| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000031822-ENSMUSG00000031821 |
CGP |
10090 |
8:120230536-120589304  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_000579_0003 [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_000579_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_000579_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000002304' => 'GINS complex subunit 2',
'ENSDARG00000062020' => 'Gse1 coiled-coil protein',
'ENSG00000131149' => 'Gse1 coiled-coil protein',
'ENSG00000131153' => 'GINS complex subunit 2 (Psf2 homolog)',
'ENSG00000263968' => 'RNA, 7SL, cytoplasmic 381, pseudogene',
'ENSMUSG00000031821' => 'GINS complex subunit 2 (Psf2 homolog)',
'ENSMUSG00000031822' => 'genetic suppressor element 1',
'ENSMUSG00000097983' => 'predicted gene, 26971',
'ENSMUSG00000098280' => 'microRNA 7687'
),
'gene_name_arr' => array(
'ENSDARG00000002304' => 'gins2',
'ENSDARG00000062020' => 'gse1',
'ENSG00000131149' => 'GSE1',
'ENSG00000131153' => 'GINS2',
'ENSG00000263968' => 'RN7SL381P',
'ENSMUSG00000031821' => 'Gins2',
'ENSMUSG00000031822' => 'Gse1',
'ENSMUSG00000097983' => 'Gm26971',
'ENSMUSG00000098280' => 'Mir7687'
),
'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) 3 => 'Adrenal',
(int) 6 => 'Brain',
(int) 12 => 'Breast',
(int) 16 => 'Colon',
(int) 20 => 'Heart',
(int) 25 => 'Kidney',
(int) 31 => 'Liver',
(int) 38 => 'Lung',
(int) 43 => 'Muscle',
(int) 49 => 'Ovary',
(int) 57 => 'Placenta',
(int) 63 => '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) 30,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000033746' => array(
'start' => '30425308',
'end' => '30443767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'gins2-001'
),
'ENSDART00000140908' => array(
'start' => '30386018',
'end' => '30421364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'gse1-001'
),
'ENST00000253458' => array(
'start' => '85613216',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-002'
),
'ENST00000393243' => array(
'start' => '85613352',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-001'
),
'ENST00000405402' => array(
'start' => '85611409',
'end' => '85673354',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-003'
),
'ENST00000411612' => array(
'start' => '85613157',
'end' => '85655872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-006'
),
'ENST00000412692' => array(
'start' => '85654432',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-005'
),
'ENST00000438180' => array(
'start' => '85663366',
'end' => '85672893',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-011'
),
'ENST00000469381' => array(
'start' => '85662291',
'end' => '85676204',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-004'
),
'ENST00000471070' => array(
'start' => '85671831',
'end' => '85672648',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GSE1-010'
),
'ENST00000479488' => array(
'start' => '85661490',
'end' => '85663353',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-007'
),
'ENST00000495192' => array(
'start' => '85664540',
'end' => '85666004',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-008'
),
'ENST00000496345' => array(
'start' => '85670628',
'end' => '85672496',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-009'
),
'ENST00000562659' => array(
'start' => '85665020',
'end' => '85666622',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-012'
),
'ENST00000253462' => array(
'start' => '85676198',
'end' => '85688999',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-001'
),
'ENST00000595355' => array(
'start' => '85678570',
'end' => '85688025',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-003'
),
'ENST00000596233' => array(
'start' => '85678623',
'end' => '85690073',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-004'
),
'ENST00000577658' => array(
'start' => '85659378',
'end' => '85659675',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL381P-201'
),
'ENSMUST00000034278' => array(
'start' => '120578633',
'end' => '120589304',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gins2-001'
),
'ENSMUST00000126094' => array(
'start' => '120582155',
'end' => '120589034',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gins2-003'
),
'ENSMUST00000146526' => array(
'start' => '120578633',
'end' => '120588980',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gins2-002'
),
'ENSMUST00000155609' => array(
'start' => '120581544',
'end' => '120586208',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gins2-004'
),
'ENSMUST00000034279' => array(
'start' => '120488447',
'end' => '120581390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-002'
),
'ENSMUST00000118136' => array(
'start' => '120537429',
'end' => '120579326',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-001'
),
'ENSMUST00000120493' => array(
'start' => '120535857',
'end' => '120579480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-003'
),
'ENSMUST00000141113' => array(
'start' => '120571329',
'end' => '120575210',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gse1-005'
),
'ENSMUST00000147327' => array(
