Notice (8): Undefined index: CIL_0007U2_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_0007U2_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000058063' => 'ATPase, class VI, type 11B',
'ENSG00000228766' => 'ribosomal protein L7-like 1 pseudogene 8',
'ENSG00000238837' => null,
'ENSG00000240063' => null,
'ENSG00000241098' => 'uncharacterized LOC401103',
'ENSG00000242012' => null,
'ENSG00000243378' => null,
'ENSG00000244199' => null,
'ENSG00000244247' => null,
'ENSG00000260377' => null,
'ENSMUSG00000093499' => 'predicted gene, 25442'
),
'gene_name_arr' => array(
'ENSG00000058063' => 'ATP11B',
'ENSG00000228766' => 'RPL7L1P8',
'ENSG00000238837' => 'RP11-646E18.2',
'ENSG00000240063' => 'RP11-225N10.1',
'ENSG00000241098' => 'FLJ46066',
'ENSG00000242012' => 'RP11-338L18.1',
'ENSG00000243378' => 'RP11-646E18.3',
'ENSG00000244199' => 'RP11-139K4.4',
'ENSG00000244247' => 'RP11-139K4.2',
'ENSG00000260377' => 'RP11-646E18.4',
'ENSMUSG00000093499' => 'Gm25442'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 25 => 'Heart',
(int) 28 => 'Kidney',
(int) 33 => 'Liver',
(int) 37 => 'Lung',
(int) 41 => 'Muscle',
(int) 45 => 'Ovary',
(int) 51 => 'Placenta',
(int) 54 => '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) 20,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000323116' => array(
'start' => '182793500',
'end' => '182921635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-001'
),
'ENST00000466758' => array(
'start' => '182873966',
'end' => '182919063',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP11B-006'
),
'ENST00000475636' => array(
'start' => '182898685',
'end' => '182913978',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP11B-008'
),
'ENST00000482070' => array(
'start' => '182879539',
'end' => '182897325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-009'
),
'ENST00000482794' => array(
'start' => '182833673',
'end' => '182848557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP11B-010'
),
'ENST00000484691' => array(
'start' => '182898607',
'end' => '182914096',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-011'
),
'ENST00000490303' => array(
'start' => '182865527',
'end' => '182914103',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP11B-005'
),
'ENST00000491699' => array(
'start' => '182897302',
'end' => '182915249',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-007'
),
'ENST00000493826' => array(
'start' => '182793503',
'end' => '182836624',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-002'
),
'ENST00000498086' => array(
'start' => '182837117',
'end' => '182918341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-004'
),
'ENST00000469911' => array(
'start' => '182610674',
'end' => '182611414',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL7L1P8-001'
),
'ENST00000492416' => array(
'start' => '182644214',
'end' => '182655880',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-646E18.2-001'
),
'ENST00000488882' => array(
'start' => '182783236',
'end' => '182793394',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-225N10.1-001'
),
'ENST00000496220' => array(
'start' => '182446970',
'end' => '182486364',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'FLJ46066-001'
),
'ENST00000473893' => array(
'start' => '182365147',
'end' => '182368256',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338L18.1-001'
),
'ENST00000491689' => array(
'start' => '182691928',
'end' => '182692285',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-646E18.3-001'
),
'ENST00000498782' => array(
'start' => '182460417',
'end' => '182461072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-139K4.4-001'
),
'ENST00000489016' => array(
'start' => '182498264',
'end' => '182507124',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-139K4.2-001'
),
'ENST00000565024' => array(
'start' => '182739669',
'end' => '182740848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-646E18.4-001'
),
'ENSMUST00000177270' => array(
'start' => '35325614',
'end' => '35325705',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25442-201'
)
),
'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_0007U2_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007U2_0001' => array(
'genes_in_region' => array(
'ENSG00000058063' => array(
[maximum depth reached]
),
'ENSG00000228766' => array(
[maximum depth reached]
),
'ENSG00000238837' => array(
