| Source ID |
Type |
Tax ID |
Position |
| ZMIZ1 |
UCNEbase |
7955 |
13:30794303-30794460  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007ML_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_0007ML_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007ML_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000108175' => 'zinc finger, MIZ-type containing 1',
'ENSG00000224596' => 'ZMIZ1 antisense RNA 1',
'ENSG00000229569' => null,
'ENSMUSG00000007817' => 'zinc finger, MIZ-type containing 1',
'ENSMUSG00000087535' => 'Zmiz1 opposite strand 1',
'ENSMUSG00000093081' => 'microRNA 3075',
'ENSMUSG00000097136' => 'predicted gene, 26772',
'ENSMUSG00000097601' => 'predicted gene, 26660'
),
'gene_name_arr' => array(
'ENSG00000108175' => 'ZMIZ1',
'ENSG00000224596' => 'ZMIZ1-AS1',
'ENSG00000229569' => 'RP11-481G8.2',
'ENSMUSG00000007817' => 'Zmiz1',
'ENSMUSG00000087535' => 'Zmiz1os1',
'ENSMUSG00000093081' => 'Mir3075',
'ENSMUSG00000097136' => 'Gm26772',
'ENSMUSG00000097601' => 'Gm26660'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 18 => 'Brain',
(int) 26 => 'Breast',
(int) 32 => 'Colon',
(int) 39 => 'Heart',
(int) 47 => 'Kidney',
(int) 54 => 'Liver',
(int) 63 => 'Lung',
(int) 70 => 'Muscle',
(int) 75 => 'Ovary',
(int) 83 => 'Placenta',
(int) 89 => '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(
'ENST00000334512' => array(
'start' => '79069035',
'end' => '79316519',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-001'
),
'ENST00000446377' => array(
'start' => '79285453',
'end' => '79316528',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-201'
),
'ENST00000472035' => array(
'start' => '79243669',
'end' => '79291085',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZMIZ1-002'
),
'ENST00000478357' => array(
'start' => '79277179',
'end' => '79296935',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZMIZ1-003'
),
'ENST00000611351' => array(
'start' => '79201595',
'end' => '79315753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-202'
),
'ENST00000428862' => array(
'start' => '78943328',
'end' => '78962394',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-004'
),
'ENST00000440151' => array(
'start' => '79044148',
'end' => '79067468',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-002'
),
'ENST00000456353' => array(
'start' => '78943328',
'end' => '79067895',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-001'
),
'ENST00000427035' => array(
'start' => '79000484',
'end' => '79003803',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-481G8.2-001'
),
'ENSMUST00000007961' => array(
'start' => '25459267',
'end' => '25664719',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-002'
),
'ENSMUST00000159766' => array(
'start' => '25459292',
'end' => '25649574',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-003'
),
'ENSMUST00000160190' => array(
'start' => '25607357',
'end' => '25643657',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1-007'
),
'ENSMUST00000160229' => array(
'start' => '25607838',
'end' => '25645735',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-008'
),
'ENSMUST00000160680' => array(
'start' => '25459555',
'end' => '25572030',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1-005'
),
'ENSMUST00000161766' => array(
'start' => '25459185',
'end' => '25538492',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-004'
),
'ENSMUST00000162546' => array(
'start' => '25656830',
'end' => '25658405',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-006'
),
'ENSMUST00000162645' => array(
'start' => '25459224',
'end' => '25666743',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-001'
),
'ENSMUST00000156682' => array(
'start' => '25455737',
'end' => '25461128',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1os1-001'
),
'ENSMUST00000175340' => array(
'start' => '25534439',
'end' => '25534523',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir3075-201'
),
'ENSMUST00000180466' => array(
'start' => '25548390',
'end' => '25554369',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26772-201'
),
'ENSMUST00000181582' => array(
'start' => '25355801',
'end' => '25378635',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26660-201'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0007ML_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007ML_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007ML_0001' => array(