'start' => '120571281',
'end' => '120573272',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gse1-004'
),
'ENSMUST00000180448' => array(
'start' => '120230536',
'end' => '120553634',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-006'
),
'ENSMUST00000182423' => array(
'start' => '120520615',
'end' => '120521686',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm26971-001'
),
'ENSMUST00000184722' => array(
'start' => '120538696',
'end' => '120538754',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7687-201'
)
),
'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_000579_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_000579_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000579_0001' => array(
'genes_in_region' => array(
'ENSDARG00000002304' => array(
[maximum depth reached]
),
'ENSDARG00000062020' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle'
)
),
'CIL_000579_0002' => array(
'genes_in_region' => array(
'ENSG00000131149' => array(
[maximum depth reached]
),
'ENSG00000131153' => array(
[maximum depth reached]
),
'ENSG00000263968' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Brain',
(int) 31 => 'Colon',
(int) 32 => 'Heart',
(int) 33 => 'Kidney',
(int) 34 => 'Liver',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Liver',
(int) 44 => 'Ovary',
(int) 45 => 'Ovary',
(int) 46 => 'Testis',
(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 => 'Lung',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000002304' => 'GINS complex subunit 2',
'ENSDARG00000062020' => 'Gse1 coiled-coil protein',
'ENSG00000131149' => 'Gse1 coiled-coil protein',
'ENSG00000131153' => 'GINS complex subunit 2 (Psf2 homolog)',
'ENSG00000263968' => 'RNA, 7SL, cytoplasmic 381, pseudogene',
'ENSMUSG00000031821' => 'GINS complex subunit 2 (Psf2 homolog)',
'ENSMUSG00000031822' => 'genetic suppressor element 1',
'ENSMUSG00000097983' => 'predicted gene, 26971',
'ENSMUSG00000098280' => 'microRNA 7687'
)
$gene_name_arr = array(
'ENSDARG00000002304' => 'gins2',
'ENSDARG00000062020' => 'gse1',
'ENSG00000131149' => 'GSE1',
'ENSG00000131153' => 'GINS2',
'ENSG00000263968' => 'RN7SL381P',
'ENSMUSG00000031821' => 'Gins2',
'ENSMUSG00000031822' => 'Gse1',
'ENSMUSG00000097983' => 'Gm26971',
'ENSMUSG00000098280' => 'Mir7687'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000579_0001',
'tax_id' => '7955',
'chromosome' => '18',
'seq_start' => '30386018',
'seq_end' => '30443767',
'region_length' => '57749',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000062020-ENSDARG00000002304'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000579_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '85611409',
'seq_end' => '85690073',
'region_length' => '78664',
'region_type' => 'CGP',
'el_id' => 'ENSG00000131149-ENSG00000131153'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000579_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '120230536',
'seq_end' => '120589304',
'region_length' => '358768',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031822-ENSMUSG00000031821'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Brain',
(int) 12 => 'Breast',
(int) 16 => 'Colon',
(int) 20 => 'Heart',
(int) 25 => 'Kidney',
(int) 31 => 'Liver',
(int) 38 => 'Lung',
(int) 43 => 'Muscle',
(int) 49 => 'Ovary',
(int) 57 => 'Placenta',
(int) 63 => '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) 30
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000033746' => array(
'start' => '30425308',
'end' => '30443767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'gins2-001'
),
'ENSDART00000140908' => array(
'start' => '30386018',
'end' => '30421364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'gse1-001'
),
'ENST00000253458' => array(
'start' => '85613216',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-002'
),
'ENST00000393243' => array(
'start' => '85613352',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-001'
),
'ENST00000405402' => array(
'start' => '85611409',
'end' => '85673354',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-003'
),
'ENST00000411612' => array(
'start' => '85613157',
'end' => '85655872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-006'
),
'ENST00000412692' => array(
'start' => '85654432',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-005'
),
'ENST00000438180' => array(
'start' => '85663366',
'end' => '85672893',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-011'
),
'ENST00000469381' => array(
'start' => '85662291',
'end' => '85676204',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-004'
),
'ENST00000471070' => array(
'start' => '85671831',
'end' => '85672648',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GSE1-010'
),
'ENST00000479488' => array(
'start' => '85661490',
'end' => '85663353',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-007'
),
'ENST00000495192' => array(
'start' => '85664540',
'end' => '85666004',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-008'
),
'ENST00000496345' => array(
'start' => '85670628',
