Notice (8): Undefined index: CIL_0007J4_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_0007J4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007J4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007J4_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000071909' => 'myosin IIIB',
'ENSG00000213981' => null,
'ENSG00000214821' => 'high mobility group box 1 pseudogene 4',
'ENSG00000222033' => 'long intergenic non-protein coding RNA 1124',
'ENSG00000275414' => 'TUC338',
'ENSMUSG00000042064' => 'myosin IIIB',
'ENSMUSG00000047965' => 'ribosomal protein L9, pseudogene 7',
'ENSMUSG00000075304' => 'trans-acting transcription factor 5',
'ENSDARG00000006892' => 'myosin IIIB'
),
'gene_name_arr' => array(
'ENSG00000071909' => 'MYO3B',
'ENSG00000213981' => 'AC007277.3',
'ENSG00000214821' => 'HMGB1P4',
'ENSG00000222033' => 'LINC01124',
'ENSG00000275414' => 'uc_338',
'ENSMUSG00000042064' => 'Myo3b',
'ENSMUSG00000047965' => 'Rpl9-ps7',
'ENSMUSG00000075304' => 'Sp5',
'ENSDARG00000006892' => 'myo3b'
),
'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) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 22 => 'Brain',
(int) 36 => 'Breast',
(int) 48 => 'Colon',
(int) 55 => 'Heart',
(int) 66 => 'Kidney',
(int) 76 => 'Liver',
(int) 88 => 'Lung',
(int) 98 => 'Muscle',
(int) 108 => 'Ovary',
(int) 121 => 'Placenta',
(int) 132 => '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) 21,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000317935' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MYO3B-003'
),
'ENST00000408978' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-004'
),
'ENST00000409044' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-001'
),
'ENST00000409940' => array(
'start' => '170178145',
'end' => '170519978',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO3B-002'
),
'ENST00000438642' => array(
'start' => '170178145',
'end' => '170651639',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-006'
),
'ENST00000442690' => array(
'start' => '170199208',
'end' => '170382766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-007'
),
'ENST00000469359' => array(
'start' => '170407730',
'end' => '170412425',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-008'
),
'ENST00000484338' => array(
'start' => '170180149',
'end' => '170499808',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-005'
),
'ENST00000602629' => array(
'start' => '170199252',
'end' => '170655171',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-009'
),
'ENST00000423519' => array(
'start' => '170618628',
'end' => '170643944',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC007277.3-002'
),
'ENST00000428156' => array(
'start' => '170640374',
'end' => '170695374',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC007277.3-001'
),
'ENST00000455362' => array(
'start' => '170601662',
'end' => '170602228',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P4-001'
),
'ENST00000409786' => array(
'start' => '170712451',
'end' => '170714567',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01124-001'
),
'ENST00000618243' => array(
'start' => '170690564',
'end' => '170690742',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'uc_338.1-212'
),
'ENSMUST00000060208' => array(
'start' => '70039126',
'end' => '70429195',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-201'
),
'ENSMUST00000112241' => array(
'start' => '70096298',
'end' => '70183267',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-001'
),
'ENSMUST00000112243' => array(
'start' => '70083074',
'end' => '70429198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-002'
),
'ENSMUST00000140507' => array(
'start' => '70458982',
'end' => '70459560',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Rpl9-ps7-001'
),
'ENSMUST00000100043' => array(
'start' => '70474923',
'end' => '70477729',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sp5-001'
),
'ENSDART00000010378' => array(
'start' => '3752080',
'end' => '3878770',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo3b-201'
),
'ENSDART00000141492' => array(
'start' => '3746250',
'end' => '3831136',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo3b-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_0007J4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007J4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007J4_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007J4_0001' => array(
'genes_in_region' => array(
'ENSG00000213981' => array(
[maximum depth reached]
),
'ENSG00000214821' => array(
[maximum depth reached]
),
'ENSG00000222033' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Bladder',
(int) 1 => 'Liver',
(int) 2 => 'Ovary',
(int) 3 => 'Testis',
(int) 4 => 'Placenta',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Liver',
(int) 10 => 'Lung',
(int) 11 => 'Ovary',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Heart',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Muscle',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis',
(int) 21 => 'Brain',
(int) 22 => 'Liver',
(int) 23 => 'Bladder',