[maximum depth reached]
),
'ENSG00000240063' => array(
[maximum depth reached]
),
'ENSG00000242012' => array(
[maximum depth reached]
),
'ENSG00000244199' => array(
[maximum depth reached]
),
'ENSG00000244247' => array(
[maximum depth reached]
),
'ENSG00000260377' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Kidney',
(int) 4 => 'Lung',
(int) 5 => 'Muscle',
(int) 6 => 'Ovary',
(int) 7 => 'Placenta',
(int) 8 => 'Testis',
(int) 9 => 'Heart',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Bladder',
(int) 14 => 'Ovary',
(int) 15 => 'Adrenal',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Muscle',
(int) 19 => 'Testis',
(int) 20 => 'Adipose',
(int) 21 => 'Adrenal',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Adrenal',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Testis',
(int) 33 => 'Adipose',
(int) 34 => 'Adrenal',
(int) 35 => 'Brain',
(int) 36 => 'Breast',
(int) 37 => 'Colon',
(int) 38 => 'Heart',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Lung',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain',
(int) 48 => 'Kidney',
(int) 49 => 'Testis',
(int) 50 => 'Testis',
(int) 51 => 'Adipose',
(int) 52 => 'Adrenal',
(int) 53 => 'Brain',
(int) 54 => 'Breast',
(int) 55 => 'Colon',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000058063' => 'ATPase, class VI, type 11B',
'ENSG00000228766' => 'ribosomal protein L7-like 1 pseudogene 8',
'ENSG00000238837' => null,
'ENSG00000240063' => null,
'ENSG00000241098' => 'uncharacterized LOC401103',
'ENSG00000242012' => null,
'ENSG00000243378' => null,
'ENSG00000244199' => null,
'ENSG00000244247' => null,
'ENSG00000260377' => null,
'ENSMUSG00000093499' => 'predicted gene, 25442'
)
$gene_name_arr = array(
'ENSG00000058063' => 'ATP11B',
'ENSG00000228766' => 'RPL7L1P8',
'ENSG00000238837' => 'RP11-646E18.2',
'ENSG00000240063' => 'RP11-225N10.1',
'ENSG00000241098' => 'FLJ46066',
'ENSG00000242012' => 'RP11-338L18.1',
'ENSG00000243378' => 'RP11-646E18.3',
'ENSG00000244199' => 'RP11-139K4.4',
'ENSG00000244247' => 'RP11-139K4.2',
'ENSG00000260377' => 'RP11-646E18.4',
'ENSMUSG00000093499' => 'Gm25442'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007U2_0001',
'tax_id' => '9606',
'chromosome' => '3',
'seq_start' => '182208439',
'seq_end' => '182810171',
'region_length' => '601732',
'region_type' => 'VISTA',
'el_id' => 'mm640'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007U2_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '35040406',
'seq_end' => '35642017',
'region_length' => '601611',
'region_type' => 'VISTA',
'el_id' => 'mm640'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 25 => 'Heart',
(int) 28 => 'Kidney',
(int) 33 => 'Liver',
(int) 37 => 'Lung',
(int) 41 => 'Muscle',
(int) 45 => 'Ovary',
(int) 51 => 'Placenta',
(int) 54 => '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) 20
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000323116' => array(
'start' => '182793500',
'end' => '182921635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-001'
),
'ENST00000466758' => array(
'start' => '182873966',
'end' => '182919063',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP11B-006'
),
'ENST00000475636' => array(
'start' => '182898685',
'end' => '182913978',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP11B-008'
),
'ENST00000482070' => array(
'start' => '182879539',
'end' => '182897325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-009'
),
'ENST00000482794' => array(
'start' => '182833673',
'end' => '182848557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP11B-010'
),
'ENST00000484691' => array(
'start' => '182898607',
'end' => '182914096',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-011'
),
'ENST00000490303' => array(
'start' => '182865527',
'end' => '182914103',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP11B-005'
),
'ENST00000491699' => array(
'start' => '182897302',
'end' => '182915249',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-007'
),
'ENST00000493826' => array(
'start' => '182793503',
'end' => '182836624',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-002'
),
'ENST00000498086' => array(
'start' => '182837117',
'end' => '182918341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-004'
),
'ENST00000469911' => array(
'start' => '182610674',
'end' => '182611414',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL7L1P8-001'
),