'end' => '85672496',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-009'
),
'ENST00000562659' => array(
'start' => '85665020',
'end' => '85666622',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-012'
),
'ENST00000253462' => array(
'start' => '85676198',
'end' => '85688999',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-001'
),
'ENST00000595355' => array(
'start' => '85678570',
'end' => '85688025',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-003'
),
'ENST00000596233' => array(
'start' => '85678623',
'end' => '85690073',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-004'
),
'ENST00000577658' => array(
'start' => '85659378',
'end' => '85659675',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL381P-201'
),
'ENSMUST00000034278' => array(
'start' => '120578633',
'end' => '120589304',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gins2-001'
),
'ENSMUST00000126094' => array(
'start' => '120582155',
'end' => '120589034',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gins2-003'
),
'ENSMUST00000146526' => array(
'start' => '120578633',
'end' => '120588980',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gins2-002'
),
'ENSMUST00000155609' => array(
'start' => '120581544',
'end' => '120586208',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gins2-004'
),
'ENSMUST00000034279' => array(
'start' => '120488447',
'end' => '120581390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-002'
),
'ENSMUST00000118136' => array(
'start' => '120537429',
'end' => '120579326',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-001'
),
'ENSMUST00000120493' => array(
'start' => '120535857',
'end' => '120579480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-003'
),
'ENSMUST00000141113' => array(
'start' => '120571329',
'end' => '120575210',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gse1-005'
),
'ENSMUST00000147327' => array(
'start' => '120571281',
'end' => '120573272',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gse1-004'
),
'ENSMUST00000180448' => array(
'start' => '120230536',
'end' => '120553634',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-006'
),
'ENSMUST00000182423' => array(
'start' => '120520615',
'end' => '120521686',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm26971-001'
),
'ENSMUST00000184722' => array(
'start' => '120538696',
'end' => '120538754',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7687-201'
)
)
$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_000579_0001' => array(
'genes_in_region' => array(
'ENSDARG00000002304' => array(
[maximum depth reached]
),
'ENSDARG00000062020' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle'
)
),
'CIL_000579_0002' => array(
'genes_in_region' => array(
'ENSG00000131149' => array(
[maximum depth reached]
),
'ENSG00000131153' => array(
[maximum depth reached]
),
'ENSG00000263968' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Brain',
(int) 31 => 'Colon',
(int) 32 => 'Heart',
(int) 33 => 'Kidney',
(int) 34 => 'Liver',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Liver',
(int) 44 => 'Ovary',
(int) 45 => 'Ovary',
(int) 46 => 'Testis',
(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 => 'Lung',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000579_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '120230536',
'seq_end' => '120589304',
'region_length' => '358768',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031822-ENSMUSG00000031821'
)
)
$gene_el = array(
'ENST00000577658' => array(
'Adipose' => array(
'average_FPKM' => '0.491',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.444',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.170',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.597',
'stddev_FPKM' => '2.13'
),
'Colon' => array(
'average_FPKM' => '1.395',
'stddev_FPKM' => '1.32'
),
'Heart' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.467',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '2.423',
'stddev_FPKM' => '2.29'
),
'Lung' => array(
'average_FPKM' => '1.016',
'stddev_FPKM' => '0.72'
),
'Ovary' => array(
'average_FPKM' => '0.448',
'stddev_FPKM' => '0.24'
),
'Placenta' => array(
'average_FPKM' => '0.429',
'stddev_FPKM' => '0.18'
),
'Testis' => array(
'average_FPKM' => '0.714',
'stddev_FPKM' => '0.02'
)
)
)
$gene_key = 'ENSG00000263968'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.491',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.444',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.170',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.597',
'stddev_FPKM' => '2.13'
),
'Colon' => array(
'average_FPKM' => '1.395',
'stddev_FPKM' => '1.32'
),
'Heart' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.467',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '2.423',
'stddev_FPKM' => '2.29'
),
'Lung' => array(
'average_FPKM' => '1.016',
'stddev_FPKM' => '0.72'
),
'Ovary' => array(
'average_FPKM' => '0.448',
'stddev_FPKM' => '0.24'
),
'Placenta' => array(
'average_FPKM' => '0.429',
'stddev_FPKM' => '0.18'
),
'Testis' => array(
'average_FPKM' => '0.714',
'stddev_FPKM' => '0.02'