(int) 24 => 'Brain',
(int) 25 => 'Placenta',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Heart',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Ovary',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Ovary',
(int) 52 => 'Testis',
(int) 53 => 'Adipose',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Heart',
(int) 57 => 'Kidney',
(int) 58 => 'Muscle',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Adipose',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Testis'
)
),
'CIL_0007J4_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000042064' => array(
[maximum depth reached]
),
'ENSMUSG00000047965' => array(
[maximum depth reached]
),
'ENSMUSG00000075304' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Bladder',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Ovary',
(int) 18 => 'Placenta',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Kidney',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Muscle',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis'
)
),
'CIL_0007J4_0004' => array(
'genes_in_region' => array(
'ENSDARG00000006892' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Kidney',
(int) 1 => 'Muscle',
(int) 2 => 'Brain',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000071909' => 'myosin IIIB',
'ENSG00000213981' => null,
'ENSG00000214821' => 'high mobility group box 1 pseudogene 4',
'ENSG00000222033' => 'long intergenic non-protein coding RNA 1124',
'ENSG00000275414' => 'TUC338',
'ENSMUSG00000042064' => 'myosin IIIB',
'ENSMUSG00000047965' => 'ribosomal protein L9, pseudogene 7',
'ENSMUSG00000075304' => 'trans-acting transcription factor 5',
'ENSDARG00000006892' => 'myosin IIIB'
)
$gene_name_arr = array(
'ENSG00000071909' => 'MYO3B',
'ENSG00000213981' => 'AC007277.3',
'ENSG00000214821' => 'HMGB1P4',
'ENSG00000222033' => 'LINC01124',
'ENSG00000275414' => 'uc_338',
'ENSMUSG00000042064' => 'Myo3b',
'ENSMUSG00000047965' => 'Rpl9-ps7',
'ENSMUSG00000075304' => 'Sp5',
'ENSDARG00000006892' => 'myo3b'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '170504394',
'seq_end' => '170715328',
'region_length' => '210934',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0002',
'tax_id' => '10090',
'chromosome' => '2',
'seq_start' => '70317822',
'seq_end' => '70475113',
'region_length' => '157291',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0003',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '3624755',
'seq_end' => '3624943',
'region_length' => '188',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '3668396',
'seq_end' => '3751590',
'region_length' => '83194',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 22 => 'Brain',
(int) 36 => 'Breast',
(int) 48 => 'Colon',
(int) 55 => 'Heart',
(int) 66 => 'Kidney',
(int) 76 => 'Liver',
(int) 88 => 'Lung',
(int) 98 => 'Muscle',
(int) 108 => 'Ovary',
(int) 121 => 'Placenta',
(int) 132 => '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) 21
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000317935' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MYO3B-003'
),
'ENST00000408978' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-004'
),
'ENST00000409044' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-001'
),
'ENST00000409940' => array(
'start' => '170178145',
'end' => '170519978',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO3B-002'
),
'ENST00000438642' => array(
'start' => '170178145',
'end' => '170651639',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-006'
),
'ENST00000442690' => array(
'start' => '170199208',
'end' => '170382766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-007'
),
'ENST00000469359' => array(
'start' => '170407730',
'end' => '170412425',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-008'
),
'ENST00000484338' => array(
'start' => '170180149',
'end' => '170499808',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-005'
),
'ENST00000602629' => array(
'start' => '170199252',
'end' => '170655171',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-009'
),
'ENST00000423519' => array(
'start' => '170618628',
'end' => '170643944',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC007277.3-002'
),
'ENST00000428156' => array(
'start' => '170640374',
'end' => '170695374',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC007277.3-001'
),
'ENST00000455362' => array(
'start' => '170601662',
'end' => '170602228',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P4-001'
),
'ENST00000409786' => array(
'start' => '170712451',
'end' => '170714567',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01124-001'
),
'ENST00000618243' => array(
'start' => '170690564',
'end' => '170690742',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'uc_338.1-212'
),
'ENSMUST00000060208' => array(
'start' => '70039126',
'end' => '70429195',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-201'
),
'ENSMUST00000112241' => array(
'start' => '70096298',
'end' => '70183267',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-001'
),
'ENSMUST00000112243' => array(
'start' => '70083074',