'genes_in_region' => array(
'ENSG00000108175' => array(
[maximum depth reached]
),
'ENSG00000224596' => array(
[maximum depth reached]
),
'ENSG00000229569' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Heart',
(int) 15 => 'Adipose',
(int) 16 => 'Lung',
(int) 17 => 'Bladder',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Brain',
(int) 24 => 'Liver',
(int) 25 => 'Adipose',
(int) 26 => 'Brain',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(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'
)
),
'CIL_0007ML_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000007817' => array(
[maximum depth reached]
),
'ENSMUSG00000097136' => array(
[maximum depth reached]
),
'ENSMUSG00000097601' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Adipose',
(int) 39 => 'Adrenal',
(int) 40 => 'Brain',
(int) 41 => 'Breast',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000108175' => 'zinc finger, MIZ-type containing 1',
'ENSG00000224596' => 'ZMIZ1 antisense RNA 1',
'ENSG00000229569' => null,
'ENSMUSG00000007817' => 'zinc finger, MIZ-type containing 1',
'ENSMUSG00000087535' => 'Zmiz1 opposite strand 1',
'ENSMUSG00000093081' => 'microRNA 3075',
'ENSMUSG00000097136' => 'predicted gene, 26772',
'ENSMUSG00000097601' => 'predicted gene, 26660'
)
$gene_name_arr = array(
'ENSG00000108175' => 'ZMIZ1',
'ENSG00000224596' => 'ZMIZ1-AS1',
'ENSG00000229569' => 'RP11-481G8.2',
'ENSMUSG00000007817' => 'Zmiz1',
'ENSMUSG00000087535' => 'Zmiz1os1',
'ENSMUSG00000093081' => 'Mir3075',
'ENSMUSG00000097136' => 'Gm26772',
'ENSMUSG00000097601' => 'Gm26660'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007ML_0001',
'tax_id' => '9606',
'chromosome' => '10',
'seq_start' => '78747884',
'seq_end' => '79316490',
'region_length' => '568606',
'region_type' => 'UCNEbase',
'el_id' => 'ZMIZ1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007ML_0002',
'tax_id' => '10090',
'chromosome' => '14',
'seq_start' => '25180100',
'seq_end' => '25666714',
'region_length' => '486614',
'region_type' => 'UCNEbase',
'el_id' => 'ZMIZ1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007ML_0003',
'tax_id' => '7955',
'chromosome' => '13',
'seq_start' => '30794303',
'seq_end' => '30794460',
'region_length' => '157',
'region_type' => 'UCNEbase',
'el_id' => 'ZMIZ1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 18 => 'Brain',
(int) 26 => 'Breast',
(int) 32 => 'Colon',
(int) 39 => 'Heart',
(int) 47 => 'Kidney',
(int) 54 => 'Liver',
(int) 63 => 'Lung',
(int) 70 => 'Muscle',
(int) 75 => 'Ovary',
(int) 83 => 'Placenta',
(int) 89 => '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(
'ENST00000334512' => array(
'start' => '79069035',
'end' => '79316519',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-001'
),
'ENST00000446377' => array(
'start' => '79285453',
'end' => '79316528',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-201'
),
'ENST00000472035' => array(
'start' => '79243669',
'end' => '79291085',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZMIZ1-002'
),
'ENST00000478357' => array(
'start' => '79277179',
'end' => '79296935',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZMIZ1-003'
),
'ENST00000611351' => array(
'start' => '79201595',
'end' => '79315753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-202'
),
'ENST00000428862' => array(
'start' => '78943328',
'end' => '78962394',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-004'
),
'ENST00000440151' => array(
'start' => '79044148',
'end' => '79067468',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-002'
),
'ENST00000456353' => array(
'start' => '78943328',
'end' => '79067895',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-001'
),
'ENST00000427035' => array(
'start' => '79000484',
'end' => '79003803',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-481G8.2-001'
),
'ENSMUST00000007961' => array(
'start' => '25459267',
'end' => '25664719',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-002'
),
'ENSMUST00000159766' => array(
'start' => '25459292',
'end' => '25649574',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-003'
),
'ENSMUST00000160190' => array(
'start' => '25607357',
