Notice (8): Undefined index: CIL_0007LX_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_0007LX_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LX_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LX_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000154473' => 'BUB3 mitotic checkpoint protein',
'ENSG00000188620' => 'H6 family homeobox 3',
'ENSG00000188816' => 'H6 family homeobox 2',
'ENSG00000225152' => null,
'ENSG00000227586' => null,
'ENSG00000230131' => null,
'ENSG00000270902' => null,
'ENSMUSG00000040148' => 'H6 homeobox 3',
'ENSMUSG00000050100' => 'H6 homeobox 2',
'ENSMUSG00000062758' => 'predicted pseudogene 16477',
'ENSMUSG00000066979' => 'budding uninhibited by benzimidazoles 3 homolog (S. cerevisiae)',
'ENSDARG00000070954' => 'H6 family homeobox 2',
'ENSDARG00000070955' => 'homeo box (H6 family) 3'
),
'gene_name_arr' => array(
'ENSG00000154473' => 'BUB3',
'ENSG00000188620' => 'HMX3',
'ENSG00000188816' => 'HMX2',
'ENSG00000225152' => 'RP11-338O1.2',
'ENSG00000227586' => 'RP11-162A23.5',
'ENSG00000230131' => 'RP11-282I1.1',
'ENSG00000270902' => 'RP11-338O1.3',
'ENSMUSG00000040148' => 'Hmx3',
'ENSMUSG00000050100' => 'Hmx2',
'ENSMUSG00000062758' => 'Gm16477',
'ENSMUSG00000066979' => 'Bub3',
'ENSDARG00000070954' => 'hmx2',
'ENSDARG00000070955' => 'hmx3'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 15 => 'Brain',
(int) 25 => 'Breast',
(int) 31 => 'Colon',
(int) 41 => 'Heart',
(int) 51 => 'Kidney',
(int) 62 => 'Liver',
(int) 69 => 'Lung',
(int) 78 => 'Muscle',
(int) 88 => 'Ovary',
(int) 95 => 'Placenta',
(int) 104 => '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) 19,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000368858' => array(
'start' => '123154415',
'end' => '123165365',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-002'
),
'ENST00000368859' => array(
'start' => '123154402',
'end' => '123165212',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-004'
),
'ENST00000368865' => array(
'start' => '123154277',
'end' => '123170467',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-001'
),
'ENST00000407911' => array(
'start' => '123154859',
'end' => '123162693',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-005'
),
'ENST00000481952' => array(
'start' => '123162254',
'end' => '123163241',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BUB3-006'
),
'ENST00000357878' => array(
'start' => '123135962',
'end' => '123137741',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HMX3-001'
),
'ENST00000339992' => array(
'start' => '123148122',
'end' => '123150672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HMX2-001'
),
'ENST00000415509' => array(
'start' => '123425713',
'end' => '123427640',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338O1.2-001'
),
'ENST00000469206' => array(
'start' => '123171535',
'end' => '123171875',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-162A23.5-001'
),
'ENST00000448347' => array(
'start' => '123356450',
'end' => '123517708',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-282I1.1-001'
),
'ENST00000448671' => array(
'start' => '123449353',
'end' => '123489336',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-282I1.1-002'
),
'ENST00000604869' => array(
'start' => '123323422',
'end' => '123323586',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-338O1.3-001'
),
'ENSMUST00000046093' => array(
'start' => '131542867',
'end' => '131544925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx3-001'
),
'ENSMUST00000051997' => array(
'start' => '131554061',
'end' => '131556589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx2-001'
),
'ENSMUST00000183219' => array(
'start' => '131548773',
'end' => '131556589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx2-002'
),
'ENSMUST00000085365' => array(
'start' => '131614188',
'end' => '131614988',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm16477-001'
),
'ENSMUST00000084502' => array(
'start' => '131560391',