'end' => '70429198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-002'
),
'ENSMUST00000140507' => array(
'start' => '70458982',
'end' => '70459560',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Rpl9-ps7-001'
),
'ENSMUST00000100043' => array(
'start' => '70474923',
'end' => '70477729',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sp5-001'
),
'ENSDART00000010378' => array(
'start' => '3752080',
'end' => '3878770',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo3b-201'
),
'ENSDART00000141492' => array(
'start' => '3746250',
'end' => '3831136',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo3b-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_0007J4_0001' => array(
'genes_in_region' => array(
'ENSG00000213981' => array(
[maximum depth reached]
),
'ENSG00000214821' => array(
[maximum depth reached]
),
'ENSG00000222033' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Bladder',
(int) 1 => 'Liver',
(int) 2 => 'Ovary',
(int) 3 => 'Testis',
(int) 4 => 'Placenta',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Liver',
(int) 10 => 'Lung',
(int) 11 => 'Ovary',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Heart',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Muscle',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis',
(int) 21 => 'Brain',
(int) 22 => 'Liver',
(int) 23 => 'Bladder',
(int) 24 => 'Brain',
(int) 25 => 'Placenta',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Heart',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Ovary',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Ovary',
(int) 52 => 'Testis',
(int) 53 => 'Adipose',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Heart',
(int) 57 => 'Kidney',
(int) 58 => 'Muscle',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Adipose',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Testis'
)
),
'CIL_0007J4_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000042064' => array(
[maximum depth reached]
),
'ENSMUSG00000047965' => array(
[maximum depth reached]
),
'ENSMUSG00000075304' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Bladder',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Ovary',
(int) 18 => 'Placenta',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Kidney',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Muscle',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis'
)
),
'CIL_0007J4_0004' => array(
'genes_in_region' => array(
'ENSDARG00000006892' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Kidney',
(int) 1 => 'Muscle',
(int) 2 => 'Brain',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0003',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '3624755',
'seq_end' => '3624943',
'region_length' => '188',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
)
$gene_el = array(
'ENSMUST00000100043' => array(
'Adipose' => array(
'average_FPKM' => '1.527',
'stddev_FPKM' => '1.07'
),
'Adrenal' => array(
'average_FPKM' => '3.442',
'stddev_FPKM' => '0.40'
),
'Bladder' => array(
'average_FPKM' => '0.125',
'stddev_FPKM' => '0.03'
),
'Brain' => array(
'average_FPKM' => '4.377',
'stddev_FPKM' => '3.01'
),
'Breast' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.02'
),
'Colon' => array(
'average_FPKM' => '0.161',
'stddev_FPKM' => '0.08'
),
'Heart' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.01'
),
'Kidney' => array(
'average_FPKM' => '2.251',
'stddev_FPKM' => '0.82'
),
'Liver' => array(
'average_FPKM' => '0.456',
'stddev_FPKM' => '0.38'
),
'Lung' => array(
'average_FPKM' => '2.452',
'stddev_FPKM' => '0.41'
),
'Muscle' => array(
'average_FPKM' => '0.038',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '1.520',
'stddev_FPKM' => '0.51'
),
'Placenta' => array(
'average_FPKM' => '0.215',
'stddev_FPKM' => '0.12'
),
'Testis' => array(
'average_FPKM' => '0.073',
'stddev_FPKM' => '0.05'
)
)
)
$gene_key = 'ENSMUSG00000075304'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '1.527',
'stddev_FPKM' => '1.07'
),
'Adrenal' => array(
'average_FPKM' => '3.442',
'stddev_FPKM' => '0.40'
),
'Bladder' => array(
'average_FPKM' => '0.125',
'stddev_FPKM' => '0.03'
),
'Brain' => array(
'average_FPKM' => '4.377',
'stddev_FPKM' => '3.01'
),
'Breast' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.02'
),
'Colon' => array(
'average_FPKM' => '0.161',
'stddev_FPKM' => '0.08'
),
'Heart' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.01'
),
'Kidney' => array(
'average_FPKM' => '2.251',
'stddev_FPKM' => '0.82'
),
'Liver' => array(
'average_FPKM' => '0.456',
'stddev_FPKM' => '0.38'
),
'Lung' => array(
'average_FPKM' => '2.452',
'stddev_FPKM' => '0.41'
),
'Muscle' => array(
'average_FPKM' => '0.038',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '1.520',
'stddev_FPKM' => '0.51'
),
'Placenta' => array(
'average_FPKM' => '0.215',
'stddev_FPKM' => '0.12'
),
'Testis' => array(
'average_FPKM' => '0.073',
'stddev_FPKM' => '0.05'
)
)
$tran_key = 'ENSMUST00000100043'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007J4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007J4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007J4_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000071909' => 'myosin IIIB',
