Notice (8): Undefined index: CIL_00043R_0002 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_00043R_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00043R_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000008370' => 'casein kinase 1, delta a',
'ENSDARG00000028583' => 'solute carrier family 16 (monocarboxylate transporter), member 3',
'ENSG00000141526' => 'solute carrier family 16 (monocarboxylate transporter), member 3',
'ENSG00000141551' => 'casein kinase 1, delta',
'ENSG00000275505' => 'microRNA 6787',
'ENSG00000275888' => null,
'ENSG00000280407' => null,
'ENSMUSG00000025161' => 'solute carrier family 16 (monocarboxylic acid transporters), member 3',
'ENSMUSG00000025162' => 'casein kinase 1, delta',
'ENSMUSG00000100629' => 'predicted gene 28192'
),
'gene_name_arr' => array(
'ENSDARG00000008370' => 'csnk1da',
'ENSDARG00000028583' => 'SLC16A3 (1 of 2)',
'ENSG00000141526' => 'SLC16A3',
'ENSG00000141551' => 'CSNK1D',
'ENSG00000275505' => 'MIR6787',
'ENSG00000275888' => 'RP13-516M14.10',
'ENSG00000280407' => 'RP13-516M14.8',
'ENSMUSG00000025161' => 'Slc16a3',
'ENSMUSG00000025162' => 'Csnk1d',
'ENSMUSG00000100629' => 'RP23-378G22.3'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 24 => 'Brain',
(int) 34 => 'Breast',
(int) 42 => 'Colon',
(int) 53 => 'Heart',
(int) 65 => 'Kidney',
(int) 77 => 'Liver',
(int) 86 => 'Lung',
(int) 93 => 'Muscle',
(int) 104 => 'Ovary',
(int) 115 => 'Placenta',
(int) 123 => '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) 71,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000025326' => array(
'start' => '36172321',
'end' => '36209462',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'csnk1da-001'
),
'ENSDART00000038525' => array(
'start' => '36160097',
'end' => '36166512',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3 (1 of 2)-001'
),
'ENST00000392339' => array(
'start' => '82232232',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-201'
),
'ENST00000392341' => array(
'start' => '82228406',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-202'
),
'ENST00000577650' => array(
'start' => '82229060',
'end' => '82237320',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-016'
),
'ENST00000578522' => array(
'start' => '82234899',
'end' => '82237177',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-008'
),
'ENST00000578574' => array(
'start' => '82229062',
'end' => '82236895',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-011'
),
'ENST00000578684' => array(
'start' => '82229058',
'end' => '82237705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-012'
),
'ENST00000578810' => array(
'start' => '82236474',
'end' => '82237416',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-017'
),
'ENST00000579572' => array(
'start' => '82229068',
'end' => '82237303',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-013'
),
'ENST00000580098' => array(
'start' => '82232232',
'end' => '82237475',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-007'
),
'ENST00000580189' => array(
'start' => '82235053',
'end' => '82237439',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-009'
),
'ENST00000581287' => array(
'start' => '82233687',
'end' => '82240086',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-001'
),
'ENST00000581642' => array(
'start' => '82228448',
'end' => '82236457',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-006'
),
'ENST00000582715' => array(
'start' => '82229093',
'end' => '82239481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-015'
),
'ENST00000582743' => array(
'start' => '82229032',
'end' => '82239479',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-002'
),
'ENST00000582946' => array(
'start' => '82235774',
'end' => '82237261',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-010'
),
'ENST00000583025' => array(
'start' => '82237170',
'end' => '82261129',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-018'
),
'ENST00000583237' => array(
'start' => '82228421',
'end' => '82237427',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-005'
),
'ENST00000583444' => array(
'start' => '82229045',
'end' => '82231926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-003'
),
'ENST00000584689' => array(
'start' => '82228397',
'end' => '82237644',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-004'
),
'ENST00000584781' => array(
'start' => '82229055',
'end' => '82237282',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SLC16A3-014'
),
'ENST00000617373' => array(
'start' => '82234899',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-203'
),
'ENST00000619321' => array(
'start' => '82235774',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-204'
),
'ENST00000269361' => array(
'start' => '82244680',
'end' => '82255516',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-022'
),
'ENST00000314028' => array(
'start' => '82242667',
'end' => '82273731',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-001'
),
'ENST00000392334' => array(
'start' => '82244362',
'end' => '82273697',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-002'
),
'ENST00000398519' => array(
'start' => '82239727',
'end' => '82273428',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-006'
),
'ENST00000403276' => array(
'start' => '82246018',
'end' => '82273431',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-005'
),
'ENST00000577578' => array(
'start' => '82244362',
'end' => '82246591',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-028'
),
'ENST00000578194' => array(
'start' => '82253220',
'end' => '82273171',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-019'
),
'ENST00000578501' => array(
'start' => '82244394',
'end' => '82249496',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-025'
),
'ENST00000578904' => array(
'start' => '82249578',
'end' => '82255546',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-009'
),
'ENST00000579308' => array(
'start' => '82265300',
'end' => '82273406',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-016'
),
'ENST00000579316' => array(
'start' => '82255130',
'end' => '82273438',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-014'
),
'ENST00000580061' => array(
'start' => '82255187',
'end' => '82266800',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-020'
),
'ENST00000580446' => array(
'start' => '82252497',
'end' => '82273431',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-015'
),
'ENST00000580565' => array(
'start' => '82246318',
'end' => '82249835',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-024'
),
'ENST00000580784' => array(
'start' => '82244645',
'end' => '82251414',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-010'
),
'ENST00000581108' => array(
