Notice (8): Undefined index: CIL_0007N4_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_0007N4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N4_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000135999' => 'enhancer of polycomb homolog 2 (Drosophila)',
'ENSG00000204406' => 'methyl-CpG binding domain protein 5',
'ENSG00000232238' => null,
'ENSMUSG00000036792' => 'methyl-CpG binding domain protein 5',
'ENSMUSG00000069495' => 'enhancer of polycomb homolog 2 (Drosophila)',
'ENSMUSG00000077769' => 'predicted gene, 25215',
'ENSMUSG00000081272' => 'predicted gene 13509',
'ENSMUSG00000084177' => 'predicted gene 13508',
'ENSDARG00000007485' => 'enhancer of polycomb homolog 2 (Drosophila)'
),
'gene_name_arr' => array(
'ENSG00000135999' => 'EPC2',
'ENSG00000204406' => 'MBD5',
'ENSG00000232238' => 'AC017080.1',
'ENSMUSG00000036792' => 'Mbd5',
'ENSMUSG00000069495' => 'Epc2',
'ENSMUSG00000077769' => 'Gm25215',
'ENSMUSG00000081272' => 'Gm13509',
'ENSMUSG00000084177' => 'Gm13508',
'ENSDARG00000007485' => 'epc2'
),
'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) 9 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 32 => 'Colon',
(int) 39 => 'Heart',
(int) 46 => 'Kidney',
(int) 54 => 'Liver',
(int) 62 => 'Lung',
(int) 70 => 'Muscle',
(int) 77 => 'Ovary',
(int) 86 => 'Placenta',
(int) 92 => '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) 36,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000258484' => array(
'start' => '148644984',
'end' => '148787568',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-001'
),
'ENST00000397424' => array(
'start' => '148645420',
'end' => '148761809',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-002'
),
'ENST00000409654' => array(
'start' => '148644999',
'end' => '148692833',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-003'
),
'ENST00000449013' => array(
'start' => '148690214',
'end' => '148692248',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-004'
),
'ENST00000457184' => array(
'start' => '148644440',
'end' => '148754020',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-006'
),
'ENST00000491099' => array(
'start' => '148753895',
'end' => '148762215',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EPC2-005'
),
'ENST00000404807' => array(
'start' => '148458630',
'end' => '148513451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-004'
),
'ENST00000407073' => array(
'start' => '148021011',
'end' => '148513451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-001'
),
'ENST00000416015' => array(
'start' => '148468725',
'end' => '148518236',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-005'
),
'ENST00000469438' => array(
'start' => '148021593',
'end' => '148041365',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-009'
),
'ENST00000470063' => array(
'start' => '148021464',
'end' => '148178793',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-011'
),
'ENST00000473478' => array(
'start' => '148021439',
'end' => '148233327',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-008'
),
'ENST00000478190' => array(
'start' => '148021238',
'end' => '148025058',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-010'
),
'ENST00000478804' => array(
'start' => '148068572',
'end' => '148458317',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-002'
),
'ENST00000488372' => array(
'start' => '148021011',
'end' => '148458497',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-007'
),
'ENST00000496158' => array(
'start' => '148021027',
'end' => '148458358',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-006'
),
'ENST00000496893' => array(
'start' => '148485116',
'end' => '148513477',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MBD5-003'
),
'ENST00000445109' => array(
'start' => '148595158',
'end' => '148595328',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC017080.1-001'
),
'ENSMUST00000047413' => array(
'start' => '49245969',
'end' => '49317069',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-001'
),
'ENSMUST00000112745' => array(
'start' => '48949510',
'end' => '49260139',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-005'
),
'ENSMUST00000112754' => array(
'start' => '49245812',
'end' => '49316972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-003'
),
'ENSMUST00000122841' => array(
'start' => '49256561',
'end' => '49316998',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-002'
),
'ENSMUST00000127085' => array(
'start' => '48949510',
'end' => '49245737',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-004'
),
'ENSMUST00000132717' => array(
'start' => '49272184',
'end' => '49322284',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Mbd5-006'
),
'ENSMUST00000142250' => array(
'start' => '48949962',
'end' => '49021440',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-009'
),
'ENSMUST00000147023' => array(
'start' => '48950149',
'end' => '49065517',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-011'
),
'ENSMUST00000147055' => array(
'start' => '48950143',
'end' => '49245557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-007'
),
'ENSMUST00000148796' => array(
'start' => '48949963',
'end' => '48954067',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-010'
),
'ENSMUST00000154653' => array(
'start' => '48949518',
'end' => '49119012',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-008'
),
'ENSMUST00000092123' => array(
'start' => '49451486',
'end' => '49551948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Epc2-001'
),