)
)
$tran_key = 'ENST00000577658'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_000579_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_000579_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000002304' => 'GINS complex subunit 2',
'ENSDARG00000062020' => 'Gse1 coiled-coil protein',
'ENSG00000131149' => 'Gse1 coiled-coil protein',
'ENSG00000131153' => 'GINS complex subunit 2 (Psf2 homolog)',
'ENSG00000263968' => 'RNA, 7SL, cytoplasmic 381, pseudogene',
'ENSMUSG00000031821' => 'GINS complex subunit 2 (Psf2 homolog)',
'ENSMUSG00000031822' => 'genetic suppressor element 1',
'ENSMUSG00000097983' => 'predicted gene, 26971',
'ENSMUSG00000098280' => 'microRNA 7687'
),
'gene_name_arr' => array(
'ENSDARG00000002304' => 'gins2',
'ENSDARG00000062020' => 'gse1',
'ENSG00000131149' => 'GSE1',
'ENSG00000131153' => 'GINS2',
'ENSG00000263968' => 'RN7SL381P',
'ENSMUSG00000031821' => 'Gins2',
'ENSMUSG00000031822' => 'Gse1',
'ENSMUSG00000097983' => 'Gm26971',
'ENSMUSG00000098280' => 'Mir7687'
),
'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) 3 => 'Adrenal',
(int) 6 => 'Brain',
(int) 12 => 'Breast',
(int) 16 => 'Colon',
(int) 20 => 'Heart',
(int) 25 => 'Kidney',
(int) 31 => 'Liver',
(int) 38 => 'Lung',
(int) 43 => 'Muscle',
(int) 49 => 'Ovary',
(int) 57 => 'Placenta',
(int) 63 => '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) 30,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000033746' => array(
'start' => '30425308',
'end' => '30443767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'gins2-001'
),
'ENSDART00000140908' => array(
'start' => '30386018',
'end' => '30421364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'gse1-001'
),
'ENST00000253458' => array(
'start' => '85613216',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-002'
),
'ENST00000393243' => array(
'start' => '85613352',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-001'
),
'ENST00000405402' => array(
'start' => '85611409',
'end' => '85673354',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-003'
),
'ENST00000411612' => array(
'start' => '85613157',
'end' => '85655872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-006'
),
'ENST00000412692' => array(
'start' => '85654432',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-005'
),
'ENST00000438180' => array(
'start' => '85663366',
'end' => '85672893',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-011'
),
'ENST00000469381' => array(
'start' => '85662291',
'end' => '85676204',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-004'
),
'ENST00000471070' => array(
'start' => '85671831',
'end' => '85672648',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GSE1-010'
),
'ENST00000479488' => array(
'start' => '85661490',
'end' => '85663353',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-007'
),
'ENST00000495192' => array(
'start' => '85664540',
'end' => '85666004',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-008'
),
'ENST00000496345' => array(
'start' => '85670628',
'end' => '85672496',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-009'
),
'ENST00000562659' => array(
'start' => '85665020',
'end' => '85666622',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-012'
),
'ENST00000253462' => array(
'start' => '85676198',
'end' => '85688999',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-001'
),
'ENST00000595355' => array(
'start' => '85678570',
'end' => '85688025',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-003'
),
'ENST00000596233' => array(
'start' => '85678623',
'end' => '85690073',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-004'
),
'ENST00000577658' => array(
'start' => '85659378',
'end' => '85659675',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL381P-201'
),
'ENSMUST00000034278' => array(
'start' => '120578633',
'end' => '120589304',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gins2-001'
),
'ENSMUST00000126094' => array(
'start' => '120582155',
'end' => '120589034',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gins2-003'
),
'ENSMUST00000146526' => array(
'start' => '120578633',
'end' => '120588980',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gins2-002'
),
'ENSMUST00000155609' => array(
'start' => '120581544',
'end' => '120586208',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gins2-004'
),
'ENSMUST00000034279' => array(
'start' => '120488447',
'end' => '120581390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-002'
),
'ENSMUST00000118136' => array(
'start' => '120537429',
'end' => '120579326',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-001'
),
'ENSMUST00000120493' => array(
'start' => '120535857',
'end' => '120579480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-003'
),
'ENSMUST00000141113' => array(
'start' => '120571329',
'end' => '120575210',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gse1-005'
),
'ENSMUST00000147327' => array(
'start' => '120571281',
'end' => '120573272',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gse1-004'
),
'ENSMUST00000180448' => array(
