| Source ID |
Type |
Tax ID |
Position |
| LMO4 |
UCNEbase |
7955 |
2:23139057-23139286  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007N8_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_0007N8_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N8_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N8_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000143013' => 'LIM domain only 4',
'ENSG00000199318' => 'RNA, 5S ribosomal pseudogene 52',
'ENSG00000221222' => null,
'ENSG00000224235' => null,
'ENSG00000227290' => 'long intergenic non-protein coding RNA 1364',
'ENSG00000267272' => 'long intergenic non-protein coding RNA 1140',
'ENSG00000267561' => 'Heparan sulfate 2-O-sulfotransferase 1 {ECO:0000313|Ensembl:ENSP00000467253}',
'ENSG00000270507' => null,
'ENSG00000279778' => null,
'ENSMUSG00000028266' => 'LIM domain only 4',
'ENSMUSG00000088851' => 'predicted gene, 24728',
'ENSDARG00000054749' => 'LIM domain only 4b',
'ENSDARG00000096974' => 'si:ch211-132f21.1',
'ENSDARG00000084243' => '5S ribosomal RNA'
),
'gene_name_arr' => array(
'ENSG00000143013' => 'LMO4',
'ENSG00000199318' => 'RNA5SP52',
'ENSG00000221222' => 'AL139139.1',
'ENSG00000224235' => 'RP5-1027O11.1',
'ENSG00000227290' => 'LINC01364',
'ENSG00000267272' => 'LINC01140',
'ENSG00000267561' => 'RP5-1052I5.2',
'ENSG00000270507' => 'CTA-21C21.1',
'ENSG00000279778' => 'RP11-60A14.1',
'ENSMUSG00000028266' => 'Lmo4',
'ENSMUSG00000088851' => 'Gm24728',
'ENSDARG00000054749' => 'lmo4b',
'ENSDARG00000096974' => 'si:ch211-132f21.1',
'ENSDARG00000084243' => '5S_rRNA'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 17 => 'Brain',
(int) 29 => 'Breast',
(int) 38 => 'Colon',
(int) 46 => 'Heart',
(int) 60 => 'Kidney',
(int) 68 => 'Liver',
(int) 75 => 'Lung',
(int) 84 => 'Muscle',
(int) 93 => 'Ovary',
(int) 102 => 'Placenta',
(int) 112 => '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) 33,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000370542' => array(
'start' => '87331668',
'end' => '87345408',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LMO4-002'
),
'ENST00000370544' => array(
'start' => '87328468',
'end' => '87348923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LMO4-001'
),
'ENST00000489303' => array(
'start' => '87331781',
'end' => '87345015',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LMO4-004'
),
'ENST00000495705' => array(
'start' => '87329099',
'end' => '87339632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LMO4-003'
),
'ENST00000362448' => array(
'start' => '87453240',
'end' => '87453373',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP52-201'
),
'ENST00000408295' => array(
'start' => '87151298',
'end' => '87151445',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL139139.1-201'
),
'ENST00000437598' => array(
'start' => '87899909',
'end' => '87905714',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-1027O11.1-001'
),
'ENST00000452509' => array(
'start' => '87353524',
'end' => '87371655',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01364-001'
),
'ENST00000461990' => array(
'start' => '87129870',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-002'
),
'ENST00000467438' => array(
'start' => '87131975',
'end' => '87134595',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-004'
),
'ENST00000469312' => array(
'start' => '87129765',
'end' => '87168505',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-009'
),
'ENST00000471417' => array(
'start' => '87129854',
'end' => '87134469',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-006'
),
'ENST00000476432' => array(
'start' => '87131969',
'end' => '87134131',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-007'
),
'ENST00000484933' => array(
'start' => '87132003',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-005'
),
'ENST00000490006' => array(
'start' => '87129774',
'end' => '87169198',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-001'
),
'ENST00000587165' => array(
'start' => '87132055',
'end' => '87162137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-010'
),
'ENST00000589455' => array(
'start' => '87132055',
'end' => '87134192',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-008'
),
'ENST00000590653' => array(
'start' => '87131955',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-003'
),
'ENST00000619924' => array(
'start' => '87132002',
'end' => '87133035',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-201'
),
'ENST00000370548' => array(
'start' => '86993009',