'ENSMUST00000152485' => array(
'start' => '49528875',
'end' => '49537081',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Epc2-002'
),
'ENSMUST00000104581' => array(
'start' => '49398395',
'end' => '49398515',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm25215-201'
),
'ENSMUST00000119733' => array(
'start' => '49308155',
'end' => '49309462',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13509-001'
),
'ENSMUST00000121639' => array(
'start' => '49327377',
'end' => '49328151',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13508-001'
),
'ENSDART00000021672' => array(
'start' => '26381159',
'end' => '26399886',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'epc2-001'
),
'ENSDART00000143524' => array(
'start' => '26392263',
'end' => '26397926',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'epc2-002'
)
),
'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_0007N4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N4_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007N4_0001' => array(
'genes_in_region' => array(
'ENSG00000135999' => array(
[maximum depth reached]
),
'ENSG00000232238' => 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 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Lung',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Muscle',
(int) 22 => 'Lung',
(int) 23 => 'Adipose',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Colon',
(int) 38 => 'Lung',
(int) 39 => 'Muscle'
)
),
'CIL_0007N4_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000036792' => array(
[maximum depth reached]
),
'ENSMUSG00000069495' => array(
[maximum depth reached]
),
'ENSMUSG00000081272' => array(
[maximum depth reached]
),
'ENSMUSG00000084177' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Ovary',
(int) 7 => 'Testis',
(int) 8 => 'Adipose',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Kidney',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Brain',
(int) 52 => 'Liver',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
),
'CIL_0007N4_0004' => array(
'genes_in_region' => array(
'ENSDARG00000007485' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000135999' => 'enhancer of polycomb homolog 2 (Drosophila)',
'ENSG00000204406' => 'methyl-CpG binding domain protein 5',
'ENSG00000232238' => null,
'ENSMUSG00000036792' => 'methyl-CpG binding domain protein 5',
'ENSMUSG00000069495' => 'enhancer of polycomb homolog 2 (Drosophila)',
'ENSMUSG00000077769' => 'predicted gene, 25215',
'ENSMUSG00000081272' => 'predicted gene 13509',
'ENSMUSG00000084177' => 'predicted gene 13508',
'ENSDARG00000007485' => 'enhancer of polycomb homolog 2 (Drosophila)'
)
$gene_name_arr = array(
'ENSG00000135999' => 'EPC2',
'ENSG00000204406' => 'MBD5',
'ENSG00000232238' => 'AC017080.1',
'ENSMUSG00000036792' => 'Mbd5',
'ENSMUSG00000069495' => 'Epc2',
'ENSMUSG00000077769' => 'Gm25215',
'ENSMUSG00000081272' => 'Gm13509',
'ENSMUSG00000084177' => 'Gm13508',
'ENSDARG00000007485' => 'epc2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '148483860',
'seq_end' => '148787579',
'region_length' => '303719',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0002',
'tax_id' => '10090',
'chromosome' => '2',
'seq_start' => '49272783',
'seq_end' => '49551184',
'region_length' => '278401',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0003',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '19353',
'seq_end' => '19486',
'region_length' => '133',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '26381135',
'seq_end' => '26381450',
'region_length' => '315',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 32 => 'Colon',
(int) 39 => 'Heart',
(int) 46 => 'Kidney',
(int) 54 => 'Liver',
(int) 62 => 'Lung',
(int) 70 => 'Muscle',
(int) 77 => 'Ovary',
(int) 86 => 'Placenta',
(int) 92 => '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) 36
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000258484' => array(
'start' => '148644984',
'end' => '148787568',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-001'
),
'ENST00000397424' => array(
'start' => '148645420',
'end' => '148761809',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-002'
),
'ENST00000409654' => array(
'start' => '148644999',
'end' => '148692833',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-003'
),
'ENST00000449013' => array(
'start' => '148690214',
'end' => '148692248',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-004'
),
'ENST00000457184' => array(
'start' => '148644440',
'end' => '148754020',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-006'
),
'ENST00000491099' => array(
'start' => '148753895',
'end' => '148762215',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EPC2-005'
),
'ENST00000404807' => array(
'start' => '148458630',
'end' => '148513451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-004'
),
'ENST00000407073' => array(
'start' => '148021011',
'end' => '148513451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-001'
),
'ENST00000416015' => array(
'start' => '148468725',
'end' => '148518236',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-005'
),
'ENST00000469438' => array(
'start' => '148021593',
'end' => '148041365',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-009'
),
'ENST00000470063' => array(
'start' => '148021464',
'end' => '148178793',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-011'
),
'ENST00000473478' => array(
'start' => '148021439',
'end' => '148233327',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-008'
),
