| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000031825-ENSMUSG00000031823 |
CGP |
10090 |
8:119992438-120101482  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0000I6_0002 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0000I6_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000103196' => 'cysteine-rich secretory protein LCCL domain containing 2',
'ENSG00000153786' => 'zinc finger, DHHC-type containing 7',
'ENSG00000260340' => null,
'ENSG00000260859' => null,
'ENSG00000265249' => null,
'ENSG00000279622' => null,
'ENSMUSG00000031823' => 'zinc finger, DHHC domain containing 7',
'ENSMUSG00000031825' => 'cysteine-rich secretory protein LCCL domain containing 2',
'ENSMUSG00000089742' => 'predicted gene 15898',
'ENSMUSG00000089776' => 'predicted gene 15684'
),
'gene_name_arr' => array(
'ENSG00000103196' => 'CRISPLD2',
'ENSG00000153786' => 'ZDHHC7',
'ENSG00000260340' => 'RP11-254F19.3',
'ENSG00000260859' => 'RP11-254F19.2',
'ENSG00000265249' => 'AC025280.1',
'ENSG00000279622' => 'RP11-254F19.4',
'ENSMUSG00000031823' => 'Zdhhc7',
'ENSMUSG00000031825' => 'Crispld2',
'ENSMUSG00000089742' => 'Gm15898',
'ENSMUSG00000089776' => 'Gm15684'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 17 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 34 => 'Kidney',
(int) 41 => 'Liver',
(int) 46 => 'Lung',
(int) 52 => 'Muscle',
(int) 56 => 'Ovary',
(int) 63 => 'Placenta',
(int) 67 => '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) 35,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000262424' => array(
'start' => '84819984',
'end' => '84909510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-001'
),
'ENST00000563066' => array(
'start' => '84842003',
'end' => '84873110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-011'
),
'ENST00000564567' => array(
'start' => '84820003',
'end' => '84880725',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-007'
),
'ENST00000565561' => array(
'start' => '84819997',
'end' => '84840023',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CRISPLD2-006'
),
'ENST00000566151' => array(
'start' => '84819985',
'end' => '84838551',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-010'
),
'ENST00000566165' => array(
'start' => '84889244',
'end' => '84920768',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CRISPLD2-013'
),
'ENST00000566431' => array(
'start' => '84819992',
'end' => '84863166',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CRISPLD2-005'
),
'ENST00000566789' => array(
'start' => '84849217',
'end' => '84866993',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-012'
),
'ENST00000567845' => array(
'start' => '84819991',
'end' => '84907112',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-002'
),
'ENST00000569090' => array(
'start' => '84820005',
'end' => '84846150',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-008'
),
'ENST00000569262' => array(
'start' => '84820017',
'end' => '84873508',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CRISPLD2-009'
),
'ENST00000313732' => array(
'start' => '84974181',
'end' => '85011535',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-001'
),
'ENST00000344861' => array(
'start' => '84974460',
'end' => '85011522',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZDHHC7-002'
),
'ENST00000564466' => array(
'start' => '84976213',
'end' => '85011502',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-008'
),
'ENST00000564526' => array(
'start' => '84976104',
'end' => '84977281',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZDHHC7-007'
),
'ENST00000566909' => array(
'start' => '84976496',
'end' => '84982117',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-005'
),
'ENST00000569017' => array(
'start' => '84990333',
'end' => '85005010',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-003'
),
'ENST00000569377' => array(
'start' => '84976246',
'end' => '84978126',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZDHHC7-006'
),
'ENST00000569488' => array(
'start' => '84977108',
'end' => '84990626',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZDHHC7-004'
),
'ENST00000569104' => array(
'start' => '84928353',
'end' => '84939603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-254F19.3-001'
),
'ENST00000562393' => array(
'start' => '84828263',
'end' => '84829242',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-254F19.2-001'
),
'ENST00000584136' => array(
'start' => '84852968',
'end' => '84853067',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC025280.1-201'
),
'ENST00000625056' => array(
'start' => '84917377',
'end' => '84919923',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-254F19.4-001'
),
'ENSMUST00000034280' => array(
'start' => '120081095',
'end' => '120101482',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zdhhc7-001'
),
'ENSMUST00000123186' => array(
'start' => '120092975',