'end' => '131571898',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Bub3-201'
),
'ENSDART00000127254' => array(
'start' => '21612058',
'end' => '21614167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'hmx2-001'
),
'ENSDART00000104612' => array(
'start' => '21620621',
'end' => '21623128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'hmx3-001'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0007LX_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LX_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LX_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007LX_0001' => array(
'genes_in_region' => array(
'ENSG00000154473' => array(
[maximum depth reached]
),
'ENSG00000188620' => array(
[maximum depth reached]
),
'ENSG00000188816' => array(
[maximum depth reached]
),
'ENSG00000225152' => array(
[maximum depth reached]
),
'ENSG00000227586' => array(
[maximum depth reached]
),
'ENSG00000230131' => 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 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Bladder',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Testis',
(int) 30 => 'Muscle',
(int) 31 => 'Adipose',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Testis',
(int) 38 => 'Bladder',
(int) 39 => 'Colon',
(int) 40 => 'Kidney',
(int) 41 => 'Lung',
(int) 42 => 'Testis',
(int) 43 => 'Heart',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Breast',
(int) 48 => 'Colon',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Placenta',
(int) 55 => 'Testis',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Testis'
)
),
'CIL_0007LX_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000040148' => array(
[maximum depth reached]
),
'ENSMUSG00000050100' => array(
[maximum depth reached]
),
'ENSMUSG00000062758' => array(
[maximum depth reached]
),
'ENSMUSG00000066979' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Placenta',
(int) 10 => 'Brain',
(int) 11 => 'Colon',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Adipose',
(int) 17 => 'Adrenal',
(int) 18 => 'Bladder',
(int) 19 => 'Brain',
(int) 20 => 'Breast',
(int) 21 => 'Colon',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Lung',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Bladder',
(int) 33 => 'Brain',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis'
)
),
'CIL_0007LX_0004' => array(
'genes_in_region' => array(
'ENSDARG00000070954' => array(
[maximum depth reached]
),
'ENSDARG00000070955' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Brain',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000154473' => 'BUB3 mitotic checkpoint protein',
'ENSG00000188620' => 'H6 family homeobox 3',
'ENSG00000188816' => 'H6 family homeobox 2',
'ENSG00000225152' => null,
'ENSG00000227586' => null,
'ENSG00000230131' => null,
'ENSG00000270902' => null,
'ENSMUSG00000040148' => 'H6 homeobox 3',
'ENSMUSG00000050100' => 'H6 homeobox 2',
'ENSMUSG00000062758' => 'predicted pseudogene 16477',
'ENSMUSG00000066979' => 'budding uninhibited by benzimidazoles 3 homolog (S. cerevisiae)',
'ENSDARG00000070954' => 'H6 family homeobox 2',
'ENSDARG00000070955' => 'homeo box (H6 family) 3'
)
$gene_name_arr = array(
'ENSG00000154473' => 'BUB3',
'ENSG00000188620' => 'HMX3',
'ENSG00000188816' => 'HMX2',
'ENSG00000225152' => 'RP11-338O1.2',
'ENSG00000227586' => 'RP11-162A23.5',
'ENSG00000230131' => 'RP11-282I1.1',
'ENSG00000270902' => 'RP11-338O1.3',
'ENSMUSG00000040148' => 'Hmx3',
'ENSMUSG00000050100' => 'Hmx2',
'ENSMUSG00000062758' => 'Gm16477',
'ENSMUSG00000066979' => 'Bub3',
'ENSDARG00000070954' => 'hmx2',
'ENSDARG00000070955' => 'hmx3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0001',
'tax_id' => '9606',
'chromosome' => '10',
'seq_start' => '123069326',
'seq_end' => '123458100',
'region_length' => '388774',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0002',
'tax_id' => '10090',
'chromosome' => '7',
'seq_start' => '131465048',
'seq_end' => '131797301',