'end' => '25643657',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1-007'
),
'ENSMUST00000160229' => array(
'start' => '25607838',
'end' => '25645735',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-008'
),
'ENSMUST00000160680' => array(
'start' => '25459555',
'end' => '25572030',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1-005'
),
'ENSMUST00000161766' => array(
'start' => '25459185',
'end' => '25538492',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-004'
),
'ENSMUST00000162546' => array(
'start' => '25656830',
'end' => '25658405',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-006'
),
'ENSMUST00000162645' => array(
'start' => '25459224',
'end' => '25666743',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-001'
),
'ENSMUST00000156682' => array(
'start' => '25455737',
'end' => '25461128',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1os1-001'
),
'ENSMUST00000175340' => array(
'start' => '25534439',
'end' => '25534523',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir3075-201'
),
'ENSMUST00000180466' => array(
'start' => '25548390',
'end' => '25554369',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26772-201'
),
'ENSMUST00000181582' => array(
'start' => '25355801',
'end' => '25378635',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26660-201'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0007ML_0001' => array(
'genes_in_region' => array(
'ENSG00000108175' => array(
[maximum depth reached]
),
'ENSG00000224596' => array(
[maximum depth reached]
),
'ENSG00000229569' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Heart',
(int) 15 => 'Adipose',
(int) 16 => 'Lung',
(int) 17 => 'Bladder',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Brain',
(int) 24 => 'Liver',
(int) 25 => 'Adipose',
(int) 26 => 'Brain',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(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'
)
),
'CIL_0007ML_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000007817' => array(
[maximum depth reached]
),
'ENSMUSG00000097136' => array(
[maximum depth reached]
),
'ENSMUSG00000097601' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Adipose',
(int) 39 => 'Adrenal',
(int) 40 => 'Brain',
(int) 41 => 'Breast',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007ML_0003',
'tax_id' => '7955',
'chromosome' => '13',
'seq_start' => '30794303',
'seq_end' => '30794460',
'region_length' => '157',
'region_type' => 'UCNEbase',
'el_id' => 'ZMIZ1'
)
)
$gene_el = array(
'ENSMUST00000181582' => array(
'Adipose' => array(
'average_FPKM' => '0.074',
'stddev_FPKM' => '0.01'
),
'Adrenal' => array(
'average_FPKM' => '0.250',
'stddev_FPKM' => '0.05'
),
'Brain' => array(
'average_FPKM' => '0.407',
'stddev_FPKM' => '0.24'
),
'Breast' => array(
'average_FPKM' => '0.192',
'stddev_FPKM' => '0.07'
),
'Colon' => array(
'average_FPKM' => '0.087',
'stddev_FPKM' => '0.02'
),
'Heart' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.03'
),
'Liver' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.05'
),
'Lung' => array(
'average_FPKM' => '0.136',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.02'
),
'Ovary' => array(
'average_FPKM' => '0.402',
'stddev_FPKM' => '0.26'
),
'Placenta' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.07'
),
'Testis' => array(
'average_FPKM' => '0.033',
'stddev_FPKM' => '0.02'
)
)
)
$gene_key = 'ENSMUSG00000097601'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.074',
'stddev_FPKM' => '0.01'
),
'Adrenal' => array(
'average_FPKM' => '0.250',
'stddev_FPKM' => '0.05'
),
'Brain' => array(
'average_FPKM' => '0.407',
'stddev_FPKM' => '0.24'
),
'Breast' => array(
'average_FPKM' => '0.192',
'stddev_FPKM' => '0.07'
),
'Colon' => array(
'average_FPKM' => '0.087',
'stddev_FPKM' => '0.02'
),
'Heart' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.03'
),
'Liver' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.05'
),
'Lung' => array(
'average_FPKM' => '0.136',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.02'
),
'Ovary' => array(
'average_FPKM' => '0.402',
'stddev_FPKM' => '0.26'
),
'Placenta' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.07'
),
'Testis' => array(
'average_FPKM' => '0.033',
'stddev_FPKM' => '0.02'
)
)
