463677',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SIM1-201'
),
'ENST00000369208' => array(
'start' => '100385015',
'end' => '100464929',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SIM1-001'
),
'ENST00000505753' => array(
'start' => '100391083',
'end' => '100394042',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SIM1-003'
),
'ENST00000511871' => array(
'start' => '100462603',
'end' => '100464889',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SIM1-002'
),
'ENST00000324696' => array(
'start' => '100647288',
'end' => '100881372',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ASCC3-003'
),
'ENST00000324723' => array(
'start' => '100848420',
'end' => '100881348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-006'
),
'ENST00000369143' => array(
'start' => '100856303',
'end' => '100881311',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-002'
),
'ENST00000369162' => array(
'start' => '100508194',
'end' => '100881364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-001'
),
'ENST00000468245' => array(
'start' => '100848004',
'end' => '100881301',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ASCC3-005'
),
'ENST00000518006' => array(
'start' => '100509218',
'end' => '100510308',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ASCC3-007'
),
'ENST00000522650' => array(
'start' => '100715130',
'end' => '100881364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-004'
),
'ENST00000281806' => array(
'start' => '99919910',
'end' => '99994223',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MCHR2-201'
),
'ENST00000369212' => array(
'start' => '99920752',
'end' => '99994247',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MCHR2-001'
),
'ENST00000447134' => array(
'start' => '100136064',
'end' => '100136663',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PRDX2P4-001'
),
'ENST00000404225' => array(
'start' => '100177209',
'end' => '100178192',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP3-344J20.1-001'
),
'ENST00000403835' => array(
'start' => '100050372',
'end' => '100051236',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'NPM1P38-001'
),
'ENST00000406773' => array(
'start' => '100530276',
'end' => '100531052',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP1-121G13.3-001'
),
'ENST00000411442' => array(
'start' => '100427118',
'end' => '100437484',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP1-121G13.2-001'
),
'ENST00000430122' => array(
'start' => '99994056',
'end' => '100076413',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-002'
),
'ENST00000443234' => array(
'start' => '99993944',
'end' => '100076411',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-003'
),
'ENST00000451220' => array(
'start' => '100000940',
'end' => '100076406',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-001'
),
'ENST00000452482' => array(
'start' => '99994066',
'end' => '100026384',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-004'
),
'ENST00000617868' => array(
'start' => '100229545',
'end' => '100229649',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL080285.1-201'
),
'ENST00000612765' => array(
'start' => '100093311',
'end' => '100093768',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP3-344J20.3-001'
),
'ENSMUST00000020071' => array(
'start' => '50895651',
'end' => '50989152',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sim1-201'
),
'ENSMUST00000035606' => array(
'start' => '50592669',
'end' => '50851202',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ascc3-201'
),
'ENSMUST00000122500' => array(
'start' => '51182299',
'end' => '51182405',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm26257-201'
),
'ENSMUST00000122686' => array(
'start' => '50866075',
'end' => '50866364',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm23883-201'
)
),
'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_0007NG_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007NG_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007NG_0001' => array(
'genes_in_region' => array(
'ENSG00000112246' => array(
[maximum depth reached]
),
'ENSG00000112249' => array(
[maximum depth reached]
),
'ENSG00000152034' => array(
[maximum depth reached]
),
'ENSG00000213177' => array(
[maximum depth reached]
),
'ENSG00000219257' => array(
[maximum depth reached]
),
'ENSG00000220695' => array(
[maximum depth reached]
),
'ENSG00000228082' => array(
[maximum depth reached]
),
'ENSG00000229315' => array(
[maximum depth reached]
),
'ENSG00000275716' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Colon',
(int) 1 => 'Kidney',
(int) 2 => 'Muscle',
(int) 3 => 'Placenta',
(int) 4 => 'Testis',
(int) 5 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 8 => 'Breast',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Lung',
(int) 13 => 'Muscle',
(int) 14 => 'Placenta',
(int) 15 => 'Bladder',
(int) 16 => 'Muscle',
(int) 17 => 'Liver',
(int) 18 => 'Adipose',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Liver',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Muscle',