'ENST00000492416' => array(
'start' => '182644214',
'end' => '182655880',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-646E18.2-001'
),
'ENST00000488882' => array(
'start' => '182783236',
'end' => '182793394',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-225N10.1-001'
),
'ENST00000496220' => array(
'start' => '182446970',
'end' => '182486364',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'FLJ46066-001'
),
'ENST00000473893' => array(
'start' => '182365147',
'end' => '182368256',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338L18.1-001'
),
'ENST00000491689' => array(
'start' => '182691928',
'end' => '182692285',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-646E18.3-001'
),
'ENST00000498782' => array(
'start' => '182460417',
'end' => '182461072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-139K4.4-001'
),
'ENST00000489016' => array(
'start' => '182498264',
'end' => '182507124',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-139K4.2-001'
),
'ENST00000565024' => array(
'start' => '182739669',
'end' => '182740848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-646E18.4-001'
),
'ENSMUST00000177270' => array(
'start' => '35325614',
'end' => '35325705',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25442-201'
)
)
$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_0007U2_0001' => array(
'genes_in_region' => array(
'ENSG00000058063' => array(
[maximum depth reached]
),
'ENSG00000228766' => array(
[maximum depth reached]
),
'ENSG00000238837' => array(
[maximum depth reached]
),
'ENSG00000240063' => array(
[maximum depth reached]
),
'ENSG00000242012' => array(
[maximum depth reached]
),
'ENSG00000244199' => array(
[maximum depth reached]
),
'ENSG00000244247' => array(
[maximum depth reached]
),
'ENSG00000260377' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Kidney',
(int) 4 => 'Lung',
(int) 5 => 'Muscle',
(int) 6 => 'Ovary',
(int) 7 => 'Placenta',
(int) 8 => 'Testis',
(int) 9 => 'Heart',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Bladder',
(int) 14 => 'Ovary',
(int) 15 => 'Adrenal',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Muscle',
(int) 19 => 'Testis',
(int) 20 => 'Adipose',
(int) 21 => 'Adrenal',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Adrenal',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Testis',
(int) 33 => 'Adipose',
(int) 34 => 'Adrenal',
(int) 35 => 'Brain',
(int) 36 => 'Breast',
(int) 37 => 'Colon',
(int) 38 => 'Heart',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Lung',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain',
(int) 48 => 'Kidney',
(int) 49 => 'Testis',
(int) 50 => 'Testis',
(int) 51 => 'Adipose',
(int) 52 => 'Adrenal',
(int) 53 => 'Brain',
(int) 54 => 'Breast',
(int) 55 => 'Colon',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007U2_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '35040406',
'seq_end' => '35642017',
'region_length' => '601611',
'region_type' => 'VISTA',
'el_id' => 'mm640'
)
)
$gene_el = array(
'ENST00000565024' => array(
'Adipose' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.151',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.070',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.042',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.012',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.022',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.099',
'stddev_FPKM' => '0.04'
),
'Muscle' => array(
'average_FPKM' => '0.032',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.043',
'stddev_FPKM' => '0.03'
),
'Testis' => array(
'average_FPKM' => '0.009',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000260377'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.151',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.070',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.042',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.012',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.022',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.099',
'stddev_FPKM' => '0.04'
),
'Muscle' => array(
'average_FPKM' => '0.032',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.043',
'stddev_FPKM' => '0.03'
),
'Testis' => array(
'average_FPKM' => '0.009',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000565024'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007U2_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000058063' => 'ATPase, class VI, type 11B',