$tran_key = 'ENSMUST00000181582'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007ML_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007ML_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000108175' => 'zinc finger, MIZ-type containing 1',
'ENSG00000224596' => 'ZMIZ1 antisense RNA 1',
'ENSG00000229569' => null,
'ENSMUSG00000007817' => 'zinc finger, MIZ-type containing 1',
'ENSMUSG00000087535' => 'Zmiz1 opposite strand 1',
'ENSMUSG00000093081' => 'microRNA 3075',
'ENSMUSG00000097136' => 'predicted gene, 26772',
'ENSMUSG00000097601' => 'predicted gene, 26660'
),
'gene_name_arr' => array(
'ENSG00000108175' => 'ZMIZ1',
'ENSG00000224596' => 'ZMIZ1-AS1',
'ENSG00000229569' => 'RP11-481G8.2',
'ENSMUSG00000007817' => 'Zmiz1',
'ENSMUSG00000087535' => 'Zmiz1os1',
'ENSMUSG00000093081' => 'Mir3075',
'ENSMUSG00000097136' => 'Gm26772',
'ENSMUSG00000097601' => 'Gm26660'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 18 => 'Brain',
(int) 26 => 'Breast',
(int) 32 => 'Colon',
(int) 39 => 'Heart',
(int) 47 => 'Kidney',
(int) 54 => 'Liver',
(int) 63 => 'Lung',
(int) 70 => 'Muscle',
(int) 75 => 'Ovary',
(int) 83 => 'Placenta',
(int) 89 => '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(
'ENST00000334512' => array(
'start' => '79069035',
'end' => '79316519',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-001'
),
'ENST00000446377' => array(
'start' => '79285453',
'end' => '79316528',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-201'
),
'ENST00000472035' => array(
'start' => '79243669',
'end' => '79291085',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZMIZ1-002'
),
'ENST00000478357' => array(
'start' => '79277179',
'end' => '79296935',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZMIZ1-003'
),
'ENST00000611351' => array(
'start' => '79201595',
'end' => '79315753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-202'
),
'ENST00000428862' => array(
'start' => '78943328',
'end' => '78962394',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-004'
),
'ENST00000440151' => array(
'start' => '79044148',
'end' => '79067468',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-002'
),
'ENST00000456353' => array(
'start' => '78943328',
'end' => '79067895',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-001'
),
'ENST00000427035' => array(
'start' => '79000484',
'end' => '79003803',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-481G8.2-001'
),
'ENSMUST00000007961' => array(
'start' => '25459267',
'end' => '25664719',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-002'
),
'ENSMUST00000159766' => array(
'start' => '25459292',
'end' => '25649574',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-003'
),
'ENSMUST00000160190' => array(
'start' => '25607357',
'end' => '25643657',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1-007'
),
'ENSMUST00000160229' => array(
'start' => '25607838',
'end' => '25645735',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-008'
),
'ENSMUST00000160680' => array(
'start' => '25459555',
'end' => '25572030',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1-005'
),
'ENSMUST00000161766' => array(
'start' => '25459185',
'end' => '25538492',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-004'
),
'ENSMUST00000162546' => array(
'start' => '25656830',
'end' => '25658405',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-006'
),
'ENSMUST00000162645' => array(
'start' => '25459224',
'end' => '25666743',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-001'
),
'ENSMUST00000156682' => array(
'start' => '25455737',
'end' => '25461128',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1os1-001'
),
'ENSMUST00000175340' => array(
'start' => '25534439',
'end' => '25534523',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir3075-201'
),
'ENSMUST00000180466' => array(
'start' => '25548390',
'end' => '25554369',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26772-201'
),
'ENSMUST00000181582' => array(
'start' => '25355801',
'end' => '25378635',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26660-201'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0007ML_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007ML_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007ML_0001' => array(
'genes_in_region' => array(
'ENSG00000108175' => array(