'ENSG00000213981' => null,
'ENSG00000214821' => 'high mobility group box 1 pseudogene 4',
'ENSG00000222033' => 'long intergenic non-protein coding RNA 1124',
'ENSG00000275414' => 'TUC338',
'ENSMUSG00000042064' => 'myosin IIIB',
'ENSMUSG00000047965' => 'ribosomal protein L9, pseudogene 7',
'ENSMUSG00000075304' => 'trans-acting transcription factor 5',
'ENSDARG00000006892' => 'myosin IIIB'
),
'gene_name_arr' => array(
'ENSG00000071909' => 'MYO3B',
'ENSG00000213981' => 'AC007277.3',
'ENSG00000214821' => 'HMGB1P4',
'ENSG00000222033' => 'LINC01124',
'ENSG00000275414' => 'uc_338',
'ENSMUSG00000042064' => 'Myo3b',
'ENSMUSG00000047965' => 'Rpl9-ps7',
'ENSMUSG00000075304' => 'Sp5',
'ENSDARG00000006892' => 'myo3b'
),
'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) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 22 => 'Brain',
(int) 36 => 'Breast',
(int) 48 => 'Colon',
(int) 55 => 'Heart',
(int) 66 => 'Kidney',
(int) 76 => 'Liver',
(int) 88 => 'Lung',
(int) 98 => 'Muscle',
(int) 108 => 'Ovary',
(int) 121 => 'Placenta',
(int) 132 => '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) 21,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000317935' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MYO3B-003'
),
'ENST00000408978' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-004'
),
'ENST00000409044' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-001'
),
'ENST00000409940' => array(
'start' => '170178145',
'end' => '170519978',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO3B-002'
),
'ENST00000438642' => array(
'start' => '170178145',
'end' => '170651639',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-006'
),
'ENST00000442690' => array(
'start' => '170199208',
'end' => '170382766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-007'
),
'ENST00000469359' => array(
'start' => '170407730',
'end' => '170412425',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-008'
),
'ENST00000484338' => array(
'start' => '170180149',
'end' => '170499808',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-005'
),
'ENST00000602629' => array(
'start' => '170199252',
'end' => '170655171',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-009'
),
'ENST00000423519' => array(
'start' => '170618628',
'end' => '170643944',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC007277.3-002'
),
'ENST00000428156' => array(
'start' => '170640374',
'end' => '170695374',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC007277.3-001'
),
'ENST00000455362' => array(
'start' => '170601662',
'end' => '170602228',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P4-001'
),
'ENST00000409786' => array(
'start' => '170712451',
'end' => '170714567',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01124-001'
),
'ENST00000618243' => array(
'start' => '170690564',
'end' => '170690742',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'uc_338.1-212'
),
'ENSMUST00000060208' => array(
'start' => '70039126',
'end' => '70429195',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-201'
),
'ENSMUST00000112241' => array(
'start' => '70096298',
'end' => '70183267',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-001'
),
'ENSMUST00000112243' => array(
'start' => '70083074',
'end' => '70429198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-002'
),
'ENSMUST00000140507' => array(
'start' => '70458982',
'end' => '70459560',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Rpl9-ps7-001'
),
'ENSMUST00000100043' => array(
'start' => '70474923',
'end' => '70477729',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sp5-001'
),
'ENSDART00000010378' => array(
'start' => '3752080',
'end' => '3878770',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo3b-201'
),
'ENSDART00000141492' => array(
'start' => '3746250',
'end' => '3831136',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo3b-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_0007J4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007J4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007J4_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007J4_0001' => array(
'genes_in_region' => array(
'ENSG00000213981' => array(
[maximum depth reached]
),
'ENSG00000214821' => array(
[maximum depth reached]
),
'ENSG00000222033' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Bladder',
(int) 1 => 'Liver',
(int) 2 => 'Ovary',
(int) 3 => 'Testis',
(int) 4 => 'Placenta',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Liver',
(int) 10 => 'Lung',
(int) 11 => 'Ovary',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Heart',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Muscle',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis',
(int) 21 => 'Brain',
(int) 22 => 'Liver',
(int) 23 => 'Bladder',
(int) 24 => 'Brain',
(int) 25 => 'Placenta',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Heart',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Ovary',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Ovary',