'end' => '120101072',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zdhhc7-002'
),
'ENSMUST00000124044' => array(
'start' => '120085222',
'end' => '120088075',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-004'
),
'ENSMUST00000141886' => array(
'start' => '120085412',
'end' => '120088268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-003'
),
'ENSMUST00000150444' => array(
'start' => '120082403',
'end' => '120086835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-005'
),
'ENSMUST00000034282' => array(
'start' => '119992508',
'end' => '120051576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-004'
),
'ENSMUST00000108972' => array(
'start' => '120002726',
'end' => '120051576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-002'
),
'ENSMUST00000132583' => array(
'start' => '119992438',
'end' => '120052793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-001'
),
'ENSMUST00000144801' => array(
'start' => '120030792',
'end' => '120050471',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Crispld2-003'
),
'ENSMUST00000151629' => array(
'start' => '120013208',
'end' => '120015690',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Crispld2-005'
),
'ENSMUST00000162213' => array(
'start' => '120095060',
'end' => '120097736',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm15898-001'
),
'ENSMUST00000160605' => array(
'start' => '120036194',
'end' => '120045287',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm15684-001'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0000I6_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0000I6_0001' => array(
'genes_in_region' => array(
'ENSG00000103196' => array(
[maximum depth reached]
),
'ENSG00000153786' => array(
[maximum depth reached]
),
'ENSG00000260340' => array(
[maximum depth reached]
),
'ENSG00000260859' => array(
[maximum depth reached]
),
'ENSG00000265249' => 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 => 'Brain',
(int) 15 => 'Kidney',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Ovary',
(int) 19 => 'Kidney',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Colon',
(int) 34 => 'Kidney',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Heart',
(int) 40 => 'Bladder',
(int) 41 => 'Adipose',
(int) 42 => 'Adrenal',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Testis',
(int) 53 => 'Adrenal',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Liver',
(int) 57 => 'Lung',
(int) 58 => 'Ovary',
(int) 59 => 'Placenta',
(int) 60 => 'Testis',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Brain',
(int) 64 => 'Breast',
(int) 65 => 'Colon',
(int) 66 => 'Heart',
(int) 67 => 'Kidney',
(int) 68 => 'Liver',
(int) 69 => 'Lung',
(int) 70 => 'Ovary',
(int) 71 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000103196' => 'cysteine-rich secretory protein LCCL domain containing 2',
'ENSG00000153786' => 'zinc finger, DHHC-type containing 7',
'ENSG00000260340' => null,
'ENSG00000260859' => null,
'ENSG00000265249' => null,
'ENSG00000279622' => null,
'ENSMUSG00000031823' => 'zinc finger, DHHC domain containing 7',
'ENSMUSG00000031825' => 'cysteine-rich secretory protein LCCL domain containing 2',
'ENSMUSG00000089742' => 'predicted gene 15898',
'ENSMUSG00000089776' => 'predicted gene 15684'
)
$gene_name_arr = array(
'ENSG00000103196' => 'CRISPLD2',
'ENSG00000153786' => 'ZDHHC7',
'ENSG00000260340' => 'RP11-254F19.3',
'ENSG00000260859' => 'RP11-254F19.2',
'ENSG00000265249' => 'AC025280.1',
'ENSG00000279622' => 'RP11-254F19.4',
'ENSMUSG00000031823' => 'Zdhhc7',
'ENSMUSG00000031825' => 'Crispld2',
'ENSMUSG00000089742' => 'Gm15898',
'ENSMUSG00000089776' => 'Gm15684'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000I6_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '84819984',
'seq_end' => '85011535',
'region_length' => '191551',
'region_type' => 'CGP',
'el_id' => 'ENSG00000103196-ENSG00000153786'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000I6_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '119992438',
'seq_end' => '120101482',
'region_length' => '109044',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031825-ENSMUSG00000031823'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 17 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 34 => 'Kidney',
(int) 41 => 'Liver',
(int) 46 => 'Lung',
(int) 52 => 'Muscle',
(int) 56 => 'Ovary',
(int) 63 => 'Placenta',
(int) 67 => '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) 35
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000262424' => array(
'start' => '84819984',
'end' => '84909510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-001'
),
'ENST00000563066' => array(
'start' => '84842003',
'end' => '84873110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-011'
),
'ENST00000564567' => array(
'start' => '84820003',
'end' => '84880725',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-007'
),
'ENST00000565561' => array(