'start' => '82249239',
'end' => '82252527',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-023'
),
'ENST00000581241' => array(
'start' => '82242673',
'end' => '82273369',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-007'
),
'ENST00000581655' => array(
'start' => '82266708',
'end' => '82273251',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-018'
),
'ENST00000581660' => array(
'start' => '82253216',
'end' => '82273457',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-013'
),
'ENST00000581737' => array(
'start' => '82244491',
'end' => '82249164',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-026'
),
'ENST00000582844' => array(
'start' => '82249489',
'end' => '82273124',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-021'
),
'ENST00000584377' => array(
'start' => '82244301',
'end' => '82254679',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-008'
),
'ENST00000584472' => array(
'start' => '82255164',
'end' => '82273466',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-012'
),
'ENST00000584672' => array(
'start' => '82239023',
'end' => '82248980',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-027'
),
'ENST00000584913' => array(
'start' => '82244722',
'end' => '82245113',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-029'
),
'ENST00000585026' => array(
'start' => '82255438',
'end' => '82273400',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-017'
),
'ENST00000616675' => array(
'start' => '82236668',
'end' => '82236728',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6787-201'
),
'ENST00000620937' => array(
'start' => '82244770',
'end' => '82245591',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP13-516M14.10-001'
),
'ENST00000622924' => array(
'start' => '82249067',
'end' => '82251827',
'transcript_biotype' => 'pseudogene',
'transcript_name' => 'RP13-516M14.8-201'
),
'ENST00000624920' => array(
'start' => '82249067',
'end' => '82251844',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP13-516M14.8-001'
),
'ENSMUST00000070653' => array(
'start' => '120948480',
'end' => '120958775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-001'
),
'ENSMUST00000100130' => array(
'start' => '120949067',
'end' => '120959000',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-201'
),
'ENSMUST00000129473' => array(
'start' => '120949071',
'end' => '120956861',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-005'
),
'ENSMUST00000133029' => array(
'start' => '120950688',
'end' => '120955273',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-003'
),
'ENSMUST00000134540' => array(
'start' => '120955226',
'end' => '120956231',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Slc16a3-004'
),
'ENSMUST00000140467' => array(
'start' => '120951138',
'end' => '120954212',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Slc16a3-006'
),
'ENSMUST00000154187' => array(
'start' => '120949053',
'end' => '120956747',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-002'
),
'ENSMUST00000168579' => array(
'start' => '120949081',
'end' => '120960868',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-202'
),
'ENSMUST00000018274' => array(
'start' => '120961749',
'end' => '120991330',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-001'
),
'ENSMUST00000070575' => array(
'start' => '120961749',
'end' => '120991092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-002'
),
'ENSMUST00000131375' => array(
'start' => '120963648',
'end' => '120965686',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-003'
),
'ENSMUST00000139267' => array(
'start' => '120967612',
'end' => '120968061',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-007'
),
'ENSMUST00000141071' => array(
'start' => '120963773',
'end' => '120971625',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-008'
),
'ENSMUST00000146837' => array(
'start' => '120972490',
'end' => '120990987',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Csnk1d-004'
),
'ENSMUST00000154483' => array(
'start' => '120972472',
'end' => '120990871',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-006'
),
'ENSMUST00000155070' => array(
'start' => '120982857',
'end' => '120991051',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Csnk1d-005'
),
'ENSMUST00000189381' => array(
'start' => '120963844',
'end' => '120964764',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP23-378G22.3-001'
)
),
'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_00043R_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00043R_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00043R_0001' => array(
'genes_in_region' => array(
'ENSDARG00000008370' => array(
[maximum depth reached]
),
'ENSDARG00000028583' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle'
)
),
'CIL_00043R_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000025161' => array(
[maximum depth reached]
),
'ENSMUSG00000025162' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Adipose',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Adrenal',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Ovary',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Adipose',
(int) 48 => 'Adrenal',
(int) 49 => 'Brain',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Kidney',
(int) 54 => 'Liver',
(int) 55 => 'Ovary',
(int) 56 => 'Adipose',
(int) 57 => 'Adrenal',
(int) 58 => 'Bladder',
(int) 59 => 'Brain',
(int) 60 => 'Breast',
(int) 61 => 'Colon',
(int) 62 => 'Heart',
(int) 63 => 'Kidney',
(int) 64 => 'Liver',
(int) 65 => 'Lung',
(int) 66 => 'Muscle',
(int) 67 => 'Ovary',
(int) 68 => 'Placenta',
(int) 69 => 'Testis',
(int) 70 => 'Adipose',
(int) 71 => 'Adrenal',
(int) 72 => 'Bladder',
(int) 73 => 'Brain',
(int) 74 => 'Breast',
(int) 75 => 'Colon',
(int) 76 => 'Heart',
(int) 77 => 'Kidney',
(int) 78 => 'Liver',
(int) 79 => 'Lung',
(int) 80 => 'Muscle',
(int) 81 => 'Ovary',
(int) 82 => 'Placenta',
(int) 83 => 'Testis',
(int) 84 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000008370' => 'casein kinase 1, delta a',
'ENSDARG00000028583' => 'solute carrier family 16 (monocarboxylate transporter), member 3',
'ENSG00000141526' => 'solute carrier family 16 (monocarboxylate transporter), member 3',
'ENSG00000141551' => 'casein kinase 1, delta',
'ENSG00000275505' => 'microRNA 6787',
'ENSG00000275888' => null,
'ENSG00000280407' => null,
'ENSMUSG00000025161' => 'solute carrier family 16 (monocarboxylic acid transporters), member 3',
'ENSMUSG00000025162' => 'casein kinase 1, delta',
'ENSMUSG00000100629' => 'predicted gene 28192'
)
$gene_name_arr = array(
'ENSDARG00000008370' => 'csnk1da',
'ENSDARG00000028583' => 'SLC16A3 (1 of 2)',
'ENSG00000141526' => 'SLC16A3',
'ENSG00000141551' => 'CSNK1D',