(int) 52 => 'Testis',
(int) 53 => 'Adipose',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Heart',
(int) 57 => 'Kidney',
(int) 58 => 'Muscle',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Adipose',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Testis'
)
),
'CIL_0007J4_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000042064' => array(
[maximum depth reached]
),
'ENSMUSG00000047965' => array(
[maximum depth reached]
),
'ENSMUSG00000075304' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Bladder',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Ovary',
(int) 18 => 'Placenta',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Kidney',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Muscle',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis'
)
),
'CIL_0007J4_0004' => array(
'genes_in_region' => array(
'ENSDARG00000006892' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Kidney',
(int) 1 => 'Muscle',
(int) 2 => 'Brain',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000071909' => 'myosin IIIB',
'ENSG00000213981' => null,
'ENSG00000214821' => 'high mobility group box 1 pseudogene 4',
'ENSG00000222033' => 'long intergenic non-protein coding RNA 1124',
'ENSG00000275414' => 'TUC338',
'ENSMUSG00000042064' => 'myosin IIIB',
'ENSMUSG00000047965' => 'ribosomal protein L9, pseudogene 7',
'ENSMUSG00000075304' => 'trans-acting transcription factor 5',
'ENSDARG00000006892' => 'myosin IIIB'
)
$gene_name_arr = array(
'ENSG00000071909' => 'MYO3B',
'ENSG00000213981' => 'AC007277.3',
'ENSG00000214821' => 'HMGB1P4',
'ENSG00000222033' => 'LINC01124',
'ENSG00000275414' => 'uc_338',
'ENSMUSG00000042064' => 'Myo3b',
'ENSMUSG00000047965' => 'Rpl9-ps7',
'ENSMUSG00000075304' => 'Sp5',
'ENSDARG00000006892' => 'myo3b'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '170504394',
'seq_end' => '170715328',
'region_length' => '210934',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0002',
'tax_id' => '10090',
'chromosome' => '2',
'seq_start' => '70317822',
'seq_end' => '70475113',
'region_length' => '157291',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0003',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '3624755',
'seq_end' => '3624943',
'region_length' => '188',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '3668396',
'seq_end' => '3751590',
'region_length' => '83194',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 22 => 'Brain',
(int) 36 => 'Breast',
(int) 48 => 'Colon',
(int) 55 => 'Heart',
(int) 66 => 'Kidney',
(int) 76 => 'Liver',
(int) 88 => 'Lung',
(int) 98 => 'Muscle',
(int) 108 => 'Ovary',
(int) 121 => 'Placenta',
(int) 132 => '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) 21
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000317935' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MYO3B-003'
),
'ENST00000408978' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-004'
),
'ENST00000409044' => array(
'start' => '170178145',
'end' => '170654481',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-001'
),
'ENST00000409940' => array(
'start' => '170178145',
'end' => '170519978',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MYO3B-002'
),
'ENST00000438642' => array(
'start' => '170178145',
'end' => '170651639',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-006'
),
'ENST00000442690' => array(
'start' => '170199208',
'end' => '170382766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-007'
),
'ENST00000469359' => array(
'start' => '170407730',
'end' => '170412425',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-008'
),
'ENST00000484338' => array(
'start' => '170180149',
'end' => '170499808',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MYO3B-005'
),
'ENST00000602629' => array(
'start' => '170199252',
'end' => '170655171',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MYO3B-009'
),
'ENST00000423519' => array(
'start' => '170618628',
'end' => '170643944',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC007277.3-002'
),
'ENST00000428156' => array(
'start' => '170640374',
'end' => '170695374',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC007277.3-001'
),
'ENST00000455362' => array(
'start' => '170601662',
'end' => '170602228',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P4-001'
),
'ENST00000409786' => array(
'start' => '170712451',
'end' => '170714567',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01124-001'
),
'ENST00000618243' => array(
'start' => '170690564',
'end' => '170690742',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'uc_338.1-212'
),
'ENSMUST00000060208' => array(
'start' => '70039126',
'end' => '70429195',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-201'
),
'ENSMUST00000112241' => array(
'start' => '70096298',
'end' => '70183267',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-001'
),
'ENSMUST00000112243' => array(
'start' => '70083074',
'end' => '70429198',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Myo3b-002'
),
'ENSMUST00000140507' => array(
'start' => '70458982',