'start' => '84819997',
'end' => '84840023',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CRISPLD2-006'
),
'ENST00000566151' => array(
'start' => '84819985',
'end' => '84838551',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-010'
),
'ENST00000566165' => array(
'start' => '84889244',
'end' => '84920768',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CRISPLD2-013'
),
'ENST00000566431' => array(
'start' => '84819992',
'end' => '84863166',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CRISPLD2-005'
),
'ENST00000566789' => array(
'start' => '84849217',
'end' => '84866993',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-012'
),
'ENST00000567845' => array(
'start' => '84819991',
'end' => '84907112',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-002'
),
'ENST00000569090' => array(
'start' => '84820005',
'end' => '84846150',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-008'
),
'ENST00000569262' => array(
'start' => '84820017',
'end' => '84873508',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CRISPLD2-009'
),
'ENST00000313732' => array(
'start' => '84974181',
'end' => '85011535',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-001'
),
'ENST00000344861' => array(
'start' => '84974460',
'end' => '85011522',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZDHHC7-002'
),
'ENST00000564466' => array(
'start' => '84976213',
'end' => '85011502',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-008'
),
'ENST00000564526' => array(
'start' => '84976104',
'end' => '84977281',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZDHHC7-007'
),
'ENST00000566909' => array(
'start' => '84976496',
'end' => '84982117',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-005'
),
'ENST00000569017' => array(
'start' => '84990333',
'end' => '85005010',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-003'
),
'ENST00000569377' => array(
'start' => '84976246',
'end' => '84978126',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZDHHC7-006'
),
'ENST00000569488' => array(
'start' => '84977108',
'end' => '84990626',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZDHHC7-004'
),
'ENST00000569104' => array(
'start' => '84928353',
'end' => '84939603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-254F19.3-001'
),
'ENST00000562393' => array(
'start' => '84828263',
'end' => '84829242',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-254F19.2-001'
),
'ENST00000584136' => array(
'start' => '84852968',
'end' => '84853067',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC025280.1-201'
),
'ENST00000625056' => array(
'start' => '84917377',
'end' => '84919923',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-254F19.4-001'
),
'ENSMUST00000034280' => array(
'start' => '120081095',
'end' => '120101482',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zdhhc7-001'
),
'ENSMUST00000123186' => array(
'start' => '120092975',
'end' => '120101072',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zdhhc7-002'
),
'ENSMUST00000124044' => array(
'start' => '120085222',
'end' => '120088075',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-004'
),
'ENSMUST00000141886' => array(
'start' => '120085412',
'end' => '120088268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-003'
),
'ENSMUST00000150444' => array(
'start' => '120082403',
'end' => '120086835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-005'
),
'ENSMUST00000034282' => array(
'start' => '119992508',
'end' => '120051576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-004'
),
'ENSMUST00000108972' => array(
'start' => '120002726',
'end' => '120051576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-002'
),
'ENSMUST00000132583' => array(
'start' => '119992438',
'end' => '120052793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-001'
),
'ENSMUST00000144801' => array(
'start' => '120030792',
'end' => '120050471',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Crispld2-003'
),
'ENSMUST00000151629' => array(
'start' => '120013208',
'end' => '120015690',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Crispld2-005'
),
'ENSMUST00000162213' => array(
'start' => '120095060',
'end' => '120097736',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm15898-001'
),
'ENSMUST00000160605' => array(
'start' => '120036194',
'end' => '120045287',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm15684-001'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0000I6_0001' => array(
'genes_in_region' => array(
'ENSG00000103196' => array(
[maximum depth reached]
),
'ENSG00000153786' => array(
[maximum depth reached]
),
'ENSG00000260340' => array(
[maximum depth reached]
),
'ENSG00000260859' => array(
[maximum depth reached]
),
'ENSG00000265249' => 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 => 'Brain',
(int) 15 => 'Kidney',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Ovary',