'end' => '87169204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RP5-1052I5.2-001'
),
'ENST00000603130' => array(
'start' => '88313153',
'end' => '88313302',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTA-21C21.1-001'
),
'ENST00000623157' => array(
'start' => '87805286',
'end' => '87808372',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-60A14.1-001'
),
'ENSMUST00000120539' => array(
'start' => '144188530',
'end' => '144205220',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-001'
),
'ENSMUST00000121112' => array(
'start' => '144188632',
'end' => '144202332',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-003'
),
'ENSMUST00000121796' => array(
'start' => '144188530',
'end' => '144202317',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-002'
),
'ENSMUST00000124891' => array(
'start' => '144201623',
'end' => '144202300',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-006'
),
'ENSMUST00000134961' => array(
'start' => '144200783',
'end' => '144205180',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-004'
),
'ENSMUST00000148128' => array(
'start' => '144189062',
'end' => '144194818',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-005'
),
'ENSMUST00000158226' => array(
'start' => '143674943',
'end' => '143675067',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24728-201'
),
'ENSDART00000076997' => array(
'start' => '25668492',
'end' => '25687604',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lmo4b-001'
),
'ENSDART00000148748' => array(
'start' => '25669249',
'end' => '25687626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lmo4b-002'
),
'ENSDART00000156456' => array(
'start' => '25526811',
'end' => '25551593',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch211-132f21.1-001'
),
'ENSDART00000119643' => array(
'start' => '215250',
'end' => '215378',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.580-201'
)
),
'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_0007N8_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N8_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N8_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007N8_0001' => array(
'genes_in_region' => array(
'ENSG00000143013' => array(
[maximum depth reached]
),
'ENSG00000224235' => array(
[maximum depth reached]
),
'ENSG00000227290' => array(
[maximum depth reached]
),
'ENSG00000267561' => array(
[maximum depth reached]
),
'ENSG00000279778' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Heart',
(int) 30 => 'Kidney',
(int) 31 => 'Liver',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Brain',
(int) 36 => 'Breast',
(int) 37 => 'Heart',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Brain',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Lung',
(int) 45 => 'Testis',
(int) 46 => 'Adipose',
(int) 47 => 'Adrenal',
(int) 48 => 'Breast',
(int) 49 => 'Colon',
(int) 50 => 'Heart',
(int) 51 => 'Lung',
(int) 52 => 'Placenta',
(int) 53 => 'Colon',
(int) 54 => 'Heart',
(int) 55 => 'Liver',
(int) 56 => 'Placenta',
(int) 57 => 'Adipose',
(int) 58 => 'Adrenal',
(int) 59 => 'Bladder',
(int) 60 => 'Brain',
(int) 61 => 'Breast',
(int) 62 => 'Colon',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Lung',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis'
)
),
'CIL_0007N8_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000028266' => 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 => 'Breast',
(int) 16 => 'Heart',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Bladder',
(int) 24 => 'Brain',
(int) 25 => 'Breast',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Breast',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta'
)
),
'CIL_0007N8_0005' => array(
'genes_in_region' => array(
'ENSDARG00000054749' => array(
[maximum depth reached]
),
'ENSDARG00000096974' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Muscle',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000143013' => 'LIM domain only 4',
'ENSG00000199318' => 'RNA, 5S ribosomal pseudogene 52',
'ENSG00000221222' => null,
'ENSG00000224235' => null,
'ENSG00000227290' => 'long intergenic non-protein coding RNA 1364',
'ENSG00000267272' => 'long intergenic non-protein coding RNA 1140',
'ENSG00000267561' => 'Heparan sulfate 2-O-sulfotransferase 1 {ECO:0000313|Ensembl:ENSP00000467253}',
'ENSG00000270507' => null,
'ENSG00000279778' => null,
'ENSMUSG00000028266' => 'LIM domain only 4',
'ENSMUSG00000088851' => 'predicted gene, 24728',
'ENSDARG00000054749' => 'LIM domain only 4b',
'ENSDARG00000096974' => 'si:ch211-132f21.1',
'ENSDARG00000084243' => '5S ribosomal RNA'
)