'ENST00000478190' => array(
'start' => '148021238',
'end' => '148025058',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-010'
),
'ENST00000478804' => array(
'start' => '148068572',
'end' => '148458317',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-002'
),
'ENST00000488372' => array(
'start' => '148021011',
'end' => '148458497',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-007'
),
'ENST00000496158' => array(
'start' => '148021027',
'end' => '148458358',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-006'
),
'ENST00000496893' => array(
'start' => '148485116',
'end' => '148513477',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MBD5-003'
),
'ENST00000445109' => array(
'start' => '148595158',
'end' => '148595328',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC017080.1-001'
),
'ENSMUST00000047413' => array(
'start' => '49245969',
'end' => '49317069',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-001'
),
'ENSMUST00000112745' => array(
'start' => '48949510',
'end' => '49260139',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-005'
),
'ENSMUST00000112754' => array(
'start' => '49245812',
'end' => '49316972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-003'
),
'ENSMUST00000122841' => array(
'start' => '49256561',
'end' => '49316998',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-002'
),
'ENSMUST00000127085' => array(
'start' => '48949510',
'end' => '49245737',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-004'
),
'ENSMUST00000132717' => array(
'start' => '49272184',
'end' => '49322284',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Mbd5-006'
),
'ENSMUST00000142250' => array(
'start' => '48949962',
'end' => '49021440',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-009'
),
'ENSMUST00000147023' => array(
'start' => '48950149',
'end' => '49065517',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-011'
),
'ENSMUST00000147055' => array(
'start' => '48950143',
'end' => '49245557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-007'
),
'ENSMUST00000148796' => array(
'start' => '48949963',
'end' => '48954067',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-010'
),
'ENSMUST00000154653' => array(
'start' => '48949518',
'end' => '49119012',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-008'
),
'ENSMUST00000092123' => array(
'start' => '49451486',
'end' => '49551948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Epc2-001'
),
'ENSMUST00000152485' => array(
'start' => '49528875',
'end' => '49537081',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Epc2-002'
),
'ENSMUST00000104581' => array(
'start' => '49398395',
'end' => '49398515',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm25215-201'
),
'ENSMUST00000119733' => array(
'start' => '49308155',
'end' => '49309462',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13509-001'
),
'ENSMUST00000121639' => array(
'start' => '49327377',
'end' => '49328151',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13508-001'
),
'ENSDART00000021672' => array(
'start' => '26381159',
'end' => '26399886',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'epc2-001'
),
'ENSDART00000143524' => array(
'start' => '26392263',
'end' => '26397926',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'epc2-002'
)
)
$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_0007N4_0001' => array(
'genes_in_region' => array(
'ENSG00000135999' => array(
[maximum depth reached]
),
'ENSG00000232238' => 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 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Lung',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Muscle',
(int) 22 => 'Lung',
(int) 23 => 'Adipose',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Colon',
(int) 38 => 'Lung',
(int) 39 => 'Muscle'
)
),
'CIL_0007N4_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000036792' => array(
[maximum depth reached]
),
'ENSMUSG00000069495' => array(
[maximum depth reached]
),
'ENSMUSG00000081272' => array(
[maximum depth reached]
),
'ENSMUSG00000084177' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Ovary',
(int) 7 => 'Testis',
(int) 8 => 'Adipose',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Kidney',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Brain',
(int) 52 => 'Liver',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
),
'CIL_0007N4_0004' => array(
'genes_in_region' => array(
'ENSDARG00000007485' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0003',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '19353',
'seq_end' => '19486',
'region_length' => '133',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
)
$gene_el = array(
'ENSMUST00000121639' => array(
'Adipose' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.03'
),
'Brain' => array(
'average_FPKM' => '0.056',
'stddev_FPKM' => '0.02'
),
'Liver' => array(
'average_FPKM' => '0.105',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.034',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.074',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000084177'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.03'
),
'Brain' => array(
'average_FPKM' => '0.056',
'stddev_FPKM' => '0.02'
),
'Liver' => array(
'average_FPKM' => '0.105',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.034',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.074',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000121639'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007N4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N4_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000135999' => 'enhancer of polycomb homolog 2 (Drosophila)',