(int) 19 => 'Kidney',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Colon',
(int) 34 => 'Kidney',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Heart',
(int) 40 => 'Bladder',
(int) 41 => 'Adipose',
(int) 42 => 'Adrenal',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Testis',
(int) 53 => 'Adrenal',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Liver',
(int) 57 => 'Lung',
(int) 58 => 'Ovary',
(int) 59 => 'Placenta',
(int) 60 => 'Testis',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Brain',
(int) 64 => 'Breast',
(int) 65 => 'Colon',
(int) 66 => 'Heart',
(int) 67 => 'Kidney',
(int) 68 => 'Liver',
(int) 69 => 'Lung',
(int) 70 => 'Ovary',
(int) 71 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0000I6_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '119992438',
'seq_end' => '120101482',
'region_length' => '109044',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031825-ENSMUSG00000031823'
)
)
$gene_el = array(
'ENST00000584136' => array(
'Adipose' => array(
'average_FPKM' => '2.095',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '6.399',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.304',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.059',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '2.603',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.271',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '3.672',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.075',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '1.504',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '87.165',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '2.300',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000265249'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '2.095',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '6.399',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.304',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.059',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '2.603',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.271',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '3.672',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.075',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '1.504',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '87.165',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '2.300',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000584136'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0000I6_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000103196' => 'cysteine-rich secretory protein LCCL domain containing 2',
'ENSG00000153786' => 'zinc finger, DHHC-type containing 7',
'ENSG00000260340' => null,
'ENSG00000260859' => null,
'ENSG00000265249' => null,
'ENSG00000279622' => null,
'ENSMUSG00000031823' => 'zinc finger, DHHC domain containing 7',
'ENSMUSG00000031825' => 'cysteine-rich secretory protein LCCL domain containing 2',
'ENSMUSG00000089742' => 'predicted gene 15898',
'ENSMUSG00000089776' => 'predicted gene 15684'
),
'gene_name_arr' => array(
'ENSG00000103196' => 'CRISPLD2',
'ENSG00000153786' => 'ZDHHC7',
'ENSG00000260340' => 'RP11-254F19.3',
'ENSG00000260859' => 'RP11-254F19.2',
'ENSG00000265249' => 'AC025280.1',
'ENSG00000279622' => 'RP11-254F19.4',
'ENSMUSG00000031823' => 'Zdhhc7',
'ENSMUSG00000031825' => 'Crispld2',
'ENSMUSG00000089742' => 'Gm15898',
'ENSMUSG00000089776' => 'Gm15684'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 17 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 34 => 'Kidney',
(int) 41 => 'Liver',
(int) 46 => 'Lung',
(int) 52 => 'Muscle',
(int) 56 => 'Ovary',
(int) 63 => 'Placenta',
(int) 67 => '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) 35,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000262424' => array(
'start' => '84819984',
'end' => '84909510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-001'
),
'ENST00000563066' => array(
'start' => '84842003',
'end' => '84873110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-011'
),
'ENST00000564567' => array(
'start' => '84820003',
'end' => '84880725',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-007'
),
'ENST00000565561' => array(
'start' => '84819997',
'end' => '84840023',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CRISPLD2-006'
),
'ENST00000566151' => array(
'start' => '84819985',
'end' => '84838551',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-010'
),
'ENST00000566165' => array(
'start' => '84889244',
'end' => '84920768',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CRISPLD2-013'
),
'ENST00000566431' => array(
'start' => '84819992',
'end' => '84863166',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CRISPLD2-005'
),
'ENST00000566789' => array(
'start' => '84849217',
'end' => '84866993',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-012'
),
'ENST00000567845' => array(