'ENSG00000275505' => 'MIR6787',
'ENSG00000275888' => 'RP13-516M14.10',
'ENSG00000280407' => 'RP13-516M14.8',
'ENSMUSG00000025161' => 'Slc16a3',
'ENSMUSG00000025162' => 'Csnk1d',
'ENSMUSG00000100629' => 'RP23-378G22.3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00043R_0001',
'tax_id' => '7955',
'chromosome' => '3',
'seq_start' => '36160097',
'seq_end' => '36209462',
'region_length' => '49365',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000028583-ENSDARG00000008370'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00043R_0002',
'tax_id' => '9606',
'chromosome' => '17',
'seq_start' => '82228397',
'seq_end' => '82273731',
'region_length' => '45334',
'region_type' => 'CGP',
'el_id' => 'ENSG00000141526-ENSG00000141551'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00043R_0003',
'tax_id' => '10090',
'chromosome' => '11',
'seq_start' => '120948480',
'seq_end' => '120991330',
'region_length' => '42850',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000025161-ENSMUSG00000025162'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 24 => 'Brain',
(int) 34 => 'Breast',
(int) 42 => 'Colon',
(int) 53 => 'Heart',
(int) 65 => 'Kidney',
(int) 77 => 'Liver',
(int) 86 => 'Lung',
(int) 93 => 'Muscle',
(int) 104 => 'Ovary',
(int) 115 => 'Placenta',
(int) 123 => '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) 71
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000025326' => array(
'start' => '36172321',
'end' => '36209462',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'csnk1da-001'
),
'ENSDART00000038525' => array(
'start' => '36160097',
'end' => '36166512',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3 (1 of 2)-001'
),
'ENST00000392339' => array(
'start' => '82232232',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-201'
),
'ENST00000392341' => array(
'start' => '82228406',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-202'
),
'ENST00000577650' => array(
'start' => '82229060',
'end' => '82237320',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-016'
),
'ENST00000578522' => array(
'start' => '82234899',
'end' => '82237177',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-008'
),
'ENST00000578574' => array(
'start' => '82229062',
'end' => '82236895',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-011'
),
'ENST00000578684' => array(
'start' => '82229058',
'end' => '82237705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-012'
),
'ENST00000578810' => array(
'start' => '82236474',
'end' => '82237416',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-017'
),
'ENST00000579572' => array(
'start' => '82229068',
'end' => '82237303',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-013'
),
'ENST00000580098' => array(
'start' => '82232232',
'end' => '82237475',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-007'
),
'ENST00000580189' => array(
'start' => '82235053',
'end' => '82237439',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-009'
),
'ENST00000581287' => array(
'start' => '82233687',
'end' => '82240086',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-001'
),
'ENST00000581642' => array(
'start' => '82228448',
'end' => '82236457',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-006'
),
'ENST00000582715' => array(
'start' => '82229093',
'end' => '82239481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-015'
),
'ENST00000582743' => array(
'start' => '82229032',
'end' => '82239479',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-002'
),
'ENST00000582946' => array(
'start' => '82235774',
'end' => '82237261',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-010'
),
'ENST00000583025' => array(
'start' => '82237170',
'end' => '82261129',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-018'
),
'ENST00000583237' => array(
'start' => '82228421',
'end' => '82237427',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-005'
),
'ENST00000583444' => array(
'start' => '82229045',
'end' => '82231926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-003'
),
'ENST00000584689' => array(
'start' => '82228397',
'end' => '82237644',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-004'
),
'ENST00000584781' => array(
'start' => '82229055',
'end' => '82237282',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SLC16A3-014'
),
'ENST00000617373' => array(
'start' => '82234899',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-203'
),
'ENST00000619321' => array(
'start' => '82235774',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-204'
),
'ENST00000269361' => array(
'start' => '82244680',
'end' => '82255516',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-022'
),
'ENST00000314028' => array(
'start' => '82242667',
'end' => '82273731',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-001'
),
'ENST00000392334' => array(
'start' => '82244362',
'end' => '82273697',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-002'
),
'ENST00000398519' => array(
'start' => '82239727',
'end' => '82273428',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-006'
),
'ENST00000403276' => array(
'start' => '82246018',
'end' => '82273431',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-005'
),
'ENST00000577578' => array(
'start' => '82244362',
'end' => '82246591',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-028'
),
'ENST00000578194' => array(
'start' => '82253220',
'end' => '82273171',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-019'
),
'ENST00000578501' => array(
'start' => '82244394',
'end' => '82249496',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-025'
),
'ENST00000578904' => array(
'start' => '82249578',
'end' => '82255546',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-009'
),
'ENST00000579308' => array(
'start' => '82265300',
'end' => '82273406',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-016'
),
'ENST00000579316' => array(
'start' => '82255130',
'end' => '82273438',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-014'
),
'ENST00000580061' => array(
'start' => '82255187',
'end' => '82266800',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-020'
),
'ENST00000580446' => array(
'start' => '82252497',
'end' => '82273431',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-015'
),
'ENST00000580565' => array(
'start' => '82246318',
'end' => '82249835',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-024'
),
'ENST00000580784' => array(
'start' => '82244645',
'end' => '82251414',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-010'
),
'ENST00000581108' => array(
'start' => '82249239',
'end' => '82252527',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-023'
),
'ENST00000581241' => array(
'start' => '82242673',