'ENSG00000204406' => 'methyl-CpG binding domain protein 5',
'ENSG00000232238' => null,
'ENSMUSG00000036792' => 'methyl-CpG binding domain protein 5',
'ENSMUSG00000069495' => 'enhancer of polycomb homolog 2 (Drosophila)',
'ENSMUSG00000077769' => 'predicted gene, 25215',
'ENSMUSG00000081272' => 'predicted gene 13509',
'ENSMUSG00000084177' => 'predicted gene 13508',
'ENSDARG00000007485' => 'enhancer of polycomb homolog 2 (Drosophila)'
),
'gene_name_arr' => array(
'ENSG00000135999' => 'EPC2',
'ENSG00000204406' => 'MBD5',
'ENSG00000232238' => 'AC017080.1',
'ENSMUSG00000036792' => 'Mbd5',
'ENSMUSG00000069495' => 'Epc2',
'ENSMUSG00000077769' => 'Gm25215',
'ENSMUSG00000081272' => 'Gm13509',
'ENSMUSG00000084177' => 'Gm13508',
'ENSDARG00000007485' => 'epc2'
),
'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) 9 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 32 => 'Colon',
(int) 39 => 'Heart',
(int) 46 => 'Kidney',
(int) 54 => 'Liver',
(int) 62 => 'Lung',
(int) 70 => 'Muscle',
(int) 77 => 'Ovary',
(int) 86 => 'Placenta',
(int) 92 => '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) 36,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000258484' => array(
'start' => '148644984',
'end' => '148787568',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-001'
),
'ENST00000397424' => array(
'start' => '148645420',
'end' => '148761809',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-002'
),
'ENST00000409654' => array(
'start' => '148644999',
'end' => '148692833',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-003'
),
'ENST00000449013' => array(
'start' => '148690214',
'end' => '148692248',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-004'
),
'ENST00000457184' => array(
'start' => '148644440',
'end' => '148754020',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-006'
),
'ENST00000491099' => array(
'start' => '148753895',
'end' => '148762215',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EPC2-005'
),
'ENST00000404807' => array(
'start' => '148458630',
'end' => '148513451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-004'
),
'ENST00000407073' => array(
'start' => '148021011',
'end' => '148513451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-001'
),
'ENST00000416015' => array(
'start' => '148468725',
'end' => '148518236',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-005'
),
'ENST00000469438' => array(
'start' => '148021593',
'end' => '148041365',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-009'
),
'ENST00000470063' => array(
'start' => '148021464',
'end' => '148178793',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-011'
),
'ENST00000473478' => array(
'start' => '148021439',
'end' => '148233327',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-008'
),
'ENST00000478190' => array(
'start' => '148021238',
'end' => '148025058',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-010'
),
'ENST00000478804' => array(
'start' => '148068572',
'end' => '148458317',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-002'
),
'ENST00000488372' => array(
'start' => '148021011',
'end' => '148458497',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-007'
),
'ENST00000496158' => array(
'start' => '148021027',
'end' => '148458358',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-006'
),
'ENST00000496893' => array(
'start' => '148485116',
'end' => '148513477',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MBD5-003'
),
'ENST00000445109' => array(
'start' => '148595158',
'end' => '148595328',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC017080.1-001'
),
'ENSMUST00000047413' => array(
'start' => '49245969',
'end' => '49317069',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-001'
),
'ENSMUST00000112745' => array(
'start' => '48949510',
'end' => '49260139',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-005'
),
'ENSMUST00000112754' => array(
'start' => '49245812',
'end' => '49316972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-003'
),
'ENSMUST00000122841' => array(
'start' => '49256561',
'end' => '49316998',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-002'
),
'ENSMUST00000127085' => array(
'start' => '48949510',
'end' => '49245737',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-004'
),
'ENSMUST00000132717' => array(
'start' => '49272184',
'end' => '49322284',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Mbd5-006'
),
'ENSMUST00000142250' => array(
'start' => '48949962',
'end' => '49021440',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-009'
),
'ENSMUST00000147023' => array(
'start' => '48950149',
'end' => '49065517',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-011'
),
'ENSMUST00000147055' => array(
'start' => '48950143',
'end' => '49245557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-007'
),
'ENSMUST00000148796' => array(
'start' => '48949963',
'end' => '48954067',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-010'
),
'ENSMUST00000154653' => array(
'start' => '48949518',
'end' => '49119012',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-008'
),
'ENSMUST00000092123' => array(
'start' => '49451486',
'end' => '49551948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Epc2-001'
),
'ENSMUST00000152485' => array(
'start' => '49528875',
'end' => '49537081',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Epc2-002'