'ENSG00000228766' => 'ribosomal protein L7-like 1 pseudogene 8',
'ENSG00000238837' => null,
'ENSG00000240063' => null,
'ENSG00000241098' => 'uncharacterized LOC401103',
'ENSG00000242012' => null,
'ENSG00000243378' => null,
'ENSG00000244199' => null,
'ENSG00000244247' => null,
'ENSG00000260377' => null,
'ENSMUSG00000093499' => 'predicted gene, 25442'
),
'gene_name_arr' => array(
'ENSG00000058063' => 'ATP11B',
'ENSG00000228766' => 'RPL7L1P8',
'ENSG00000238837' => 'RP11-646E18.2',
'ENSG00000240063' => 'RP11-225N10.1',
'ENSG00000241098' => 'FLJ46066',
'ENSG00000242012' => 'RP11-338L18.1',
'ENSG00000243378' => 'RP11-646E18.3',
'ENSG00000244199' => 'RP11-139K4.4',
'ENSG00000244247' => 'RP11-139K4.2',
'ENSG00000260377' => 'RP11-646E18.4',
'ENSMUSG00000093499' => 'Gm25442'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 25 => 'Heart',
(int) 28 => 'Kidney',
(int) 33 => 'Liver',
(int) 37 => 'Lung',
(int) 41 => 'Muscle',
(int) 45 => 'Ovary',
(int) 51 => 'Placenta',
(int) 54 => '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) 20,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000323116' => array(
'start' => '182793500',
'end' => '182921635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-001'
),
'ENST00000466758' => array(
'start' => '182873966',
'end' => '182919063',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP11B-006'
),
'ENST00000475636' => array(
'start' => '182898685',
'end' => '182913978',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP11B-008'
),
'ENST00000482070' => array(
'start' => '182879539',
'end' => '182897325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-009'
),
'ENST00000482794' => array(
'start' => '182833673',
'end' => '182848557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP11B-010'
),
'ENST00000484691' => array(
'start' => '182898607',
'end' => '182914096',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-011'
),
'ENST00000490303' => array(
'start' => '182865527',
'end' => '182914103',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP11B-005'
),
'ENST00000491699' => array(
'start' => '182897302',
'end' => '182915249',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-007'
),
'ENST00000493826' => array(
'start' => '182793503',
'end' => '182836624',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-002'
),
'ENST00000498086' => array(
'start' => '182837117',
'end' => '182918341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-004'
),
'ENST00000469911' => array(
'start' => '182610674',
'end' => '182611414',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL7L1P8-001'
),
'ENST00000492416' => array(
'start' => '182644214',
'end' => '182655880',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-646E18.2-001'
),
'ENST00000488882' => array(
'start' => '182783236',
'end' => '182793394',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-225N10.1-001'
),
'ENST00000496220' => array(
'start' => '182446970',
'end' => '182486364',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'FLJ46066-001'
),
'ENST00000473893' => array(
'start' => '182365147',
'end' => '182368256',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338L18.1-001'
),
'ENST00000491689' => array(
'start' => '182691928',
'end' => '182692285',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-646E18.3-001'
),
'ENST00000498782' => array(
'start' => '182460417',
'end' => '182461072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-139K4.4-001'
),
'ENST00000489016' => array(
'start' => '182498264',
'end' => '182507124',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-139K4.2-001'
),
'ENST00000565024' => array(
'start' => '182739669',
'end' => '182740848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-646E18.4-001'
),
'ENSMUST00000177270' => array(
'start' => '35325614',
'end' => '35325705',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25442-201'
)
),
'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_0007U2_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007U2_0001' => array(
'genes_in_region' => array(
'ENSG00000058063' => array(
[maximum depth reached]
),
'ENSG00000228766' => array(
[maximum depth reached]
),
'ENSG00000238837' => array(
[maximum depth reached]
),
'ENSG00000240063' => array(
[maximum depth reached]
),
'ENSG00000242012' => array(
[maximum depth reached]
),