'end' => '82273369',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-007'
),
'ENST00000581655' => array(
'start' => '82266708',
'end' => '82273251',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-018'
),
'ENST00000581660' => array(
'start' => '82253216',
'end' => '82273457',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-013'
),
'ENST00000581737' => array(
'start' => '82244491',
'end' => '82249164',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-026'
),
'ENST00000582844' => array(
'start' => '82249489',
'end' => '82273124',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-021'
),
'ENST00000584377' => array(
'start' => '82244301',
'end' => '82254679',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-008'
),
'ENST00000584472' => array(
'start' => '82255164',
'end' => '82273466',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-012'
),
'ENST00000584672' => array(
'start' => '82239023',
'end' => '82248980',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-027'
),
'ENST00000584913' => array(
'start' => '82244722',
'end' => '82245113',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-029'
),
'ENST00000585026' => array(
'start' => '82255438',
'end' => '82273400',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-017'
),
'ENST00000616675' => array(
'start' => '82236668',
'end' => '82236728',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6787-201'
),
'ENST00000620937' => array(
'start' => '82244770',
'end' => '82245591',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP13-516M14.10-001'
),
'ENST00000622924' => array(
'start' => '82249067',
'end' => '82251827',
'transcript_biotype' => 'pseudogene',
'transcript_name' => 'RP13-516M14.8-201'
),
'ENST00000624920' => array(
'start' => '82249067',
'end' => '82251844',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP13-516M14.8-001'
),
'ENSMUST00000070653' => array(
'start' => '120948480',
'end' => '120958775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-001'
),
'ENSMUST00000100130' => array(
'start' => '120949067',
'end' => '120959000',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-201'
),
'ENSMUST00000129473' => array(
'start' => '120949071',
'end' => '120956861',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-005'
),
'ENSMUST00000133029' => array(
'start' => '120950688',
'end' => '120955273',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-003'
),
'ENSMUST00000134540' => array(
'start' => '120955226',
'end' => '120956231',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Slc16a3-004'
),
'ENSMUST00000140467' => array(
'start' => '120951138',
'end' => '120954212',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Slc16a3-006'
),
'ENSMUST00000154187' => array(
'start' => '120949053',
'end' => '120956747',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-002'
),
'ENSMUST00000168579' => array(
'start' => '120949081',
'end' => '120960868',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-202'
),
'ENSMUST00000018274' => array(
'start' => '120961749',
'end' => '120991330',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-001'
),
'ENSMUST00000070575' => array(
'start' => '120961749',
'end' => '120991092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-002'
),
'ENSMUST00000131375' => array(
'start' => '120963648',
'end' => '120965686',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-003'
),
'ENSMUST00000139267' => array(
'start' => '120967612',
'end' => '120968061',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-007'
),
'ENSMUST00000141071' => array(
'start' => '120963773',
'end' => '120971625',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-008'
),
'ENSMUST00000146837' => array(
'start' => '120972490',
'end' => '120990987',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Csnk1d-004'
),
'ENSMUST00000154483' => array(
'start' => '120972472',
'end' => '120990871',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-006'
),
'ENSMUST00000155070' => array(
'start' => '120982857',
'end' => '120991051',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Csnk1d-005'
),
'ENSMUST00000189381' => array(
'start' => '120963844',
'end' => '120964764',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP23-378G22.3-001'
)
)
$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_00043R_0001' => array(
'genes_in_region' => array(
'ENSDARG00000008370' => array(
[maximum depth reached]
),
'ENSDARG00000028583' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle'
)
),
'CIL_00043R_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000025161' => array(
[maximum depth reached]
),
'ENSMUSG00000025162' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Adipose',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Adrenal',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Ovary',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Adipose',
(int) 48 => 'Adrenal',
(int) 49 => 'Brain',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Kidney',
(int) 54 => 'Liver',
(int) 55 => 'Ovary',
(int) 56 => 'Adipose',
(int) 57 => 'Adrenal',
(int) 58 => 'Bladder',
(int) 59 => 'Brain',
(int) 60 => 'Breast',
(int) 61 => 'Colon',
(int) 62 => 'Heart',
(int) 63 => 'Kidney',
(int) 64 => 'Liver',
(int) 65 => 'Lung',
(int) 66 => 'Muscle',
(int) 67 => 'Ovary',
(int) 68 => 'Placenta',
(int) 69 => 'Testis',
(int) 70 => 'Adipose',
(int) 71 => 'Adrenal',
(int) 72 => 'Bladder',
(int) 73 => 'Brain',
(int) 74 => 'Breast',
(int) 75 => 'Colon',
(int) 76 => 'Heart',
(int) 77 => 'Kidney',
(int) 78 => 'Liver',
(int) 79 => 'Lung',
(int) 80 => 'Muscle',
(int) 81 => 'Ovary',
(int) 82 => 'Placenta',
(int) 83 => 'Testis',
(int) 84 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00043R_0002',
'tax_id' => '9606',
'chromosome' => '17',
'seq_start' => '82228397',
'seq_end' => '82273731',
'region_length' => '45334',
'region_type' => 'CGP',
'el_id' => 'ENSG00000141526-ENSG00000141551'
)
)
$gene_el = array(
'ENSDART00000038525' => array(
'Brain' => array(
'average_FPKM' => '2.052',
'stddev_FPKM' => '0.87'
),
'Heart' => array(
'average_FPKM' => '0.614',
'stddev_FPKM' => '0.25'
),
'Kidney' => array(
'average_FPKM' => '0.666',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.474',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000028583'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '2.052',
'stddev_FPKM' => '0.87'
),
'Heart' => array(
'average_FPKM' => '0.614',
'stddev_FPKM' => '0.25'
),
'Kidney' => array(
'average_FPKM' => '0.666',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.474',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000038525'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00043R_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00043R_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000008370' => 'casein kinase 1, delta a',