'region_length' => '332253',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0003',
'tax_id' => '7955',
'chromosome' => '12',
'seq_start' => '50667887',
'seq_end' => '50668118',
'region_length' => '231',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0004',
'tax_id' => '7955',
'chromosome' => '17',
'seq_start' => '21498898',
'seq_end' => '21643986',
'region_length' => '145088',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 15 => 'Brain',
(int) 25 => 'Breast',
(int) 31 => 'Colon',
(int) 41 => 'Heart',
(int) 51 => 'Kidney',
(int) 62 => 'Liver',
(int) 69 => 'Lung',
(int) 78 => 'Muscle',
(int) 88 => 'Ovary',
(int) 95 => 'Placenta',
(int) 104 => '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) 19
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000368858' => array(
'start' => '123154415',
'end' => '123165365',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-002'
),
'ENST00000368859' => array(
'start' => '123154402',
'end' => '123165212',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-004'
),
'ENST00000368865' => array(
'start' => '123154277',
'end' => '123170467',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-001'
),
'ENST00000407911' => array(
'start' => '123154859',
'end' => '123162693',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-005'
),
'ENST00000481952' => array(
'start' => '123162254',
'end' => '123163241',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BUB3-006'
),
'ENST00000357878' => array(
'start' => '123135962',
'end' => '123137741',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HMX3-001'
),
'ENST00000339992' => array(
'start' => '123148122',
'end' => '123150672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HMX2-001'
),
'ENST00000415509' => array(
'start' => '123425713',
'end' => '123427640',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338O1.2-001'
),
'ENST00000469206' => array(
'start' => '123171535',
'end' => '123171875',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-162A23.5-001'
),
'ENST00000448347' => array(
'start' => '123356450',
'end' => '123517708',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-282I1.1-001'
),
'ENST00000448671' => array(
'start' => '123449353',
'end' => '123489336',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-282I1.1-002'
),
'ENST00000604869' => array(
'start' => '123323422',
'end' => '123323586',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-338O1.3-001'
),
'ENSMUST00000046093' => array(
'start' => '131542867',
'end' => '131544925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx3-001'
),
'ENSMUST00000051997' => array(
'start' => '131554061',
'end' => '131556589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx2-001'
),
'ENSMUST00000183219' => array(
'start' => '131548773',
'end' => '131556589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx2-002'
),
'ENSMUST00000085365' => array(
'start' => '131614188',
'end' => '131614988',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm16477-001'
),
'ENSMUST00000084502' => array(
'start' => '131560391',
'end' => '131571898',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Bub3-201'
),
'ENSDART00000127254' => array(
'start' => '21612058',
'end' => '21614167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'hmx2-001'
),
'ENSDART00000104612' => array(
'start' => '21620621',
'end' => '21623128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'hmx3-001'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0007LX_0001' => array(
'genes_in_region' => array(
'ENSG00000154473' => array(
[maximum depth reached]
),
'ENSG00000188620' => array(
[maximum depth reached]
),
'ENSG00000188816' => array(
[maximum depth reached]
),
'ENSG00000225152' => array(
[maximum depth reached]
),
'ENSG00000227586' => array(
[maximum depth reached]
),
'ENSG00000230131' => 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 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Bladder',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Testis',