$gene_name_arr = array(
'ENSG00000143013' => 'LMO4',
'ENSG00000199318' => 'RNA5SP52',
'ENSG00000221222' => 'AL139139.1',
'ENSG00000224235' => 'RP5-1027O11.1',
'ENSG00000227290' => 'LINC01364',
'ENSG00000267272' => 'LINC01140',
'ENSG00000267561' => 'RP5-1052I5.2',
'ENSG00000270507' => 'CTA-21C21.1',
'ENSG00000279778' => 'RP11-60A14.1',
'ENSMUSG00000028266' => 'Lmo4',
'ENSMUSG00000088851' => 'Gm24728',
'ENSDARG00000054749' => 'lmo4b',
'ENSDARG00000096974' => 'si:ch211-132f21.1',
'ENSDARG00000084243' => '5S_rRNA'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0001',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '87150228',
'seq_end' => '88462394',
'region_length' => '1312166',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '143101318',
'seq_end' => '144382743',
'region_length' => '1281425',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0003',
'tax_id' => '7955',
'chromosome' => '2',
'seq_start' => '23139057',
'seq_end' => '23139286',
'region_length' => '229',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0004',
'tax_id' => '7955',
'chromosome' => '5',
'seq_start' => '34574816',
'seq_end' => '34575288',
'region_length' => '472',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0005',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '25381261',
'seq_end' => '25718815',
'region_length' => '337554',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 5 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0006',
'tax_id' => '7955',
'chromosome' => '8',
'seq_start' => '55027279',
'seq_end' => '55027446',
'region_length' => '167',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 6 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0007',
'tax_id' => '7955',
'chromosome' => 'Zv9_scaffold3471',
'seq_start' => '185031',
'seq_end' => '588459',
'region_length' => '403428',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 17 => 'Brain',
(int) 29 => 'Breast',
(int) 38 => 'Colon',
(int) 46 => 'Heart',
(int) 60 => 'Kidney',
(int) 68 => 'Liver',
(int) 75 => 'Lung',
(int) 84 => 'Muscle',
(int) 93 => 'Ovary',
(int) 102 => 'Placenta',
(int) 112 => '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) 33
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000370542' => array(
'start' => '87331668',
'end' => '87345408',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LMO4-002'
),
'ENST00000370544' => array(
'start' => '87328468',
'end' => '87348923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LMO4-001'
),
'ENST00000489303' => array(
'start' => '87331781',
'end' => '87345015',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LMO4-004'
),
'ENST00000495705' => array(
'start' => '87329099',
'end' => '87339632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LMO4-003'
),
'ENST00000362448' => array(
'start' => '87453240',
'end' => '87453373',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP52-201'
),
'ENST00000408295' => array(
'start' => '87151298',
'end' => '87151445',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL139139.1-201'
),
'ENST00000437598' => array(
'start' => '87899909',
'end' => '87905714',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-1027O11.1-001'
),
'ENST00000452509' => array(
'start' => '87353524',
'end' => '87371655',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01364-001'
),
'ENST00000461990' => array(
'start' => '87129870',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-002'
),
'ENST00000467438' => array(
'start' => '87131975',
'end' => '87134595',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-004'
),
'ENST00000469312' => array(
'start' => '87129765',
'end' => '87168505',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-009'
),
'ENST00000471417' => array(
'start' => '87129854',
'end' => '87134469',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-006'
),
'ENST00000476432' => array(
'start' => '87131969',
'end' => '87134131',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-007'
),
'ENST00000484933' => array(
'start' => '87132003',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-005'
),
'ENST00000490006' => array(
'start' => '87129774',
'end' => '87169198',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-001'
),
'ENST00000587165' => array(
'start' => '87132055',
'end' => '87162137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-010'
),
'ENST00000589455' => array(
'start' => '87132055',
'end' => '87134192',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-008'
),
'ENST00000590653' => array(
'start' => '87131955',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-003'