'ENSDARG00000028583' => 'solute carrier family 16 (monocarboxylate transporter), member 3',
'ENSG00000141526' => 'solute carrier family 16 (monocarboxylate transporter), member 3',
'ENSG00000141551' => 'casein kinase 1, delta',
'ENSG00000275505' => 'microRNA 6787',
'ENSG00000275888' => null,
'ENSG00000280407' => null,
'ENSMUSG00000025161' => 'solute carrier family 16 (monocarboxylic acid transporters), member 3',
'ENSMUSG00000025162' => 'casein kinase 1, delta',
'ENSMUSG00000100629' => 'predicted gene 28192'
),
'gene_name_arr' => array(
'ENSDARG00000008370' => 'csnk1da',
'ENSDARG00000028583' => 'SLC16A3 (1 of 2)',
'ENSG00000141526' => 'SLC16A3',
'ENSG00000141551' => 'CSNK1D',
'ENSG00000275505' => 'MIR6787',
'ENSG00000275888' => 'RP13-516M14.10',
'ENSG00000280407' => 'RP13-516M14.8',
'ENSMUSG00000025161' => 'Slc16a3',
'ENSMUSG00000025162' => 'Csnk1d',
'ENSMUSG00000100629' => 'RP23-378G22.3'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 24 => 'Brain',
(int) 34 => 'Breast',
(int) 42 => 'Colon',
(int) 53 => 'Heart',
(int) 65 => 'Kidney',
(int) 77 => 'Liver',
(int) 86 => 'Lung',
(int) 93 => 'Muscle',
(int) 104 => 'Ovary',
(int) 115 => 'Placenta',
(int) 123 => '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) 71,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000025326' => array(
'start' => '36172321',
'end' => '36209462',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'csnk1da-001'
),
'ENSDART00000038525' => array(
'start' => '36160097',
'end' => '36166512',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3 (1 of 2)-001'
),
'ENST00000392339' => array(
'start' => '82232232',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-201'
),
'ENST00000392341' => array(
'start' => '82228406',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-202'
),
'ENST00000577650' => array(
'start' => '82229060',
'end' => '82237320',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-016'
),
'ENST00000578522' => array(
'start' => '82234899',
'end' => '82237177',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-008'
),
'ENST00000578574' => array(
'start' => '82229062',
'end' => '82236895',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-011'
),
'ENST00000578684' => array(
'start' => '82229058',
'end' => '82237705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-012'
),
'ENST00000578810' => array(
'start' => '82236474',
'end' => '82237416',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-017'
),
'ENST00000579572' => array(
'start' => '82229068',
'end' => '82237303',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-013'
),
'ENST00000580098' => array(
'start' => '82232232',
'end' => '82237475',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-007'
),
'ENST00000580189' => array(
'start' => '82235053',
'end' => '82237439',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-009'
),
'ENST00000581287' => array(
'start' => '82233687',
'end' => '82240086',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-001'
),
'ENST00000581642' => array(
'start' => '82228448',
'end' => '82236457',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-006'
),
'ENST00000582715' => array(
'start' => '82229093',
'end' => '82239481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-015'
),
'ENST00000582743' => array(
'start' => '82229032',
'end' => '82239479',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-002'
),
'ENST00000582946' => array(
'start' => '82235774',
'end' => '82237261',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-010'
),
'ENST00000583025' => array(
'start' => '82237170',
'end' => '82261129',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-018'
),
'ENST00000583237' => array(
'start' => '82228421',
'end' => '82237427',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-005'
),
'ENST00000583444' => array(
'start' => '82229045',
'end' => '82231926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-003'
),
'ENST00000584689' => array(
'start' => '82228397',
'end' => '82237644',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-004'
),
'ENST00000584781' => array(
'start' => '82229055',
'end' => '82237282',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SLC16A3-014'
),
'ENST00000617373' => array(
'start' => '82234899',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-203'
),
'ENST00000619321' => array(
'start' => '82235774',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-204'
),
'ENST00000269361' => array(
'start' => '82244680',
'end' => '82255516',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-022'
),
'ENST00000314028' => array(
'start' => '82242667',
'end' => '82273731',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-001'
),
'ENST00000392334' => array(
'start' => '82244362',
'end' => '82273697',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-002'
),
'ENST00000398519' => array(
'start' => '82239727',
'end' => '82273428',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-006'
),
'ENST00000403276' => array(
'start' => '82246018',
'end' => '82273431',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-005'
),
'ENST00000577578' => array(
'start' => '82244362',
'end' => '82246591',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-028'
),
'ENST00000578194' => array(
'start' => '82253220',
'end' => '82273171',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-019'
),
'ENST00000578501' => array(
'start' => '82244394',
'end' => '82249496',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-025'
),
'ENST00000578904' => array(
'start' => '82249578',
'end' => '82255546',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-009'
),
'ENST00000579308' => array(
'start' => '82265300',
'end' => '82273406',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-016'
),
'ENST00000579316' => array(
'start' => '82255130',
'end' => '82273438',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-014'
),
'ENST00000580061' => array(
'start' => '82255187',
'end' => '82266800',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-020'
),
'ENST00000580446' => array(
'start' => '82252497',
'end' => '82273431',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-015'
),
'ENST00000580565' => array(
'start' => '82246318',
'end' => '82249835',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-024'
),
'ENST00000580784' => array(
'start' => '82244645',
'end' => '82251414',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-010'
),
'ENST00000581108' => array(
'start' => '82249239',
'end' => '82252527',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-023'
),
'ENST00000581241' => array(
'start' => '82242673',