(int) 42 => 'Adrenal',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Kidney',
(int) 47 => 'Ovary',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Liver',
(int) 51 => 'Brain',
(int) 52 => 'Colon',
(int) 53 => 'Muscle',
(int) 54 => 'Ovary',
(int) 55 => 'Adrenal',
(int) 56 => 'Colon',
(int) 57 => 'Lung',
(int) 58 => 'Muscle',
(int) 59 => 'Testis',
(int) 60 => 'Bladder',
(int) 61 => 'Kidney',
(int) 62 => 'Ovary',
(int) 63 => 'Testis',
(int) 64 => 'Testis',
(int) 65 => 'Testis',
(int) 66 => 'Heart',
(int) 67 => 'Testis',
(int) 68 => 'Placenta',
(int) 69 => 'Testis'
)
),
'CIL_0007NG_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000019913' => array(
[maximum depth reached]
),
'ENSMUSG00000038774' => array(
[maximum depth reached]
),
'ENSMUSG00000084635' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Liver',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000112246' => 'single-minded family bHLH transcription factor 1',
'ENSG00000112249' => 'activating signal cointegrator 1 complex subunit 3',
'ENSG00000152034' => 'melanin-concentrating hormone receptor 2',
'ENSG00000213177' => 'peroxiredoxin 2 pseudogene 4',
'ENSG00000216378' => null,
'ENSG00000219257' => 'nucleophosmin 1 (nucleolar phosphoprotein B23, numatrin) pseudogene 38',
'ENSG00000220695' => null,
'ENSG00000228082' => null,
'ENSG00000229315' => 'MCHR2 antisense RNA 1',
'ENSG00000275020' => null,
'ENSG00000275716' => null,
'ENSMUSG00000019913' => 'single-minded homolog 1 (Drosophila)',
'ENSMUSG00000038774' => 'activating signal cointegrator 1 complex subunit 3',
'ENSMUSG00000084449' => 'predicted gene, 26257',
'ENSMUSG00000084635' => 'predicted gene, 23883'
)
$gene_name_arr = array(
'ENSG00000112246' => 'SIM1',
'ENSG00000112249' => 'ASCC3',
'ENSG00000152034' => 'MCHR2',
'ENSG00000213177' => 'PRDX2P4',
'ENSG00000216378' => 'RP3-344J20.1',
'ENSG00000219257' => 'NPM1P38',
'ENSG00000220695' => 'RP1-121G13.3',
'ENSG00000228082' => 'RP1-121G13.2',
'ENSG00000229315' => 'MCHR2-AS1',
'ENSG00000275020' => 'AL080285.1',
'ENSG00000275716' => 'RP3-344J20.3',
'ENSMUSG00000019913' => 'Sim1',
'ENSMUSG00000038774' => 'Ascc3',
'ENSMUSG00000084449' => 'Gm26257',
'ENSMUSG00000084635' => 'Gm23883'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0001',
'tax_id' => '9606',
'chromosome' => '6',
'seq_start' => '99749802',
'seq_end' => '100612540',
'region_length' => '862738',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0002',
'tax_id' => '10090',
'chromosome' => '10',
'seq_start' => '50743535',
'seq_end' => '51257731',
'region_length' => '514196',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0003',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '1453092',
'seq_end' => '1453346',
'region_length' => '254',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0004',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '21532354',
'seq_end' => '21532586',
'region_length' => '232',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0005',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '2540150',
'seq_end' => '2548274',
'region_length' => '8124',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
),
(int) 5 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0006',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '35109233',
'seq_end' => '35109442',
'region_length' => '209',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 31 => 'Colon',
(int) 38 => 'Heart',
(int) 42 => 'Kidney',
(int) 49 => 'Liver',
(int) 56 => 'Lung',
(int) 61 => 'Muscle',
(int) 70 => 'Ovary',
(int) 77 => 'Placenta',
(int) 84 => '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) 28
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000262901' => array(
'start' => '100388872',
'end' => '100463677',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SIM1-201'
),
'ENST00000369208' => array(
'start' => '100385015',
'end' => '100464929',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SIM1-001'
),
'ENST00000505753' => array(
'start' => '100391083',
'end' => '100394042',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SIM1-003'
),
'ENST00000511871' => array(
'start' => '100462603',
'end' => '100464889',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SIM1-002'
),
'ENST00000324696' => array(
'start' => '100647288',
'end' => '100881372',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ASCC3-003'
),
'ENST00000324723' => array(
'start' => '100848420',
'end' => '100881348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-006'
),
'ENST00000369143' => array(
'start' => '100856303',
'end' => '100881311',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-002'
),
'ENST00000369162' => array(
'start' => '100508194',
'end' => '100881364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-001'
),
'ENST00000468245' => array(
'start' => '100848004',
'end' => '100881301',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ASCC3-005'
),
'ENST00000518006' => array(
'start' => '100509218',
'end' => '100510308',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ASCC3-007'
),
'ENST00000522650' => array(
'start' => '100715130',