),
'ENST00000619924' => array(
'start' => '87132002',
'end' => '87133035',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-201'
),
'ENST00000370548' => array(
'start' => '86993009',
'end' => '87169204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RP5-1052I5.2-001'
),
'ENST00000603130' => array(
'start' => '88313153',
'end' => '88313302',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTA-21C21.1-001'
),
'ENST00000623157' => array(
'start' => '87805286',
'end' => '87808372',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-60A14.1-001'
),
'ENSMUST00000120539' => array(
'start' => '144188530',
'end' => '144205220',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-001'
),
'ENSMUST00000121112' => array(
'start' => '144188632',
'end' => '144202332',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-003'
),
'ENSMUST00000121796' => array(
'start' => '144188530',
'end' => '144202317',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-002'
),
'ENSMUST00000124891' => array(
'start' => '144201623',
'end' => '144202300',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-006'
),
'ENSMUST00000134961' => array(
'start' => '144200783',
'end' => '144205180',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-004'
),
'ENSMUST00000148128' => array(
'start' => '144189062',
'end' => '144194818',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-005'
),
'ENSMUST00000158226' => array(
'start' => '143674943',
'end' => '143675067',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24728-201'
),
'ENSDART00000076997' => array(
'start' => '25668492',
'end' => '25687604',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lmo4b-001'
),
'ENSDART00000148748' => array(
'start' => '25669249',
'end' => '25687626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lmo4b-002'
),
'ENSDART00000156456' => array(
'start' => '25526811',
'end' => '25551593',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch211-132f21.1-001'
),
'ENSDART00000119643' => array(
'start' => '215250',
'end' => '215378',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.580-201'
)
)
$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_0007N8_0001' => array(
'genes_in_region' => array(
'ENSG00000143013' => array(
[maximum depth reached]
),
'ENSG00000224235' => array(
[maximum depth reached]
),
'ENSG00000227290' => array(
[maximum depth reached]
),
'ENSG00000267561' => array(
[maximum depth reached]
),
'ENSG00000279778' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Heart',
(int) 30 => 'Kidney',
(int) 31 => 'Liver',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Brain',
(int) 36 => 'Breast',
(int) 37 => 'Heart',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Brain',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Lung',
(int) 45 => 'Testis',
(int) 46 => 'Adipose',
(int) 47 => 'Adrenal',
(int) 48 => 'Breast',
(int) 49 => 'Colon',
(int) 50 => 'Heart',
(int) 51 => 'Lung',
(int) 52 => 'Placenta',
(int) 53 => 'Colon',
(int) 54 => 'Heart',
(int) 55 => 'Liver',
(int) 56 => 'Placenta',
(int) 57 => 'Adipose',
(int) 58 => 'Adrenal',
(int) 59 => 'Bladder',
(int) 60 => 'Brain',
(int) 61 => 'Breast',
(int) 62 => 'Colon',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Lung',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis'
)
),
'CIL_0007N8_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000028266' => 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 => 'Breast',
(int) 16 => 'Heart',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Bladder',
(int) 24 => 'Brain',
(int) 25 => 'Breast',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Breast',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta'
)
),
'CIL_0007N8_0005' => array(
'genes_in_region' => array(
'ENSDARG00000054749' => array(
[maximum depth reached]
),
'ENSDARG00000096974' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Muscle',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0003',
'tax_id' => '7955',
'chromosome' => '2',
'seq_start' => '23139057',
'seq_end' => '23139286',
'region_length' => '229',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
)
$gene_el = array(
'ENSMUST00000120539' => array(
'Adipose' => array(
'average_FPKM' => '19.553',
'stddev_FPKM' => '7.55'
),
'Adrenal' => array(
'average_FPKM' => '35.040',
'stddev_FPKM' => '6.58'
),
'Bladder' => array(
'average_FPKM' => '54.415',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '19.649',
'stddev_FPKM' => '6.43'
),
'Breast' => array(
'average_FPKM' => '15.750',