'start' => '84819991',
'end' => '84907112',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-002'
),
'ENST00000569090' => array(
'start' => '84820005',
'end' => '84846150',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-008'
),
'ENST00000569262' => array(
'start' => '84820017',
'end' => '84873508',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CRISPLD2-009'
),
'ENST00000313732' => array(
'start' => '84974181',
'end' => '85011535',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-001'
),
'ENST00000344861' => array(
'start' => '84974460',
'end' => '85011522',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZDHHC7-002'
),
'ENST00000564466' => array(
'start' => '84976213',
'end' => '85011502',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-008'
),
'ENST00000564526' => array(
'start' => '84976104',
'end' => '84977281',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZDHHC7-007'
),
'ENST00000566909' => array(
'start' => '84976496',
'end' => '84982117',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-005'
),
'ENST00000569017' => array(
'start' => '84990333',
'end' => '85005010',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-003'
),
'ENST00000569377' => array(
'start' => '84976246',
'end' => '84978126',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZDHHC7-006'
),
'ENST00000569488' => array(
'start' => '84977108',
'end' => '84990626',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZDHHC7-004'
),
'ENST00000569104' => array(
'start' => '84928353',
'end' => '84939603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-254F19.3-001'
),
'ENST00000562393' => array(
'start' => '84828263',
'end' => '84829242',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-254F19.2-001'
),
'ENST00000584136' => array(
'start' => '84852968',
'end' => '84853067',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC025280.1-201'
),
'ENST00000625056' => array(
'start' => '84917377',
'end' => '84919923',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-254F19.4-001'
),
'ENSMUST00000034280' => array(
'start' => '120081095',
'end' => '120101482',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zdhhc7-001'
),
'ENSMUST00000123186' => array(
'start' => '120092975',
'end' => '120101072',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zdhhc7-002'
),
'ENSMUST00000124044' => array(
'start' => '120085222',
'end' => '120088075',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-004'
),
'ENSMUST00000141886' => array(
'start' => '120085412',
'end' => '120088268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-003'
),
'ENSMUST00000150444' => array(
'start' => '120082403',
'end' => '120086835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-005'
),
'ENSMUST00000034282' => array(
'start' => '119992508',
'end' => '120051576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-004'
),
'ENSMUST00000108972' => array(
'start' => '120002726',
'end' => '120051576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-002'
),
'ENSMUST00000132583' => array(
'start' => '119992438',
'end' => '120052793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-001'
),
'ENSMUST00000144801' => array(
'start' => '120030792',
'end' => '120050471',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Crispld2-003'
),
'ENSMUST00000151629' => array(
'start' => '120013208',
'end' => '120015690',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Crispld2-005'
),
'ENSMUST00000162213' => array(
'start' => '120095060',
'end' => '120097736',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm15898-001'
),
'ENSMUST00000160605' => array(
'start' => '120036194',
'end' => '120045287',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm15684-001'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0000I6_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0000I6_0001' => array(
'genes_in_region' => array(
'ENSG00000103196' => array(
[maximum depth reached]
),
'ENSG00000153786' => array(
[maximum depth reached]
),
'ENSG00000260340' => array(
[maximum depth reached]
),
'ENSG00000260859' => array(
[maximum depth reached]
),
'ENSG00000265249' => 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 => 'Brain',
(int) 15 => 'Kidney',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Ovary',
(int) 19 => 'Kidney',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Colon',
(int) 34 => 'Kidney',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Heart',
(int) 40 => 'Bladder',
(int) 41 => 'Adipose',
(int) 42 => 'Adrenal',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Testis',
(int) 53 => 'Adrenal',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Liver',
(int) 57 => 'Lung',
(int) 58 => 'Ovary',
(int) 59 => 'Placenta',
(int) 60 => 'Testis',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Brain',
(int) 64 => 'Breast',
(int) 65 => 'Colon',
(int) 66 => 'Heart',
(int) 67 => 'Kidney',