(int) 30 => 'Muscle',
(int) 31 => 'Adipose',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Testis',
(int) 38 => 'Bladder',
(int) 39 => 'Colon',
(int) 40 => 'Kidney',
(int) 41 => 'Lung',
(int) 42 => 'Testis',
(int) 43 => 'Heart',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Breast',
(int) 48 => 'Colon',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Placenta',
(int) 55 => 'Testis',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Testis'
)
),
'CIL_0007LX_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000040148' => array(
[maximum depth reached]
),
'ENSMUSG00000050100' => array(
[maximum depth reached]
),
'ENSMUSG00000062758' => array(
[maximum depth reached]
),
'ENSMUSG00000066979' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Placenta',
(int) 10 => 'Brain',
(int) 11 => 'Colon',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Adipose',
(int) 17 => 'Adrenal',
(int) 18 => 'Bladder',
(int) 19 => 'Brain',
(int) 20 => 'Breast',
(int) 21 => 'Colon',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Lung',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Bladder',
(int) 33 => 'Brain',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis'
)
),
'CIL_0007LX_0004' => array(
'genes_in_region' => array(
'ENSDARG00000070954' => array(
[maximum depth reached]
),
'ENSDARG00000070955' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Brain',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0003',
'tax_id' => '7955',
'chromosome' => '12',
'seq_start' => '50667887',
'seq_end' => '50668118',
'region_length' => '231',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
)
$gene_el = array(
'ENSMUST00000084502' => array(
'Adipose' => array(
'average_FPKM' => '36.989',
'stddev_FPKM' => '6.78'
),
'Adrenal' => array(
'average_FPKM' => '44.633',
'stddev_FPKM' => '0.78'
),
'Bladder' => array(
'average_FPKM' => '13.140',
'stddev_FPKM' => '1.91'
),
'Brain' => array(
'average_FPKM' => '30.796',
'stddev_FPKM' => '20.56'
),
'Breast' => array(
'average_FPKM' => '35.316',
'stddev_FPKM' => '5.21'
),
'Colon' => array(
'average_FPKM' => '33.210',
'stddev_FPKM' => '3.57'
),
'Heart' => array(
'average_FPKM' => '19.589',
'stddev_FPKM' => '0.95'
),
'Kidney' => array(
'average_FPKM' => '30.086',
'stddev_FPKM' => '1.51'
),
'Liver' => array(
'average_FPKM' => '25.139',
'stddev_FPKM' => '19.29'
),
'Lung' => array(
'average_FPKM' => '44.272',
'stddev_FPKM' => '2.78'
),
'Muscle' => array(
'average_FPKM' => '11.801',
'stddev_FPKM' => '0.94'
),
'Ovary' => array(
'average_FPKM' => '49.360',
'stddev_FPKM' => '14.45'
),
'Placenta' => array(
'average_FPKM' => '21.775',
'stddev_FPKM' => '10.22'
),
'Testis' => array(
'average_FPKM' => '18.581',
'stddev_FPKM' => '8.82'
)
)
)
$gene_key = 'ENSMUSG00000066979'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '36.989',
'stddev_FPKM' => '6.78'
),
'Adrenal' => array(
'average_FPKM' => '44.633',
'stddev_FPKM' => '0.78'
),
'Bladder' => array(
'average_FPKM' => '13.140',
'stddev_FPKM' => '1.91'
),
'Brain' => array(
'average_FPKM' => '30.796',
'stddev_FPKM' => '20.56'
),
'Breast' => array(
'average_FPKM' => '35.316',
'stddev_FPKM' => '5.21'
),
'Colon' => array(
'average_FPKM' => '33.210',
'stddev_FPKM' => '3.57'
),
'Heart' => array(
'average_FPKM' => '19.589',
'stddev_FPKM' => '0.95'
),
'Kidney' => array(
'average_FPKM' => '30.086',
'stddev_FPKM' => '1.51'
),
'Liver' => array(
'average_FPKM' => '25.139',
'stddev_FPKM' => '19.29'
),
'Lung' => array(
'average_FPKM' => '44.272',
'stddev_FPKM' => '2.78'
),
'Muscle' => array(
'average_FPKM' => '11.801',
'stddev_FPKM' => '0.94'
),
'Ovary' => array(
'average_FPKM' => '49.360',
'stddev_FPKM' => '14.45'
),
'Placenta' => array(
'average_FPKM' => '21.775',
'stddev_FPKM' => '10.22'
),
'Testis' => array(
'average_FPKM' => '18.581',
'stddev_FPKM' => '8.82'
)
)
$tran_key = 'ENSMUST00000084502'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007LX_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LX_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LX_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000154473' => 'BUB3 mitotic checkpoint protein',