),
'ENSMUST00000104581' => array(
'start' => '49398395',
'end' => '49398515',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm25215-201'
),
'ENSMUST00000119733' => array(
'start' => '49308155',
'end' => '49309462',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13509-001'
),
'ENSMUST00000121639' => array(
'start' => '49327377',
'end' => '49328151',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13508-001'
),
'ENSDART00000021672' => array(
'start' => '26381159',
'end' => '26399886',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'epc2-001'
),
'ENSDART00000143524' => array(
'start' => '26392263',
'end' => '26397926',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'epc2-002'
)
),
'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_0007N4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N4_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007N4_0001' => array(
'genes_in_region' => array(
'ENSG00000135999' => array(
[maximum depth reached]
),
'ENSG00000232238' => 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 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Lung',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Muscle',
(int) 22 => 'Lung',
(int) 23 => 'Adipose',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Colon',
(int) 38 => 'Lung',
(int) 39 => 'Muscle'
)
),
'CIL_0007N4_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000036792' => array(
[maximum depth reached]
),
'ENSMUSG00000069495' => array(
[maximum depth reached]
),
'ENSMUSG00000081272' => array(
[maximum depth reached]
),
'ENSMUSG00000084177' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Ovary',
(int) 7 => 'Testis',
(int) 8 => 'Adipose',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Kidney',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Brain',
(int) 52 => 'Liver',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
),
'CIL_0007N4_0004' => array(
'genes_in_region' => array(
'ENSDARG00000007485' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000135999' => 'enhancer of polycomb homolog 2 (Drosophila)',
'ENSG00000204406' => 'methyl-CpG binding domain protein 5',
'ENSG00000232238' => null,
'ENSMUSG00000036792' => 'methyl-CpG binding domain protein 5',
'ENSMUSG00000069495' => 'enhancer of polycomb homolog 2 (Drosophila)',
'ENSMUSG00000077769' => 'predicted gene, 25215',
'ENSMUSG00000081272' => 'predicted gene 13509',
'ENSMUSG00000084177' => 'predicted gene 13508',
'ENSDARG00000007485' => 'enhancer of polycomb homolog 2 (Drosophila)'
)
$gene_name_arr = array(
'ENSG00000135999' => 'EPC2',
'ENSG00000204406' => 'MBD5',
'ENSG00000232238' => 'AC017080.1',
'ENSMUSG00000036792' => 'Mbd5',
'ENSMUSG00000069495' => 'Epc2',
'ENSMUSG00000077769' => 'Gm25215',
'ENSMUSG00000081272' => 'Gm13509',
'ENSMUSG00000084177' => 'Gm13508',
'ENSDARG00000007485' => 'epc2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '148483860',
'seq_end' => '148787579',
'region_length' => '303719',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0002',
'tax_id' => '10090',
'chromosome' => '2',
'seq_start' => '49272783',
'seq_end' => '49551184',
'region_length' => '278401',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0003',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '19353',
'seq_end' => '19486',
'region_length' => '133',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '26381135',
'seq_end' => '26381450',
'region_length' => '315',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 32 => 'Colon',
(int) 39 => 'Heart',
(int) 46 => 'Kidney',
(int) 54 => 'Liver',
(int) 62 => 'Lung',
(int) 70 => 'Muscle',
(int) 77 => 'Ovary',
(int) 86 => 'Placenta',
(int) 92 => '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) 36
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000258484' => array(
'start' => '148644984',
'end' => '148787568',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-001'
),
'ENST00000397424' => array(
'start' => '148645420',
'end' => '148761809',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-002'
),
'ENST00000409654' => array(
'start' => '148644999',
'end' => '148692833',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-003'
),
'ENST00000449013' => array(
'start' => '148690214',
'end' => '148692248',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-004'
),
'ENST00000457184' => array(
'start' => '148644440',
'end' => '148754020',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EPC2-006'
),
'ENST00000491099' => array(
'start' => '148753895',
'end' => '148762215',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'EPC2-005'
),
'ENST00000404807' => array(
'start' => '148458630',
'end' => '148513451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-004'
),
'ENST00000407073' => array(
'start' => '148021011',
'end' => '148513451',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-001'
),
'ENST00000416015' => array(
'start' => '148468725',
'end' => '148518236',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MBD5-005'
),
'ENST00000469438' => array(
'start' => '148021593',
'end' => '148041365',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-009'
),
'ENST00000470063' => array(
'start' => '148021464',
'end' => '148178793',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-011'
),
'ENST00000473478' => array(
'start' => '148021439',
'end' => '148233327',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-008'
),
'ENST00000478190' => array(
'start' => '148021238',
'end' => '148025058',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-010'