[maximum depth reached]
),
'ENSG00000224596' => array(
[maximum depth reached]
),
'ENSG00000229569' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Heart',
(int) 15 => 'Adipose',
(int) 16 => 'Lung',
(int) 17 => 'Bladder',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Brain',
(int) 24 => 'Liver',
(int) 25 => 'Adipose',
(int) 26 => 'Brain',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(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'
)
),
'CIL_0007ML_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000007817' => array(
[maximum depth reached]
),
'ENSMUSG00000097136' => array(
[maximum depth reached]
),
'ENSMUSG00000097601' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Adipose',
(int) 39 => 'Adrenal',
(int) 40 => 'Brain',
(int) 41 => 'Breast',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000108175' => 'zinc finger, MIZ-type containing 1',
'ENSG00000224596' => 'ZMIZ1 antisense RNA 1',
'ENSG00000229569' => null,
'ENSMUSG00000007817' => 'zinc finger, MIZ-type containing 1',
'ENSMUSG00000087535' => 'Zmiz1 opposite strand 1',
'ENSMUSG00000093081' => 'microRNA 3075',
'ENSMUSG00000097136' => 'predicted gene, 26772',
'ENSMUSG00000097601' => 'predicted gene, 26660'
)
$gene_name_arr = array(
'ENSG00000108175' => 'ZMIZ1',
'ENSG00000224596' => 'ZMIZ1-AS1',
'ENSG00000229569' => 'RP11-481G8.2',
'ENSMUSG00000007817' => 'Zmiz1',
'ENSMUSG00000087535' => 'Zmiz1os1',
'ENSMUSG00000093081' => 'Mir3075',
'ENSMUSG00000097136' => 'Gm26772',
'ENSMUSG00000097601' => 'Gm26660'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007ML_0001',
'tax_id' => '9606',
'chromosome' => '10',
'seq_start' => '78747884',
'seq_end' => '79316490',
'region_length' => '568606',
'region_type' => 'UCNEbase',
'el_id' => 'ZMIZ1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007ML_0002',
'tax_id' => '10090',
'chromosome' => '14',
'seq_start' => '25180100',
'seq_end' => '25666714',
'region_length' => '486614',
'region_type' => 'UCNEbase',
'el_id' => 'ZMIZ1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007ML_0003',
'tax_id' => '7955',
'chromosome' => '13',
'seq_start' => '30794303',
'seq_end' => '30794460',
'region_length' => '157',
'region_type' => 'UCNEbase',
'el_id' => 'ZMIZ1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 18 => 'Brain',
(int) 26 => 'Breast',
(int) 32 => 'Colon',
(int) 39 => 'Heart',
(int) 47 => 'Kidney',
(int) 54 => 'Liver',
(int) 63 => 'Lung',
(int) 70 => 'Muscle',
(int) 75 => 'Ovary',
(int) 83 => 'Placenta',
(int) 89 => '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(
'ENST00000334512' => array(
'start' => '79069035',
'end' => '79316519',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-001'
),
'ENST00000446377' => array(
'start' => '79285453',
'end' => '79316528',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-201'
),
'ENST00000472035' => array(
'start' => '79243669',
'end' => '79291085',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZMIZ1-002'
),
'ENST00000478357' => array(
'start' => '79277179',
'end' => '79296935',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZMIZ1-003'
),
'ENST00000611351' => array(
'start' => '79201595',
'end' => '79315753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZMIZ1-202'
),
'ENST00000428862' => array(
'start' => '78943328',
'end' => '78962394',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-004'
),
'ENST00000440151' => array(
'start' => '79044148',
'end' => '79067468',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-002'
),
'ENST00000456353' => array(
'start' => '78943328',
'end' => '79067895',
'transcript_biotype' => 'antisense',
'transcript_name' => 'ZMIZ1-AS1-001'
),
'ENST00000427035' => array(
'start' => '79000484',
'end' => '79003803',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-481G8.2-001'
),
'ENSMUST00000007961' => array(
'start' => '25459267',
'end' => '25664719',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-002'
),
'ENSMUST00000159766' => array(
'start' => '25459292',
'end' => '25649574',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-003'
),
'ENSMUST00000160190' => array(
'start' => '25607357',
'end' => '25643657',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1-007'
),
'ENSMUST00000160229' => array(
'start' => '25607838',