'ENSG00000188620' => 'H6 family homeobox 3',
'ENSG00000188816' => 'H6 family homeobox 2',
'ENSG00000225152' => null,
'ENSG00000227586' => null,
'ENSG00000230131' => null,
'ENSG00000270902' => null,
'ENSMUSG00000040148' => 'H6 homeobox 3',
'ENSMUSG00000050100' => 'H6 homeobox 2',
'ENSMUSG00000062758' => 'predicted pseudogene 16477',
'ENSMUSG00000066979' => 'budding uninhibited by benzimidazoles 3 homolog (S. cerevisiae)',
'ENSDARG00000070954' => 'H6 family homeobox 2',
'ENSDARG00000070955' => 'homeo box (H6 family) 3'
),
'gene_name_arr' => array(
'ENSG00000154473' => 'BUB3',
'ENSG00000188620' => 'HMX3',
'ENSG00000188816' => 'HMX2',
'ENSG00000225152' => 'RP11-338O1.2',
'ENSG00000227586' => 'RP11-162A23.5',
'ENSG00000230131' => 'RP11-282I1.1',
'ENSG00000270902' => 'RP11-338O1.3',
'ENSMUSG00000040148' => 'Hmx3',
'ENSMUSG00000050100' => 'Hmx2',
'ENSMUSG00000062758' => 'Gm16477',
'ENSMUSG00000066979' => 'Bub3',
'ENSDARG00000070954' => 'hmx2',
'ENSDARG00000070955' => 'hmx3'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 15 => 'Brain',
(int) 25 => 'Breast',
(int) 31 => 'Colon',
(int) 41 => 'Heart',
(int) 51 => 'Kidney',
(int) 62 => 'Liver',
(int) 69 => 'Lung',
(int) 78 => 'Muscle',
(int) 88 => 'Ovary',
(int) 95 => 'Placenta',
(int) 104 => '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) 19,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000368858' => array(
'start' => '123154415',
'end' => '123165365',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-002'
),
'ENST00000368859' => array(
'start' => '123154402',
'end' => '123165212',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-004'
),
'ENST00000368865' => array(
'start' => '123154277',
'end' => '123170467',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-001'
),
'ENST00000407911' => array(
'start' => '123154859',
'end' => '123162693',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-005'
),
'ENST00000481952' => array(
'start' => '123162254',
'end' => '123163241',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BUB3-006'
),
'ENST00000357878' => array(
'start' => '123135962',
'end' => '123137741',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HMX3-001'
),
'ENST00000339992' => array(
'start' => '123148122',
'end' => '123150672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HMX2-001'
),
'ENST00000415509' => array(
'start' => '123425713',
'end' => '123427640',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338O1.2-001'
),
'ENST00000469206' => array(
'start' => '123171535',
'end' => '123171875',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-162A23.5-001'
),
'ENST00000448347' => array(
'start' => '123356450',
'end' => '123517708',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-282I1.1-001'
),
'ENST00000448671' => array(
'start' => '123449353',
'end' => '123489336',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-282I1.1-002'
),
'ENST00000604869' => array(
'start' => '123323422',
'end' => '123323586',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-338O1.3-001'
),
'ENSMUST00000046093' => array(
'start' => '131542867',
'end' => '131544925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx3-001'
),
'ENSMUST00000051997' => array(
'start' => '131554061',
'end' => '131556589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx2-001'
),
'ENSMUST00000183219' => array(
'start' => '131548773',
'end' => '131556589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx2-002'
),
'ENSMUST00000085365' => array(
'start' => '131614188',
'end' => '131614988',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm16477-001'
),
'ENSMUST00000084502' => array(
'start' => '131560391',
'end' => '131571898',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Bub3-201'
),
'ENSDART00000127254' => array(
'start' => '21612058',