'end' => '82273369',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-007'
),
'ENST00000581655' => array(
'start' => '82266708',
'end' => '82273251',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-018'
),
'ENST00000581660' => array(
'start' => '82253216',
'end' => '82273457',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-013'
),
'ENST00000581737' => array(
'start' => '82244491',
'end' => '82249164',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-026'
),
'ENST00000582844' => array(
'start' => '82249489',
'end' => '82273124',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-021'
),
'ENST00000584377' => array(
'start' => '82244301',
'end' => '82254679',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-008'
),
'ENST00000584472' => array(
'start' => '82255164',
'end' => '82273466',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-012'
),
'ENST00000584672' => array(
'start' => '82239023',
'end' => '82248980',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-027'
),
'ENST00000584913' => array(
'start' => '82244722',
'end' => '82245113',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-029'
),
'ENST00000585026' => array(
'start' => '82255438',
'end' => '82273400',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-017'
),
'ENST00000616675' => array(
'start' => '82236668',
'end' => '82236728',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6787-201'
),
'ENST00000620937' => array(
'start' => '82244770',
'end' => '82245591',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP13-516M14.10-001'
),
'ENST00000622924' => array(
'start' => '82249067',
'end' => '82251827',
'transcript_biotype' => 'pseudogene',
'transcript_name' => 'RP13-516M14.8-201'
),
'ENST00000624920' => array(
'start' => '82249067',
'end' => '82251844',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP13-516M14.8-001'
),
'ENSMUST00000070653' => array(
'start' => '120948480',
'end' => '120958775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-001'
),
'ENSMUST00000100130' => array(
'start' => '120949067',
'end' => '120959000',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-201'
),
'ENSMUST00000129473' => array(
'start' => '120949071',
'end' => '120956861',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-005'
),
'ENSMUST00000133029' => array(
'start' => '120950688',
'end' => '120955273',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-003'
),
'ENSMUST00000134540' => array(
'start' => '120955226',
'end' => '120956231',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Slc16a3-004'
),
'ENSMUST00000140467' => array(
'start' => '120951138',
'end' => '120954212',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Slc16a3-006'
),
'ENSMUST00000154187' => array(
'start' => '120949053',
'end' => '120956747',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-002'
),
'ENSMUST00000168579' => array(
'start' => '120949081',
'end' => '120960868',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-202'
),
'ENSMUST00000018274' => array(
'start' => '120961749',
'end' => '120991330',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-001'
),
'ENSMUST00000070575' => array(
'start' => '120961749',
'end' => '120991092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-002'
),
'ENSMUST00000131375' => array(
'start' => '120963648',
'end' => '120965686',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-003'
),
'ENSMUST00000139267' => array(
'start' => '120967612',
'end' => '120968061',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-007'
),
'ENSMUST00000141071' => array(
'start' => '120963773',
'end' => '120971625',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-008'
),
'ENSMUST00000146837' => array(
'start' => '120972490',
'end' => '120990987',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Csnk1d-004'
),
'ENSMUST00000154483' => array(
'start' => '120972472',
'end' => '120990871',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-006'
),
'ENSMUST00000155070' => array(
'start' => '120982857',
'end' => '120991051',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Csnk1d-005'
),
'ENSMUST00000189381' => array(
'start' => '120963844',
'end' => '120964764',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP23-378G22.3-001'
)
),
'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_00043R_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00043R_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00043R_0001' => array(
'genes_in_region' => array(
'ENSDARG00000008370' => array(
[maximum depth reached]
),
'ENSDARG00000028583' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle'
)
),
'CIL_00043R_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000025161' => array(
[maximum depth reached]
),
'ENSMUSG00000025162' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Adipose',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Adrenal',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Ovary',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Adipose',
(int) 48 => 'Adrenal',
(int) 49 => 'Brain',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Kidney',
(int) 54 => 'Liver',
(int) 55 => 'Ovary',
(int) 56 => 'Adipose',
(int) 57 => 'Adrenal',
(int) 58 => 'Bladder',
(int) 59 => 'Brain',
(int) 60 => 'Breast',
(int) 61 => 'Colon',
(int) 62 => 'Heart',
(int) 63 => 'Kidney',
(int) 64 => 'Liver',
(int) 65 => 'Lung',
(int) 66 => 'Muscle',
(int) 67 => 'Ovary',
(int) 68 => 'Placenta',
(int) 69 => 'Testis',
(int) 70 => 'Adipose',
(int) 71 => 'Adrenal',
(int) 72 => 'Bladder',
(int) 73 => 'Brain',
(int) 74 => 'Breast',
(int) 75 => 'Colon',
(int) 76 => 'Heart',
(int) 77 => 'Kidney',
(int) 78 => 'Liver',
(int) 79 => 'Lung',
(int) 80 => 'Muscle',
(int) 81 => 'Ovary',
(int) 82 => 'Placenta',
(int) 83 => 'Testis',
(int) 84 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000008370' => 'casein kinase 1, delta a',
'ENSDARG00000028583' => 'solute carrier family 16 (monocarboxylate transporter), member 3',
'ENSG00000141526' => 'solute carrier family 16 (monocarboxylate transporter), member 3',
'ENSG00000141551' => 'casein kinase 1, delta',
'ENSG00000275505' => 'microRNA 6787',
'ENSG00000275888' => null,
'ENSG00000280407' => null,
'ENSMUSG00000025161' => 'solute carrier family 16 (monocarboxylic acid transporters), member 3',
'ENSMUSG00000025162' => 'casein kinase 1, delta',
'ENSMUSG00000100629' => 'predicted gene 28192'
)
$gene_name_arr = array(
'ENSDARG00000008370' => 'csnk1da',
'ENSDARG00000028583' => 'SLC16A3 (1 of 2)',
'ENSG00000141526' => 'SLC16A3',
'ENSG00000141551' => 'CSNK1D',
'ENSG00000275505' => 'MIR6787',
'ENSG00000275888' => 'RP13-516M14.10',
'ENSG00000280407' => 'RP13-516M14.8',
'ENSMUSG00000025161' => 'Slc16a3',
'ENSMUSG00000025162' => 'Csnk1d',