'ENSG00000244199' => array(
[maximum depth reached]
),
'ENSG00000244247' => array(
[maximum depth reached]
),
'ENSG00000260377' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Kidney',
(int) 4 => 'Lung',
(int) 5 => 'Muscle',
(int) 6 => 'Ovary',
(int) 7 => 'Placenta',
(int) 8 => 'Testis',
(int) 9 => 'Heart',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Bladder',
(int) 14 => 'Ovary',
(int) 15 => 'Adrenal',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Muscle',
(int) 19 => 'Testis',
(int) 20 => 'Adipose',
(int) 21 => 'Adrenal',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Adrenal',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Testis',
(int) 33 => 'Adipose',
(int) 34 => 'Adrenal',
(int) 35 => 'Brain',
(int) 36 => 'Breast',
(int) 37 => 'Colon',
(int) 38 => 'Heart',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Lung',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain',
(int) 48 => 'Kidney',
(int) 49 => 'Testis',
(int) 50 => 'Testis',
(int) 51 => 'Adipose',
(int) 52 => 'Adrenal',
(int) 53 => 'Brain',
(int) 54 => 'Breast',
(int) 55 => 'Colon',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000058063' => 'ATPase, class VI, type 11B',
'ENSG00000228766' => 'ribosomal protein L7-like 1 pseudogene 8',
'ENSG00000238837' => null,
'ENSG00000240063' => null,
'ENSG00000241098' => 'uncharacterized LOC401103',
'ENSG00000242012' => null,
'ENSG00000243378' => null,
'ENSG00000244199' => null,
'ENSG00000244247' => null,
'ENSG00000260377' => null,
'ENSMUSG00000093499' => 'predicted gene, 25442'
)
$gene_name_arr = array(
'ENSG00000058063' => 'ATP11B',
'ENSG00000228766' => 'RPL7L1P8',
'ENSG00000238837' => 'RP11-646E18.2',
'ENSG00000240063' => 'RP11-225N10.1',
'ENSG00000241098' => 'FLJ46066',
'ENSG00000242012' => 'RP11-338L18.1',
'ENSG00000243378' => 'RP11-646E18.3',
'ENSG00000244199' => 'RP11-139K4.4',
'ENSG00000244247' => 'RP11-139K4.2',
'ENSG00000260377' => 'RP11-646E18.4',
'ENSMUSG00000093499' => 'Gm25442'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007U2_0001',
'tax_id' => '9606',
'chromosome' => '3',
'seq_start' => '182208439',
'seq_end' => '182810171',
'region_length' => '601732',
'region_type' => 'VISTA',
'el_id' => 'mm640'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007U2_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '35040406',
'seq_end' => '35642017',
'region_length' => '601611',
'region_type' => 'VISTA',
'el_id' => 'mm640'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 25 => 'Heart',
(int) 28 => 'Kidney',
(int) 33 => 'Liver',
(int) 37 => 'Lung',
(int) 41 => 'Muscle',
(int) 45 => 'Ovary',
(int) 51 => 'Placenta',
(int) 54 => '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) 20
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000323116' => array(
'start' => '182793500',
'end' => '182921635',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-001'
),
'ENST00000466758' => array(
'start' => '182873966',
'end' => '182919063',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ATP11B-006'
),
'ENST00000475636' => array(
'start' => '182898685',
'end' => '182913978',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP11B-008'
),
'ENST00000482070' => array(
'start' => '182879539',
'end' => '182897325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-009'
),
'ENST00000482794' => array(
'start' => '182833673',
'end' => '182848557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ATP11B-010'
),
'ENST00000484691' => array(
'start' => '182898607',
'end' => '182914096',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-011'
),
'ENST00000490303' => array(
'start' => '182865527',
'end' => '182914103',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ATP11B-005'
),
'ENST00000491699' => array(
'start' => '182897302',
'end' => '182915249',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-007'
),
'ENST00000493826' => array(
'start' => '182793503',
'end' => '182836624',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-002'
),
'ENST00000498086' => array(
'start' => '182837117',
'end' => '182918341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ATP11B-004'
),
'ENST00000469911' => array(
'start' => '182610674',
'end' => '182611414',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPL7L1P8-001'
),
'ENST00000492416' => array(
'start' => '182644214',
'end' => '182655880',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-646E18.2-001'