),
'ENST00000478804' => array(
'start' => '148068572',
'end' => '148458317',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-002'
),
'ENST00000488372' => array(
'start' => '148021011',
'end' => '148458497',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-007'
),
'ENST00000496158' => array(
'start' => '148021027',
'end' => '148458358',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MBD5-006'
),
'ENST00000496893' => array(
'start' => '148485116',
'end' => '148513477',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MBD5-003'
),
'ENST00000445109' => array(
'start' => '148595158',
'end' => '148595328',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC017080.1-001'
),
'ENSMUST00000047413' => array(
'start' => '49245969',
'end' => '49317069',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-001'
),
'ENSMUST00000112745' => array(
'start' => '48949510',
'end' => '49260139',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-005'
),
'ENSMUST00000112754' => array(
'start' => '49245812',
'end' => '49316972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-003'
),
'ENSMUST00000122841' => array(
'start' => '49256561',
'end' => '49316998',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mbd5-002'
),
'ENSMUST00000127085' => array(
'start' => '48949510',
'end' => '49245737',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-004'
),
'ENSMUST00000132717' => array(
'start' => '49272184',
'end' => '49322284',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Mbd5-006'
),
'ENSMUST00000142250' => array(
'start' => '48949962',
'end' => '49021440',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-009'
),
'ENSMUST00000147023' => array(
'start' => '48950149',
'end' => '49065517',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-011'
),
'ENSMUST00000147055' => array(
'start' => '48950143',
'end' => '49245557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-007'
),
'ENSMUST00000148796' => array(
'start' => '48949963',
'end' => '48954067',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-010'
),
'ENSMUST00000154653' => array(
'start' => '48949518',
'end' => '49119012',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mbd5-008'
),
'ENSMUST00000092123' => array(
'start' => '49451486',
'end' => '49551948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Epc2-001'
),
'ENSMUST00000152485' => array(
'start' => '49528875',
'end' => '49537081',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Epc2-002'
),
'ENSMUST00000104581' => array(
'start' => '49398395',
'end' => '49398515',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm25215-201'
),
'ENSMUST00000119733' => array(
'start' => '49308155',
'end' => '49309462',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13509-001'
),
'ENSMUST00000121639' => array(
'start' => '49327377',
'end' => '49328151',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13508-001'
),
'ENSDART00000021672' => array(
'start' => '26381159',
'end' => '26399886',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'epc2-001'
),
'ENSDART00000143524' => array(
'start' => '26392263',
'end' => '26397926',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'epc2-002'
)
)
$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_0007N4_0001' => array(
'genes_in_region' => array(
'ENSG00000135999' => array(
[maximum depth reached]
),
'ENSG00000232238' => 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 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Lung',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Muscle',
(int) 22 => 'Lung',
(int) 23 => 'Adipose',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Colon',
(int) 38 => 'Lung',
(int) 39 => 'Muscle'
)
),
'CIL_0007N4_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000036792' => array(
[maximum depth reached]
),
'ENSMUSG00000069495' => array(
[maximum depth reached]
),
'ENSMUSG00000081272' => array(
[maximum depth reached]
),
'ENSMUSG00000084177' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Ovary',
(int) 7 => 'Testis',
(int) 8 => 'Adipose',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Kidney',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Brain',
(int) 52 => 'Liver',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
),
'CIL_0007N4_0004' => array(
'genes_in_region' => array(
'ENSDARG00000007485' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N4_0003',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '19353',
'seq_end' => '19486',
'region_length' => '133',
'region_type' => 'UCNEbase',
'el_id' => 'MBD5'
)
)
$gene_el = array(
'ENSMUST00000121639' => array(
'Adipose' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.03'
),
'Brain' => array(
'average_FPKM' => '0.056',
'stddev_FPKM' => '0.02'
),
'Liver' => array(
'average_FPKM' => '0.105',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.034',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.074',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000084177'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.03'
),
'Brain' => array(
'average_FPKM' => '0.056',
'stddev_FPKM' => '0.02'
),
'Liver' => array(
'average_FPKM' => '0.105',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.034',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.074',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000121639'
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 |
| MBD5 |
UCNEbase |
7955 |
6:19353-19486  |
| Gene | Transcript | Position | Biotype |
|---|
(EPC2)