'ENSMUSG00000100629' => 'RP23-378G22.3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00043R_0001',
'tax_id' => '7955',
'chromosome' => '3',
'seq_start' => '36160097',
'seq_end' => '36209462',
'region_length' => '49365',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000028583-ENSDARG00000008370'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00043R_0002',
'tax_id' => '9606',
'chromosome' => '17',
'seq_start' => '82228397',
'seq_end' => '82273731',
'region_length' => '45334',
'region_type' => 'CGP',
'el_id' => 'ENSG00000141526-ENSG00000141551'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00043R_0003',
'tax_id' => '10090',
'chromosome' => '11',
'seq_start' => '120948480',
'seq_end' => '120991330',
'region_length' => '42850',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000025161-ENSMUSG00000025162'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 24 => 'Brain',
(int) 34 => 'Breast',
(int) 42 => 'Colon',
(int) 53 => 'Heart',
(int) 65 => 'Kidney',
(int) 77 => 'Liver',
(int) 86 => 'Lung',
(int) 93 => 'Muscle',
(int) 104 => 'Ovary',
(int) 115 => 'Placenta',
(int) 123 => '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) 71
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000025326' => array(
'start' => '36172321',
'end' => '36209462',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'csnk1da-001'
),
'ENSDART00000038525' => array(
'start' => '36160097',
'end' => '36166512',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3 (1 of 2)-001'
),
'ENST00000392339' => array(
'start' => '82232232',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-201'
),
'ENST00000392341' => array(
'start' => '82228406',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-202'
),
'ENST00000577650' => array(
'start' => '82229060',
'end' => '82237320',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-016'
),
'ENST00000578522' => array(
'start' => '82234899',
'end' => '82237177',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-008'
),
'ENST00000578574' => array(
'start' => '82229062',
'end' => '82236895',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-011'
),
'ENST00000578684' => array(
'start' => '82229058',
'end' => '82237705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-012'
),
'ENST00000578810' => array(
'start' => '82236474',
'end' => '82237416',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-017'
),
'ENST00000579572' => array(
'start' => '82229068',
'end' => '82237303',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-013'
),
'ENST00000580098' => array(
'start' => '82232232',
'end' => '82237475',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-007'
),
'ENST00000580189' => array(
'start' => '82235053',
'end' => '82237439',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-009'
),
'ENST00000581287' => array(
'start' => '82233687',
'end' => '82240086',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-001'
),
'ENST00000581642' => array(
'start' => '82228448',
'end' => '82236457',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-006'
),
'ENST00000582715' => array(
'start' => '82229093',
'end' => '82239481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-015'
),
'ENST00000582743' => array(
'start' => '82229032',
'end' => '82239479',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-002'
),
'ENST00000582946' => array(
'start' => '82235774',
'end' => '82237261',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-010'
),
'ENST00000583025' => array(
'start' => '82237170',
'end' => '82261129',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-018'
),
'ENST00000583237' => array(
'start' => '82228421',
'end' => '82237427',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-005'
),
'ENST00000583444' => array(
'start' => '82229045',
'end' => '82231926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC16A3-003'
),
'ENST00000584689' => array(
'start' => '82228397',
'end' => '82237644',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-004'
),
'ENST00000584781' => array(
'start' => '82229055',
'end' => '82237282',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SLC16A3-014'
),
'ENST00000617373' => array(
'start' => '82234899',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-203'
),
'ENST00000619321' => array(
'start' => '82235774',
'end' => '82239498',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC16A3-204'
),
'ENST00000269361' => array(
'start' => '82244680',
'end' => '82255516',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-022'
),
'ENST00000314028' => array(
'start' => '82242667',
'end' => '82273731',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-001'
),
'ENST00000392334' => array(
'start' => '82244362',
'end' => '82273697',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-002'
),
'ENST00000398519' => array(
'start' => '82239727',
'end' => '82273428',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-006'
),
'ENST00000403276' => array(
'start' => '82246018',
'end' => '82273431',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-005'
),
'ENST00000577578' => array(
'start' => '82244362',
'end' => '82246591',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-028'
),
'ENST00000578194' => array(
'start' => '82253220',
'end' => '82273171',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-019'
),
'ENST00000578501' => array(
'start' => '82244394',
'end' => '82249496',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-025'
),
'ENST00000578904' => array(
'start' => '82249578',
'end' => '82255546',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-009'
),
'ENST00000579308' => array(
'start' => '82265300',
'end' => '82273406',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-016'
),
'ENST00000579316' => array(
'start' => '82255130',
'end' => '82273438',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-014'
),
'ENST00000580061' => array(
'start' => '82255187',
'end' => '82266800',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-020'
),
'ENST00000580446' => array(
'start' => '82252497',
'end' => '82273431',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CSNK1D-015'
),
'ENST00000580565' => array(
'start' => '82246318',
'end' => '82249835',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-024'
),
'ENST00000580784' => array(
'start' => '82244645',
'end' => '82251414',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-010'
),
'ENST00000581108' => array(
'start' => '82249239',
'end' => '82252527',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-023'
),
'ENST00000581241' => array(
'start' => '82242673',
'end' => '82273369',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-007'
),
'ENST00000581655' => array(