'end' => '21614167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'hmx2-001'
),
'ENSDART00000104612' => array(
'start' => '21620621',
'end' => '21623128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'hmx3-001'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0007LX_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LX_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LX_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007LX_0001' => array(
'genes_in_region' => array(
'ENSG00000154473' => array(
[maximum depth reached]
),
'ENSG00000188620' => array(
[maximum depth reached]
),
'ENSG00000188816' => array(
[maximum depth reached]
),
'ENSG00000225152' => array(
[maximum depth reached]
),
'ENSG00000227586' => array(
[maximum depth reached]
),
'ENSG00000230131' => 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 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Bladder',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Testis',
(int) 30 => 'Muscle',
(int) 31 => 'Adipose',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Testis',
(int) 38 => 'Bladder',
(int) 39 => 'Colon',
(int) 40 => 'Kidney',
(int) 41 => 'Lung',
(int) 42 => 'Testis',
(int) 43 => 'Heart',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Breast',
(int) 48 => 'Colon',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Placenta',
(int) 55 => 'Testis',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Testis'
)
),
'CIL_0007LX_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000040148' => array(
[maximum depth reached]
),
'ENSMUSG00000050100' => array(
[maximum depth reached]
),
'ENSMUSG00000062758' => array(
[maximum depth reached]
),
'ENSMUSG00000066979' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Placenta',
(int) 10 => 'Brain',
(int) 11 => 'Colon',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Adipose',
(int) 17 => 'Adrenal',
(int) 18 => 'Bladder',
(int) 19 => 'Brain',
(int) 20 => 'Breast',
(int) 21 => 'Colon',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Lung',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Bladder',
(int) 33 => 'Brain',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis'
)
),
'CIL_0007LX_0004' => array(
'genes_in_region' => array(
'ENSDARG00000070954' => array(
[maximum depth reached]
),
'ENSDARG00000070955' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Brain',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000154473' => 'BUB3 mitotic checkpoint protein',
'ENSG00000188620' => 'H6 family homeobox 3',
'ENSG00000188816' => 'H6 family homeobox 2',
'ENSG00000225152' => null,
'ENSG00000227586' => null,
'ENSG00000230131' => null,
'ENSG00000270902' => null,
'ENSMUSG00000040148' => 'H6 homeobox 3',
'ENSMUSG00000050100' => 'H6 homeobox 2',
'ENSMUSG00000062758' => 'predicted pseudogene 16477',
'ENSMUSG00000066979' => 'budding uninhibited by benzimidazoles 3 homolog (S. cerevisiae)',
'ENSDARG00000070954' => 'H6 family homeobox 2',
'ENSDARG00000070955' => 'homeo box (H6 family) 3'
)
$gene_name_arr = array(
'ENSG00000154473' => 'BUB3',
'ENSG00000188620' => 'HMX3',
'ENSG00000188816' => 'HMX2',
'ENSG00000225152' => 'RP11-338O1.2',
'ENSG00000227586' => 'RP11-162A23.5',
'ENSG00000230131' => 'RP11-282I1.1',
'ENSG00000270902' => 'RP11-338O1.3',
'ENSMUSG00000040148' => 'Hmx3',
'ENSMUSG00000050100' => 'Hmx2',
'ENSMUSG00000062758' => 'Gm16477',
'ENSMUSG00000066979' => 'Bub3',
'ENSDARG00000070954' => 'hmx2',
'ENSDARG00000070955' => 'hmx3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0001',
'tax_id' => '9606',
'chromosome' => '10',
'seq_start' => '123069326',
'seq_end' => '123458100',
'region_length' => '388774',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0002',
'tax_id' => '10090',
'chromosome' => '7',
'seq_start' => '131465048',
'seq_end' => '131797301',
'region_length' => '332253',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0003',
'tax_id' => '7955',
'chromosome' => '12',
'seq_start' => '50667887',
'seq_end' => '50668118',