'start' => '120230536',
'end' => '120553634',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-006'
),
'ENSMUST00000182423' => array(
'start' => '120520615',
'end' => '120521686',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm26971-001'
),
'ENSMUST00000184722' => array(
'start' => '120538696',
'end' => '120538754',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7687-201'
)
),
'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_000579_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_000579_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000579_0001' => array(
'genes_in_region' => array(
'ENSDARG00000002304' => array(
[maximum depth reached]
),
'ENSDARG00000062020' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle'
)
),
'CIL_000579_0002' => array(
'genes_in_region' => array(
'ENSG00000131149' => array(
[maximum depth reached]
),
'ENSG00000131153' => array(
[maximum depth reached]
),
'ENSG00000263968' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Brain',
(int) 31 => 'Colon',
(int) 32 => 'Heart',
(int) 33 => 'Kidney',
(int) 34 => 'Liver',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Liver',
(int) 44 => 'Ovary',
(int) 45 => 'Ovary',
(int) 46 => 'Testis',
(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 => 'Lung',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000002304' => 'GINS complex subunit 2',
'ENSDARG00000062020' => 'Gse1 coiled-coil protein',
'ENSG00000131149' => 'Gse1 coiled-coil protein',
'ENSG00000131153' => 'GINS complex subunit 2 (Psf2 homolog)',
'ENSG00000263968' => 'RNA, 7SL, cytoplasmic 381, pseudogene',
'ENSMUSG00000031821' => 'GINS complex subunit 2 (Psf2 homolog)',
'ENSMUSG00000031822' => 'genetic suppressor element 1',
'ENSMUSG00000097983' => 'predicted gene, 26971',
'ENSMUSG00000098280' => 'microRNA 7687'
)
$gene_name_arr = array(
'ENSDARG00000002304' => 'gins2',
'ENSDARG00000062020' => 'gse1',
'ENSG00000131149' => 'GSE1',
'ENSG00000131153' => 'GINS2',
'ENSG00000263968' => 'RN7SL381P',
'ENSMUSG00000031821' => 'Gins2',
'ENSMUSG00000031822' => 'Gse1',
'ENSMUSG00000097983' => 'Gm26971',
'ENSMUSG00000098280' => 'Mir7687'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000579_0001',
'tax_id' => '7955',
'chromosome' => '18',
'seq_start' => '30386018',
'seq_end' => '30443767',
'region_length' => '57749',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000062020-ENSDARG00000002304'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000579_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '85611409',
'seq_end' => '85690073',
'region_length' => '78664',
'region_type' => 'CGP',
'el_id' => 'ENSG00000131149-ENSG00000131153'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000579_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '120230536',
'seq_end' => '120589304',
'region_length' => '358768',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031822-ENSMUSG00000031821'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Brain',
(int) 12 => 'Breast',
(int) 16 => 'Colon',
(int) 20 => 'Heart',
(int) 25 => 'Kidney',
(int) 31 => 'Liver',
(int) 38 => 'Lung',
(int) 43 => 'Muscle',
(int) 49 => 'Ovary',
(int) 57 => 'Placenta',
(int) 63 => '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) 30
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000033746' => array(
'start' => '30425308',
'end' => '30443767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'gins2-001'
),
'ENSDART00000140908' => array(
'start' => '30386018',
'end' => '30421364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'gse1-001'
),
'ENST00000253458' => array(
'start' => '85613216',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-002'
),
'ENST00000393243' => array(
'start' => '85613352',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-001'
),
'ENST00000405402' => array(
'start' => '85611409',
'end' => '85673354',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-003'
),
'ENST00000411612' => array(
'start' => '85613157',
'end' => '85655872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-006'
),
'ENST00000412692' => array(
'start' => '85654432',
'end' => '85676204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-005'
),
'ENST00000438180' => array(
'start' => '85663366',
'end' => '85672893',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GSE1-011'
),
'ENST00000469381' => array(
'start' => '85662291',
'end' => '85676204',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-004'
),
'ENST00000471070' => array(
'start' => '85671831',
'end' => '85672648',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GSE1-010'
),
'ENST00000479488' => array(
'start' => '85661490',
'end' => '85663353',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-007'
),
'ENST00000495192' => array(
'start' => '85664540',
'end' => '85666004',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-008'
),
'ENST00000496345' => array(
'start' => '85670628',
'end' => '85672496',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-009'
),
'ENST00000562659' => array(
'start' => '85665020',