),
'ENST00000488882' => array(
'start' => '182783236',
'end' => '182793394',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-225N10.1-001'
),
'ENST00000496220' => array(
'start' => '182446970',
'end' => '182486364',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'FLJ46066-001'
),
'ENST00000473893' => array(
'start' => '182365147',
'end' => '182368256',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338L18.1-001'
),
'ENST00000491689' => array(
'start' => '182691928',
'end' => '182692285',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-646E18.3-001'
),
'ENST00000498782' => array(
'start' => '182460417',
'end' => '182461072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-139K4.4-001'
),
'ENST00000489016' => array(
'start' => '182498264',
'end' => '182507124',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-139K4.2-001'
),
'ENST00000565024' => array(
'start' => '182739669',
'end' => '182740848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-646E18.4-001'
),
'ENSMUST00000177270' => array(
'start' => '35325614',
'end' => '35325705',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm25442-201'
)
)
$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_0007U2_0001' => array(
'genes_in_region' => array(
'ENSG00000058063' => array(
[maximum depth reached]
),
'ENSG00000228766' => array(
[maximum depth reached]
),
'ENSG00000238837' => array(
[maximum depth reached]
),
'ENSG00000240063' => array(
[maximum depth reached]
),
'ENSG00000242012' => array(
[maximum depth reached]
),
'ENSG00000244199' => array(
[maximum depth reached]
),
'ENSG00000244247' => array(
[maximum depth reached]
),
'ENSG00000260377' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Kidney',
(int) 4 => 'Lung',
(int) 5 => 'Muscle',
(int) 6 => 'Ovary',
(int) 7 => 'Placenta',
(int) 8 => 'Testis',
(int) 9 => 'Heart',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Bladder',
(int) 14 => 'Ovary',
(int) 15 => 'Adrenal',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Muscle',
(int) 19 => 'Testis',
(int) 20 => 'Adipose',
(int) 21 => 'Adrenal',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Adrenal',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Testis',
(int) 33 => 'Adipose',
(int) 34 => 'Adrenal',
(int) 35 => 'Brain',
(int) 36 => 'Breast',
(int) 37 => 'Colon',
(int) 38 => 'Heart',
(int) 39 => 'Kidney',
(int) 40 => 'Liver',
(int) 41 => 'Lung',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain',
(int) 48 => 'Kidney',
(int) 49 => 'Testis',
(int) 50 => 'Testis',
(int) 51 => 'Adipose',
(int) 52 => 'Adrenal',
(int) 53 => 'Brain',
(int) 54 => 'Breast',
(int) 55 => 'Colon',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007U2_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '35040406',
'seq_end' => '35642017',
'region_length' => '601611',
'region_type' => 'VISTA',
'el_id' => 'mm640'
)
)
$gene_el = array(
'ENST00000565024' => array(
'Adipose' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.151',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.070',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.042',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.012',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.022',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.099',
'stddev_FPKM' => '0.04'
),
'Muscle' => array(
'average_FPKM' => '0.032',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.043',
'stddev_FPKM' => '0.03'
),
'Testis' => array(
'average_FPKM' => '0.009',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000260377'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.044',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.151',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.070',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.042',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.012',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.022',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.099',
'stddev_FPKM' => '0.04'
),
'Muscle' => array(
'average_FPKM' => '0.032',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.043',
'stddev_FPKM' => '0.03'
),
'Testis' => array(
'average_FPKM' => '0.009',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000565024'
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 |
| mm640 |
VISTA |
10090 |
3:35040406-35642017  |
| Gene | Transcript | Position | Biotype |
|---|
(ATP11B)