'end' => '25645735',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-008'
),
'ENSMUST00000160680' => array(
'start' => '25459555',
'end' => '25572030',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1-005'
),
'ENSMUST00000161766' => array(
'start' => '25459185',
'end' => '25538492',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-004'
),
'ENSMUST00000162546' => array(
'start' => '25656830',
'end' => '25658405',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zmiz1-006'
),
'ENSMUST00000162645' => array(
'start' => '25459224',
'end' => '25666743',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zmiz1-001'
),
'ENSMUST00000156682' => array(
'start' => '25455737',
'end' => '25461128',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zmiz1os1-001'
),
'ENSMUST00000175340' => array(
'start' => '25534439',
'end' => '25534523',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir3075-201'
),
'ENSMUST00000180466' => array(
'start' => '25548390',
'end' => '25554369',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26772-201'
),
'ENSMUST00000181582' => array(
'start' => '25355801',
'end' => '25378635',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26660-201'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0007ML_0001' => array(
'genes_in_region' => array(
'ENSG00000108175' => array(
[maximum depth reached]
),
'ENSG00000224596' => array(
[maximum depth reached]
),
'ENSG00000229569' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Heart',
(int) 15 => 'Adipose',
(int) 16 => 'Lung',
(int) 17 => 'Bladder',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Brain',
(int) 24 => 'Liver',
(int) 25 => 'Adipose',
(int) 26 => 'Brain',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(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'
)
),
'CIL_0007ML_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000007817' => array(
[maximum depth reached]
),
'ENSMUSG00000097136' => array(
[maximum depth reached]
),
'ENSMUSG00000097601' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Heart',
(int) 17 => 'Kidney',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Adipose',
(int) 39 => 'Adrenal',
(int) 40 => 'Brain',
(int) 41 => 'Breast',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007ML_0003',
'tax_id' => '7955',
'chromosome' => '13',
'seq_start' => '30794303',
'seq_end' => '30794460',
'region_length' => '157',
'region_type' => 'UCNEbase',
'el_id' => 'ZMIZ1'
)
)
$gene_el = array(
'ENSMUST00000181582' => array(
'Adipose' => array(
'average_FPKM' => '0.074',
'stddev_FPKM' => '0.01'
),
'Adrenal' => array(
'average_FPKM' => '0.250',
'stddev_FPKM' => '0.05'
),
'Brain' => array(
'average_FPKM' => '0.407',
'stddev_FPKM' => '0.24'
),
'Breast' => array(
'average_FPKM' => '0.192',
'stddev_FPKM' => '0.07'
),
'Colon' => array(
'average_FPKM' => '0.087',
'stddev_FPKM' => '0.02'
),
'Heart' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.03'
),
'Liver' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.05'
),
'Lung' => array(
'average_FPKM' => '0.136',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.02'
),
'Ovary' => array(
'average_FPKM' => '0.402',
'stddev_FPKM' => '0.26'
),
'Placenta' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.07'
),
'Testis' => array(
'average_FPKM' => '0.033',
'stddev_FPKM' => '0.02'
)
)
)
$gene_key = 'ENSMUSG00000097601'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.074',
'stddev_FPKM' => '0.01'
),
'Adrenal' => array(
'average_FPKM' => '0.250',
'stddev_FPKM' => '0.05'
),
'Brain' => array(
'average_FPKM' => '0.407',
'stddev_FPKM' => '0.24'
),
'Breast' => array(
'average_FPKM' => '0.192',
'stddev_FPKM' => '0.07'
),
'Colon' => array(
'average_FPKM' => '0.087',
'stddev_FPKM' => '0.02'
),
'Heart' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.03'
),
'Liver' => array(
'average_FPKM' => '0.051',
'stddev_FPKM' => '0.05'
),
'Lung' => array(
'average_FPKM' => '0.136',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.02'
),
'Ovary' => array(
'average_FPKM' => '0.402',
'stddev_FPKM' => '0.26'
),
'Placenta' => array(
'average_FPKM' => '0.090',
'stddev_FPKM' => '0.07'
),
'Testis' => array(
'average_FPKM' => '0.033',
'stddev_FPKM' => '0.02'
)
)
$tran_key = 'ENSMUST00000181582'
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
(ZMIZ1)