'end' => '70459560',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Rpl9-ps7-001'
),
'ENSMUST00000100043' => array(
'start' => '70474923',
'end' => '70477729',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sp5-001'
),
'ENSDART00000010378' => array(
'start' => '3752080',
'end' => '3878770',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo3b-201'
),
'ENSDART00000141492' => array(
'start' => '3746250',
'end' => '3831136',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'myo3b-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_0007J4_0001' => array(
'genes_in_region' => array(
'ENSG00000213981' => array(
[maximum depth reached]
),
'ENSG00000214821' => array(
[maximum depth reached]
),
'ENSG00000222033' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Bladder',
(int) 1 => 'Liver',
(int) 2 => 'Ovary',
(int) 3 => 'Testis',
(int) 4 => 'Placenta',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Liver',
(int) 10 => 'Lung',
(int) 11 => 'Ovary',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Heart',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Muscle',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis',
(int) 21 => 'Brain',
(int) 22 => 'Liver',
(int) 23 => 'Bladder',
(int) 24 => 'Brain',
(int) 25 => 'Placenta',
(int) 26 => 'Brain',
(int) 27 => 'Breast',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Heart',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Ovary',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Ovary',
(int) 52 => 'Testis',
(int) 53 => 'Adipose',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Heart',
(int) 57 => 'Kidney',
(int) 58 => 'Muscle',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Adipose',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Testis'
)
),
'CIL_0007J4_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000042064' => array(
[maximum depth reached]
),
'ENSMUSG00000047965' => array(
[maximum depth reached]
),
'ENSMUSG00000075304' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Bladder',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Ovary',
(int) 18 => 'Placenta',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Kidney',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adipose',
(int) 46 => 'Adrenal',
(int) 47 => 'Bladder',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Muscle',
(int) 56 => 'Ovary',
(int) 57 => 'Placenta',
(int) 58 => 'Testis'
)
),
'CIL_0007J4_0004' => array(
'genes_in_region' => array(
'ENSDARG00000006892' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Kidney',
(int) 1 => 'Muscle',
(int) 2 => 'Brain',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007J4_0003',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '3624755',
'seq_end' => '3624943',
'region_length' => '188',
'region_type' => 'UCNEbase',
'el_id' => 'SP5'
)
)
$gene_el = array(
'ENSMUST00000100043' => array(
'Adipose' => array(
'average_FPKM' => '1.527',
'stddev_FPKM' => '1.07'
),
'Adrenal' => array(
'average_FPKM' => '3.442',
'stddev_FPKM' => '0.40'
),
'Bladder' => array(
'average_FPKM' => '0.125',
'stddev_FPKM' => '0.03'
),
'Brain' => array(
'average_FPKM' => '4.377',
'stddev_FPKM' => '3.01'
),
'Breast' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.02'
),
'Colon' => array(
'average_FPKM' => '0.161',
'stddev_FPKM' => '0.08'
),
'Heart' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.01'
),
'Kidney' => array(
'average_FPKM' => '2.251',
'stddev_FPKM' => '0.82'
),
'Liver' => array(
'average_FPKM' => '0.456',
'stddev_FPKM' => '0.38'
),
'Lung' => array(
'average_FPKM' => '2.452',
'stddev_FPKM' => '0.41'
),
'Muscle' => array(
'average_FPKM' => '0.038',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '1.520',
'stddev_FPKM' => '0.51'
),
'Placenta' => array(
'average_FPKM' => '0.215',
'stddev_FPKM' => '0.12'
),
'Testis' => array(
'average_FPKM' => '0.073',
'stddev_FPKM' => '0.05'
)
)
)
$gene_key = 'ENSMUSG00000075304'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '1.527',
'stddev_FPKM' => '1.07'
),
'Adrenal' => array(
'average_FPKM' => '3.442',
'stddev_FPKM' => '0.40'
),
'Bladder' => array(
'average_FPKM' => '0.125',
'stddev_FPKM' => '0.03'
),
'Brain' => array(
'average_FPKM' => '4.377',
'stddev_FPKM' => '3.01'
),
'Breast' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.02'
),
'Colon' => array(
'average_FPKM' => '0.161',
'stddev_FPKM' => '0.08'
),
'Heart' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.01'
),
'Kidney' => array(
'average_FPKM' => '2.251',
'stddev_FPKM' => '0.82'
),
'Liver' => array(
'average_FPKM' => '0.456',
'stddev_FPKM' => '0.38'
),
'Lung' => array(
'average_FPKM' => '2.452',
'stddev_FPKM' => '0.41'
),
'Muscle' => array(
'average_FPKM' => '0.038',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '1.520',
'stddev_FPKM' => '0.51'
),
'Placenta' => array(
'average_FPKM' => '0.215',
'stddev_FPKM' => '0.12'
),
'Testis' => array(
'average_FPKM' => '0.073',
'stddev_FPKM' => '0.05'
)
)
$tran_key = 'ENSMUST00000100043'
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 |
| SP5 |
UCNEbase |
7955 |
6:3624755-3624943  |
| Gene | Transcript | Position | Biotype |
|---|
(AC007277.3)