'region_length' => '231',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0004',
'tax_id' => '7955',
'chromosome' => '17',
'seq_start' => '21498898',
'seq_end' => '21643986',
'region_length' => '145088',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 15 => 'Brain',
(int) 25 => 'Breast',
(int) 31 => 'Colon',
(int) 41 => 'Heart',
(int) 51 => 'Kidney',
(int) 62 => 'Liver',
(int) 69 => 'Lung',
(int) 78 => 'Muscle',
(int) 88 => 'Ovary',
(int) 95 => 'Placenta',
(int) 104 => '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) 19
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000368858' => array(
'start' => '123154415',
'end' => '123165365',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-002'
),
'ENST00000368859' => array(
'start' => '123154402',
'end' => '123165212',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-004'
),
'ENST00000368865' => array(
'start' => '123154277',
'end' => '123170467',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-001'
),
'ENST00000407911' => array(
'start' => '123154859',
'end' => '123162693',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BUB3-005'
),
'ENST00000481952' => array(
'start' => '123162254',
'end' => '123163241',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'BUB3-006'
),
'ENST00000357878' => array(
'start' => '123135962',
'end' => '123137741',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HMX3-001'
),
'ENST00000339992' => array(
'start' => '123148122',
'end' => '123150672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HMX2-001'
),
'ENST00000415509' => array(
'start' => '123425713',
'end' => '123427640',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-338O1.2-001'
),
'ENST00000469206' => array(
'start' => '123171535',
'end' => '123171875',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-162A23.5-001'
),
'ENST00000448347' => array(
'start' => '123356450',
'end' => '123517708',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-282I1.1-001'
),
'ENST00000448671' => array(
'start' => '123449353',
'end' => '123489336',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-282I1.1-002'
),
'ENST00000604869' => array(
'start' => '123323422',
'end' => '123323586',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-338O1.3-001'
),
'ENSMUST00000046093' => array(
'start' => '131542867',
'end' => '131544925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx3-001'
),
'ENSMUST00000051997' => array(
'start' => '131554061',
'end' => '131556589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx2-001'
),
'ENSMUST00000183219' => array(
'start' => '131548773',
'end' => '131556589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hmx2-002'
),
'ENSMUST00000085365' => array(
'start' => '131614188',
'end' => '131614988',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm16477-001'
),
'ENSMUST00000084502' => array(
'start' => '131560391',
'end' => '131571898',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Bub3-201'
),
'ENSDART00000127254' => array(
'start' => '21612058',
'end' => '21614167',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'hmx2-001'
),
'ENSDART00000104612' => array(
'start' => '21620621',
'end' => '21623128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'hmx3-001'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0007LX_0001' => array(
'genes_in_region' => array(
'ENSG00000154473' => array(
[maximum depth reached]
),
'ENSG00000188620' => array(
[maximum depth reached]
),
'ENSG00000188816' => array(
[maximum depth reached]
),
'ENSG00000225152' => array(
[maximum depth reached]
),
'ENSG00000227586' => array(
[maximum depth reached]
),
'ENSG00000230131' => 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 => 'Bladder',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Bladder',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Testis',
(int) 30 => 'Muscle',
(int) 31 => 'Adipose',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Testis',
(int) 38 => 'Bladder',
(int) 39 => 'Colon',