(int) 68 => 'Liver',
(int) 69 => 'Lung',
(int) 70 => 'Ovary',
(int) 71 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000103196' => 'cysteine-rich secretory protein LCCL domain containing 2',
'ENSG00000153786' => 'zinc finger, DHHC-type containing 7',
'ENSG00000260340' => null,
'ENSG00000260859' => null,
'ENSG00000265249' => null,
'ENSG00000279622' => null,
'ENSMUSG00000031823' => 'zinc finger, DHHC domain containing 7',
'ENSMUSG00000031825' => 'cysteine-rich secretory protein LCCL domain containing 2',
'ENSMUSG00000089742' => 'predicted gene 15898',
'ENSMUSG00000089776' => 'predicted gene 15684'
)
$gene_name_arr = array(
'ENSG00000103196' => 'CRISPLD2',
'ENSG00000153786' => 'ZDHHC7',
'ENSG00000260340' => 'RP11-254F19.3',
'ENSG00000260859' => 'RP11-254F19.2',
'ENSG00000265249' => 'AC025280.1',
'ENSG00000279622' => 'RP11-254F19.4',
'ENSMUSG00000031823' => 'Zdhhc7',
'ENSMUSG00000031825' => 'Crispld2',
'ENSMUSG00000089742' => 'Gm15898',
'ENSMUSG00000089776' => 'Gm15684'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000I6_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '84819984',
'seq_end' => '85011535',
'region_length' => '191551',
'region_type' => 'CGP',
'el_id' => 'ENSG00000103196-ENSG00000153786'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000I6_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '119992438',
'seq_end' => '120101482',
'region_length' => '109044',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031825-ENSMUSG00000031823'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 17 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 34 => 'Kidney',
(int) 41 => 'Liver',
(int) 46 => 'Lung',
(int) 52 => 'Muscle',
(int) 56 => 'Ovary',
(int) 63 => 'Placenta',
(int) 67 => '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) 35
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000262424' => array(
'start' => '84819984',
'end' => '84909510',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-001'
),
'ENST00000563066' => array(
'start' => '84842003',
'end' => '84873110',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-011'
),
'ENST00000564567' => array(
'start' => '84820003',
'end' => '84880725',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-007'
),
'ENST00000565561' => array(
'start' => '84819997',
'end' => '84840023',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CRISPLD2-006'
),
'ENST00000566151' => array(
'start' => '84819985',
'end' => '84838551',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-010'
),
'ENST00000566165' => array(
'start' => '84889244',
'end' => '84920768',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CRISPLD2-013'
),
'ENST00000566431' => array(
'start' => '84819992',
'end' => '84863166',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CRISPLD2-005'
),
'ENST00000566789' => array(
'start' => '84849217',
'end' => '84866993',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-012'
),
'ENST00000567845' => array(
'start' => '84819991',
'end' => '84907112',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-002'
),
'ENST00000569090' => array(
'start' => '84820005',
'end' => '84846150',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CRISPLD2-008'
),
'ENST00000569262' => array(
'start' => '84820017',
'end' => '84873508',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CRISPLD2-009'
),
'ENST00000313732' => array(
'start' => '84974181',
'end' => '85011535',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-001'
),
'ENST00000344861' => array(
'start' => '84974460',
'end' => '85011522',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZDHHC7-002'
),
'ENST00000564466' => array(
'start' => '84976213',
'end' => '85011502',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-008'
),
'ENST00000564526' => array(
'start' => '84976104',
'end' => '84977281',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZDHHC7-007'
),
'ENST00000566909' => array(
'start' => '84976496',
'end' => '84982117',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-005'
),
'ENST00000569017' => array(
'start' => '84990333',
'end' => '85005010',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZDHHC7-003'
),
'ENST00000569377' => array(
'start' => '84976246',
'end' => '84978126',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZDHHC7-006'
),
'ENST00000569488' => array(
'start' => '84977108',
'end' => '84990626',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZDHHC7-004'
),
'ENST00000569104' => array(
'start' => '84928353',
'end' => '84939603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-254F19.3-001'
),
'ENST00000562393' => array(
'start' => '84828263',
'end' => '84829242',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-254F19.2-001'
),
'ENST00000584136' => array(
'start' => '84852968',
'end' => '84853067',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC025280.1-201'
),