'end' => '100881364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ASCC3-004'
),
'ENST00000281806' => array(
'start' => '99919910',
'end' => '99994223',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MCHR2-201'
),
'ENST00000369212' => array(
'start' => '99920752',
'end' => '99994247',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MCHR2-001'
),
'ENST00000447134' => array(
'start' => '100136064',
'end' => '100136663',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'PRDX2P4-001'
),
'ENST00000404225' => array(
'start' => '100177209',
'end' => '100178192',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP3-344J20.1-001'
),
'ENST00000403835' => array(
'start' => '100050372',
'end' => '100051236',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'NPM1P38-001'
),
'ENST00000406773' => array(
'start' => '100530276',
'end' => '100531052',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP1-121G13.3-001'
),
'ENST00000411442' => array(
'start' => '100427118',
'end' => '100437484',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP1-121G13.2-001'
),
'ENST00000430122' => array(
'start' => '99994056',
'end' => '100076413',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-002'
),
'ENST00000443234' => array(
'start' => '99993944',
'end' => '100076411',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-003'
),
'ENST00000451220' => array(
'start' => '100000940',
'end' => '100076406',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-001'
),
'ENST00000452482' => array(
'start' => '99994066',
'end' => '100026384',
'transcript_biotype' => 'antisense',
'transcript_name' => 'MCHR2-AS1-004'
),
'ENST00000617868' => array(
'start' => '100229545',
'end' => '100229649',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL080285.1-201'
),
'ENST00000612765' => array(
'start' => '100093311',
'end' => '100093768',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP3-344J20.3-001'
),
'ENSMUST00000020071' => array(
'start' => '50895651',
'end' => '50989152',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sim1-201'
),
'ENSMUST00000035606' => array(
'start' => '50592669',
'end' => '50851202',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ascc3-201'
),
'ENSMUST00000122500' => array(
'start' => '51182299',
'end' => '51182405',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm26257-201'
),
'ENSMUST00000122686' => array(
'start' => '50866075',
'end' => '50866364',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm23883-201'
)
)
$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_0007NG_0001' => array(
'genes_in_region' => array(
'ENSG00000112246' => array(
[maximum depth reached]
),
'ENSG00000112249' => array(
[maximum depth reached]
),
'ENSG00000152034' => array(
[maximum depth reached]
),
'ENSG00000213177' => array(
[maximum depth reached]
),
'ENSG00000219257' => array(
[maximum depth reached]
),
'ENSG00000220695' => array(
[maximum depth reached]
),
'ENSG00000228082' => array(
[maximum depth reached]
),
'ENSG00000229315' => array(
[maximum depth reached]
),
'ENSG00000275716' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Colon',
(int) 1 => 'Kidney',
(int) 2 => 'Muscle',
(int) 3 => 'Placenta',
(int) 4 => 'Testis',
(int) 5 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 8 => 'Breast',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Lung',
(int) 13 => 'Muscle',
(int) 14 => 'Placenta',
(int) 15 => 'Bladder',
(int) 16 => 'Muscle',
(int) 17 => 'Liver',
(int) 18 => 'Adipose',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Liver',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Muscle',
(int) 42 => 'Adrenal',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Kidney',
(int) 47 => 'Ovary',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Liver',
(int) 51 => 'Brain',
(int) 52 => 'Colon',
(int) 53 => 'Muscle',
(int) 54 => 'Ovary',
(int) 55 => 'Adrenal',
(int) 56 => 'Colon',
(int) 57 => 'Lung',
(int) 58 => 'Muscle',
(int) 59 => 'Testis',
(int) 60 => 'Bladder',
(int) 61 => 'Kidney',
(int) 62 => 'Ovary',
(int) 63 => 'Testis',
(int) 64 => 'Testis',
(int) 65 => 'Testis',
(int) 66 => 'Heart',
(int) 67 => 'Testis',
(int) 68 => 'Placenta',
(int) 69 => 'Testis'
)
),
'CIL_0007NG_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000019913' => array(
[maximum depth reached]
),
'ENSMUSG00000038774' => array(
[maximum depth reached]
),
'ENSMUSG00000084635' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Liver',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NG_0004',
'tax_id' => '10090',
'chromosome' => '4',
'seq_start' => '21532354',
'seq_end' => '21532586',
'region_length' => '232',
'region_type' => 'UCNEbase',
'el_id' => 'PRDM13'
)
)
$gene_el = array(
'ENSMUST00000122686' => array(
'Testis' => array(
'average_FPKM' => '0.228',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000084635'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '0.228',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000122686'
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 |
| PRDM13 |
UCNEbase |
10090 |
4:21532354-21532586  |
| Gene | Transcript | Position | Biotype |
|---|
(SIM1)