(int) 40 => 'Kidney',
(int) 41 => 'Lung',
(int) 42 => 'Testis',
(int) 43 => 'Heart',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Breast',
(int) 48 => 'Colon',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Placenta',
(int) 55 => 'Testis',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Testis'
)
),
'CIL_0007LX_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000040148' => array(
[maximum depth reached]
),
'ENSMUSG00000050100' => array(
[maximum depth reached]
),
'ENSMUSG00000062758' => array(
[maximum depth reached]
),
'ENSMUSG00000066979' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Placenta',
(int) 7 => 'Testis',
(int) 8 => 'Brain',
(int) 9 => 'Placenta',
(int) 10 => 'Brain',
(int) 11 => 'Colon',
(int) 12 => 'Kidney',
(int) 13 => 'Liver',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Adipose',
(int) 17 => 'Adrenal',
(int) 18 => 'Bladder',
(int) 19 => 'Brain',
(int) 20 => 'Breast',
(int) 21 => 'Colon',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Lung',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Bladder',
(int) 33 => 'Brain',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis'
)
),
'CIL_0007LX_0004' => array(
'genes_in_region' => array(
'ENSDARG00000070954' => array(
[maximum depth reached]
),
'ENSDARG00000070955' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Brain',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LX_0003',
'tax_id' => '7955',
'chromosome' => '12',
'seq_start' => '50667887',
'seq_end' => '50668118',
'region_length' => '231',
'region_type' => 'UCNEbase',
'el_id' => 'HMX2'
)
)
$gene_el = array(
'ENSMUST00000084502' => array(
'Adipose' => array(
'average_FPKM' => '36.989',
'stddev_FPKM' => '6.78'
),
'Adrenal' => array(
'average_FPKM' => '44.633',
'stddev_FPKM' => '0.78'
),
'Bladder' => array(
'average_FPKM' => '13.140',
'stddev_FPKM' => '1.91'
),
'Brain' => array(
'average_FPKM' => '30.796',
'stddev_FPKM' => '20.56'
),
'Breast' => array(
'average_FPKM' => '35.316',
'stddev_FPKM' => '5.21'
),
'Colon' => array(
'average_FPKM' => '33.210',
'stddev_FPKM' => '3.57'
),
'Heart' => array(
'average_FPKM' => '19.589',
'stddev_FPKM' => '0.95'
),
'Kidney' => array(
'average_FPKM' => '30.086',
'stddev_FPKM' => '1.51'
),
'Liver' => array(
'average_FPKM' => '25.139',
'stddev_FPKM' => '19.29'
),
'Lung' => array(
'average_FPKM' => '44.272',
'stddev_FPKM' => '2.78'
),
'Muscle' => array(
'average_FPKM' => '11.801',
'stddev_FPKM' => '0.94'
),
'Ovary' => array(
'average_FPKM' => '49.360',
'stddev_FPKM' => '14.45'
),
'Placenta' => array(
'average_FPKM' => '21.775',
'stddev_FPKM' => '10.22'
),
'Testis' => array(
'average_FPKM' => '18.581',
'stddev_FPKM' => '8.82'
)
)
)
$gene_key = 'ENSMUSG00000066979'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '36.989',
'stddev_FPKM' => '6.78'
),
'Adrenal' => array(
'average_FPKM' => '44.633',
'stddev_FPKM' => '0.78'
),
'Bladder' => array(
'average_FPKM' => '13.140',
'stddev_FPKM' => '1.91'
),
'Brain' => array(
'average_FPKM' => '30.796',
'stddev_FPKM' => '20.56'
),
'Breast' => array(
'average_FPKM' => '35.316',
'stddev_FPKM' => '5.21'
),
'Colon' => array(
'average_FPKM' => '33.210',
'stddev_FPKM' => '3.57'
),
'Heart' => array(
'average_FPKM' => '19.589',
'stddev_FPKM' => '0.95'
),
'Kidney' => array(
'average_FPKM' => '30.086',
'stddev_FPKM' => '1.51'
),
'Liver' => array(
'average_FPKM' => '25.139',
'stddev_FPKM' => '19.29'
),
'Lung' => array(
'average_FPKM' => '44.272',
'stddev_FPKM' => '2.78'
),
'Muscle' => array(
'average_FPKM' => '11.801',
'stddev_FPKM' => '0.94'
),
'Ovary' => array(
'average_FPKM' => '49.360',
'stddev_FPKM' => '14.45'
),
'Placenta' => array(
'average_FPKM' => '21.775',
'stddev_FPKM' => '10.22'
),
'Testis' => array(
'average_FPKM' => '18.581',
'stddev_FPKM' => '8.82'
)
)
$tran_key = 'ENSMUST00000084502'
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 |
| HMX2 |
UCNEbase |
7955 |
12:50667887-50668118  |
| Gene | Transcript | Position | Biotype |
|---|
(BUB3)