'ENST00000625056' => array(
'start' => '84917377',
'end' => '84919923',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-254F19.4-001'
),
'ENSMUST00000034280' => array(
'start' => '120081095',
'end' => '120101482',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zdhhc7-001'
),
'ENSMUST00000123186' => array(
'start' => '120092975',
'end' => '120101072',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Zdhhc7-002'
),
'ENSMUST00000124044' => array(
'start' => '120085222',
'end' => '120088075',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-004'
),
'ENSMUST00000141886' => array(
'start' => '120085412',
'end' => '120088268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-003'
),
'ENSMUST00000150444' => array(
'start' => '120082403',
'end' => '120086835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zdhhc7-005'
),
'ENSMUST00000034282' => array(
'start' => '119992508',
'end' => '120051576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-004'
),
'ENSMUST00000108972' => array(
'start' => '120002726',
'end' => '120051576',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-002'
),
'ENSMUST00000132583' => array(
'start' => '119992438',
'end' => '120052793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Crispld2-001'
),
'ENSMUST00000144801' => array(
'start' => '120030792',
'end' => '120050471',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Crispld2-003'
),
'ENSMUST00000151629' => array(
'start' => '120013208',
'end' => '120015690',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Crispld2-005'
),
'ENSMUST00000162213' => array(
'start' => '120095060',
'end' => '120097736',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'Gm15898-001'
),
'ENSMUST00000160605' => array(
'start' => '120036194',
'end' => '120045287',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm15684-001'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0000I6_0001' => array(
'genes_in_region' => array(
'ENSG00000103196' => array(
[maximum depth reached]
),
'ENSG00000153786' => array(
[maximum depth reached]
),
'ENSG00000260340' => array(
[maximum depth reached]
),
'ENSG00000260859' => array(
[maximum depth reached]
),
'ENSG00000265249' => 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 => 'Brain',
(int) 15 => 'Kidney',
(int) 16 => 'Heart',
(int) 17 => 'Liver',
(int) 18 => 'Ovary',
(int) 19 => 'Kidney',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis',
(int) 31 => 'Bladder',
(int) 32 => 'Brain',
(int) 33 => 'Colon',
(int) 34 => 'Kidney',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Heart',
(int) 40 => 'Bladder',
(int) 41 => 'Adipose',
(int) 42 => 'Adrenal',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Testis',
(int) 53 => 'Adrenal',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Liver',
(int) 57 => 'Lung',
(int) 58 => 'Ovary',
(int) 59 => 'Placenta',
(int) 60 => 'Testis',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Brain',
(int) 64 => 'Breast',
(int) 65 => 'Colon',
(int) 66 => 'Heart',
(int) 67 => 'Kidney',
(int) 68 => 'Liver',
(int) 69 => 'Lung',
(int) 70 => 'Ovary',
(int) 71 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0000I6_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '119992438',
'seq_end' => '120101482',
'region_length' => '109044',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031825-ENSMUSG00000031823'
)
)
$gene_el = array(
'ENST00000584136' => array(
'Adipose' => array(
'average_FPKM' => '2.095',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '6.399',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.304',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.059',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '2.603',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.271',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '3.672',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.075',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '1.504',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '87.165',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '2.300',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000265249'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '2.095',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '6.399',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.304',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.059',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '2.603',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.271',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '3.672',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.075',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '1.504',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '87.165',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '2.300',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000584136'
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
(CRISPLD2)