'end' => '85666622',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GSE1-012'
),
'ENST00000253462' => array(
'start' => '85676198',
'end' => '85688999',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-001'
),
'ENST00000595355' => array(
'start' => '85678570',
'end' => '85688025',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-003'
),
'ENST00000596233' => array(
'start' => '85678623',
'end' => '85690073',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GINS2-004'
),
'ENST00000577658' => array(
'start' => '85659378',
'end' => '85659675',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL381P-201'
),
'ENSMUST00000034278' => array(
'start' => '120578633',
'end' => '120589304',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gins2-001'
),
'ENSMUST00000126094' => array(
'start' => '120582155',
'end' => '120589034',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gins2-003'
),
'ENSMUST00000146526' => array(
'start' => '120578633',
'end' => '120588980',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gins2-002'
),
'ENSMUST00000155609' => array(
'start' => '120581544',
'end' => '120586208',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gins2-004'
),
'ENSMUST00000034279' => array(
'start' => '120488447',
'end' => '120581390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-002'
),
'ENSMUST00000118136' => array(
'start' => '120537429',
'end' => '120579326',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-001'
),
'ENSMUST00000120493' => array(
'start' => '120535857',
'end' => '120579480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-003'
),
'ENSMUST00000141113' => array(
'start' => '120571329',
'end' => '120575210',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gse1-005'
),
'ENSMUST00000147327' => array(
'start' => '120571281',
'end' => '120573272',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Gse1-004'
),
'ENSMUST00000180448' => array(
'start' => '120230536',
'end' => '120553634',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gse1-006'
),
'ENSMUST00000182423' => array(
'start' => '120520615',
'end' => '120521686',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm26971-001'
),
'ENSMUST00000184722' => array(
'start' => '120538696',
'end' => '120538754',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7687-201'
)
)
$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_000579_0001' => array(
'genes_in_region' => array(
'ENSDARG00000002304' => array(
[maximum depth reached]
),
'ENSDARG00000062020' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Muscle'
)
),
'CIL_000579_0002' => array(
'genes_in_region' => array(
'ENSG00000131149' => array(
[maximum depth reached]
),
'ENSG00000131153' => array(
[maximum depth reached]
),
'ENSG00000263968' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Brain',
(int) 31 => 'Colon',
(int) 32 => 'Heart',
(int) 33 => 'Kidney',
(int) 34 => 'Liver',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Liver',
(int) 44 => 'Ovary',
(int) 45 => 'Ovary',
(int) 46 => 'Testis',
(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 => 'Lung',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000579_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '120230536',
'seq_end' => '120589304',
'region_length' => '358768',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031822-ENSMUSG00000031821'
)
)
$gene_el = array(
'ENST00000577658' => array(
'Adipose' => array(
'average_FPKM' => '0.491',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.444',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.170',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.597',
'stddev_FPKM' => '2.13'
),
'Colon' => array(
'average_FPKM' => '1.395',
'stddev_FPKM' => '1.32'
),
'Heart' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.467',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '2.423',
'stddev_FPKM' => '2.29'
),
'Lung' => array(
'average_FPKM' => '1.016',
'stddev_FPKM' => '0.72'
),
'Ovary' => array(
'average_FPKM' => '0.448',
'stddev_FPKM' => '0.24'
),
'Placenta' => array(
'average_FPKM' => '0.429',
'stddev_FPKM' => '0.18'
),
'Testis' => array(
'average_FPKM' => '0.714',
'stddev_FPKM' => '0.02'
)
)
)
$gene_key = 'ENSG00000263968'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.491',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.444',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.170',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.597',
'stddev_FPKM' => '2.13'
),
'Colon' => array(
'average_FPKM' => '1.395',
'stddev_FPKM' => '1.32'
),
'Heart' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.467',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '2.423',
'stddev_FPKM' => '2.29'
),
'Lung' => array(
'average_FPKM' => '1.016',
'stddev_FPKM' => '0.72'
),
'Ovary' => array(
'average_FPKM' => '0.448',
'stddev_FPKM' => '0.24'
),
'Placenta' => array(
'average_FPKM' => '0.429',
'stddev_FPKM' => '0.18'
),
'Testis' => array(
'average_FPKM' => '0.714',
'stddev_FPKM' => '0.02'
)
)
$tran_key = 'ENST00000577658'
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
(gins2)