'start' => '82266708',
'end' => '82273251',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-018'
),
'ENST00000581660' => array(
'start' => '82253216',
'end' => '82273457',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-013'
),
'ENST00000581737' => array(
'start' => '82244491',
'end' => '82249164',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-026'
),
'ENST00000582844' => array(
'start' => '82249489',
'end' => '82273124',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-021'
),
'ENST00000584377' => array(
'start' => '82244301',
'end' => '82254679',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CSNK1D-008'
),
'ENST00000584472' => array(
'start' => '82255164',
'end' => '82273466',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-012'
),
'ENST00000584672' => array(
'start' => '82239023',
'end' => '82248980',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-027'
),
'ENST00000584913' => array(
'start' => '82244722',
'end' => '82245113',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CSNK1D-029'
),
'ENST00000585026' => array(
'start' => '82255438',
'end' => '82273400',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CSNK1D-017'
),
'ENST00000616675' => array(
'start' => '82236668',
'end' => '82236728',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6787-201'
),
'ENST00000620937' => array(
'start' => '82244770',
'end' => '82245591',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP13-516M14.10-001'
),
'ENST00000622924' => array(
'start' => '82249067',
'end' => '82251827',
'transcript_biotype' => 'pseudogene',
'transcript_name' => 'RP13-516M14.8-201'
),
'ENST00000624920' => array(
'start' => '82249067',
'end' => '82251844',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP13-516M14.8-001'
),
'ENSMUST00000070653' => array(
'start' => '120948480',
'end' => '120958775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-001'
),
'ENSMUST00000100130' => array(
'start' => '120949067',
'end' => '120959000',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-201'
),
'ENSMUST00000129473' => array(
'start' => '120949071',
'end' => '120956861',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-005'
),
'ENSMUST00000133029' => array(
'start' => '120950688',
'end' => '120955273',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-003'
),
'ENSMUST00000134540' => array(
'start' => '120955226',
'end' => '120956231',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Slc16a3-004'
),
'ENSMUST00000140467' => array(
'start' => '120951138',
'end' => '120954212',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Slc16a3-006'
),
'ENSMUST00000154187' => array(
'start' => '120949053',
'end' => '120956747',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-002'
),
'ENSMUST00000168579' => array(
'start' => '120949081',
'end' => '120960868',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc16a3-202'
),
'ENSMUST00000018274' => array(
'start' => '120961749',
'end' => '120991330',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-001'
),
'ENSMUST00000070575' => array(
'start' => '120961749',
'end' => '120991092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-002'
),
'ENSMUST00000131375' => array(
'start' => '120963648',
'end' => '120965686',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-003'
),
'ENSMUST00000139267' => array(
'start' => '120967612',
'end' => '120968061',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-007'
),
'ENSMUST00000141071' => array(
'start' => '120963773',
'end' => '120971625',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Csnk1d-008'
),
'ENSMUST00000146837' => array(
'start' => '120972490',
'end' => '120990987',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Csnk1d-004'
),
'ENSMUST00000154483' => array(
'start' => '120972472',
'end' => '120990871',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Csnk1d-006'
),
'ENSMUST00000155070' => array(
'start' => '120982857',
'end' => '120991051',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Csnk1d-005'
),
'ENSMUST00000189381' => array(
'start' => '120963844',
'end' => '120964764',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP23-378G22.3-001'
)
)
$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_00043R_0001' => array(
'genes_in_region' => array(
'ENSDARG00000008370' => array(
[maximum depth reached]
),
'ENSDARG00000028583' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle'
)
),
'CIL_00043R_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000025161' => array(
[maximum depth reached]
),
'ENSMUSG00000025162' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Adipose',
(int) 14 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Adrenal',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Ovary',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Adipose',
(int) 48 => 'Adrenal',
(int) 49 => 'Brain',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Kidney',
(int) 54 => 'Liver',
(int) 55 => 'Ovary',
(int) 56 => 'Adipose',
(int) 57 => 'Adrenal',
(int) 58 => 'Bladder',
(int) 59 => 'Brain',
(int) 60 => 'Breast',
(int) 61 => 'Colon',
(int) 62 => 'Heart',
(int) 63 => 'Kidney',
(int) 64 => 'Liver',
(int) 65 => 'Lung',
(int) 66 => 'Muscle',
(int) 67 => 'Ovary',
(int) 68 => 'Placenta',
(int) 69 => 'Testis',
(int) 70 => 'Adipose',
(int) 71 => 'Adrenal',
(int) 72 => 'Bladder',
(int) 73 => 'Brain',
(int) 74 => 'Breast',
(int) 75 => 'Colon',
(int) 76 => 'Heart',
(int) 77 => 'Kidney',
(int) 78 => 'Liver',
(int) 79 => 'Lung',
(int) 80 => 'Muscle',
(int) 81 => 'Ovary',
(int) 82 => 'Placenta',
(int) 83 => 'Testis',
(int) 84 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00043R_0002',
'tax_id' => '9606',
'chromosome' => '17',
'seq_start' => '82228397',
'seq_end' => '82273731',
'region_length' => '45334',
'region_type' => 'CGP',
'el_id' => 'ENSG00000141526-ENSG00000141551'
)
)
$gene_el = array(
'ENSDART00000038525' => array(
'Brain' => array(
'average_FPKM' => '2.052',
'stddev_FPKM' => '0.87'
),
'Heart' => array(
'average_FPKM' => '0.614',
'stddev_FPKM' => '0.25'
),
'Kidney' => array(
'average_FPKM' => '0.666',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.474',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000028583'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '2.052',
'stddev_FPKM' => '0.87'
),
'Heart' => array(
'average_FPKM' => '0.614',
'stddev_FPKM' => '0.25'
),
'Kidney' => array(
'average_FPKM' => '0.666',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.474',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000038525'
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 |
| ENSG00000141526-ENSG00000141551 |
CGP |
9606 |
17:82228397-82273731  |
| Gene | Transcript | Position | Biotype |
|---|
(csnk1da)