'stddev_FPKM' => '5.84'
),
'Colon' => array(
'average_FPKM' => '11.277',
'stddev_FPKM' => '1.47'
),
'Heart' => array(
'average_FPKM' => '3.536',
'stddev_FPKM' => '1.00'
),
'Kidney' => array(
'average_FPKM' => '13.602',
'stddev_FPKM' => '4.02'
),
'Liver' => array(
'average_FPKM' => '5.800',
'stddev_FPKM' => '5.18'
),
'Lung' => array(
'average_FPKM' => '12.496',
'stddev_FPKM' => '1.22'
),
'Muscle' => array(
'average_FPKM' => '5.350',
'stddev_FPKM' => '1.42'
),
'Ovary' => array(
'average_FPKM' => '19.151',
'stddev_FPKM' => '6.16'
),
'Placenta' => array(
'average_FPKM' => '4.006',
'stddev_FPKM' => '3.38'
),
'Testis' => array(
'average_FPKM' => '1.431',
'stddev_FPKM' => '0.76'
)
),
'ENSMUST00000121112' => array(
'Brain' => array(
'average_FPKM' => '6.490',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '13.199',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3.361',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '5.887',
'stddev_FPKM' => '0.73'
),
'Muscle' => array(
'average_FPKM' => '3.039',
'stddev_FPKM' => '0.45'
),
'Ovary' => array(
'average_FPKM' => '3.776',
'stddev_FPKM' => '2.06'
),
'Placenta' => array(
'average_FPKM' => '1.043',
'stddev_FPKM' => '0.17'
)
),
'ENSMUST00000121796' => array(
'Adipose' => array(
'average_FPKM' => '48.538',
'stddev_FPKM' => '22.92'
),
'Adrenal' => array(
'average_FPKM' => '46.103',
'stddev_FPKM' => '9.65'
),
'Bladder' => array(
'average_FPKM' => '57.334',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '16.284',
'stddev_FPKM' => '8.05'
),
'Breast' => array(
'average_FPKM' => '35.879',
'stddev_FPKM' => '5.57'
),
'Colon' => array(
'average_FPKM' => '13.500',
'stddev_FPKM' => '3.35'
),
'Heart' => array(
'average_FPKM' => '12.799',
'stddev_FPKM' => '2.44'
),
'Kidney' => array(
'average_FPKM' => '40.969',
'stddev_FPKM' => '4.19'
),
'Liver' => array(
'average_FPKM' => '6.121',
'stddev_FPKM' => '1.39'
),
'Lung' => array(
'average_FPKM' => '30.711',
'stddev_FPKM' => '5.64'
),
'Muscle' => array(
'average_FPKM' => '3.325',
'stddev_FPKM' => '1.92'
),
'Ovary' => array(
'average_FPKM' => '24.258',
'stddev_FPKM' => '6.42'
),
'Placenta' => array(
'average_FPKM' => '4.531',
'stddev_FPKM' => '1.97'
),
'Testis' => array(
'average_FPKM' => '4.126',
'stddev_FPKM' => '1.88'
)
),
'ENSMUST00000124891' => array(),
'ENSMUST00000134961' => array(),
'ENSMUST00000148128' => array(
'Breast' => array(
'average_FPKM' => '10.593',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '12.248',
'stddev_FPKM' => '0.15'
),
'Placenta' => array(
'average_FPKM' => '3.990',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000028266'
$is_first = false
$tran_el = array(
'Breast' => array(
'average_FPKM' => '10.593',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '12.248',
'stddev_FPKM' => '0.15'
),
'Placenta' => array(
'average_FPKM' => '3.990',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000148128'include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007N8_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N8_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N8_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000143013' => 'LIM domain only 4',
'ENSG00000199318' => 'RNA, 5S ribosomal pseudogene 52',
'ENSG00000221222' => null,
'ENSG00000224235' => null,
'ENSG00000227290' => 'long intergenic non-protein coding RNA 1364',
'ENSG00000267272' => 'long intergenic non-protein coding RNA 1140',
'ENSG00000267561' => 'Heparan sulfate 2-O-sulfotransferase 1 {ECO:0000313|Ensembl:ENSP00000467253}',
'ENSG00000270507' => null,
'ENSG00000279778' => null,
'ENSMUSG00000028266' => 'LIM domain only 4',
'ENSMUSG00000088851' => 'predicted gene, 24728',
'ENSDARG00000054749' => 'LIM domain only 4b',
'ENSDARG00000096974' => 'si:ch211-132f21.1',
'ENSDARG00000084243' => '5S ribosomal RNA'
),
'gene_name_arr' => array(
'ENSG00000143013' => 'LMO4',
'ENSG00000199318' => 'RNA5SP52',
'ENSG00000221222' => 'AL139139.1',
'ENSG00000224235' => 'RP5-1027O11.1',
'ENSG00000227290' => 'LINC01364',
'ENSG00000267272' => 'LINC01140',
'ENSG00000267561' => 'RP5-1052I5.2',
'ENSG00000270507' => 'CTA-21C21.1',
'ENSG00000279778' => 'RP11-60A14.1',
'ENSMUSG00000028266' => 'Lmo4',
'ENSMUSG00000088851' => 'Gm24728',
'ENSDARG00000054749' => 'lmo4b',
'ENSDARG00000096974' => 'si:ch211-132f21.1',
'ENSDARG00000084243' => '5S_rRNA'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 17 => 'Brain',
(int) 29 => 'Breast',
(int) 38 => 'Colon',
(int) 46 => 'Heart',
(int) 60 => 'Kidney',
(int) 68 => 'Liver',
(int) 75 => 'Lung',
(int) 84 => 'Muscle',
(int) 93 => 'Ovary',
(int) 102 => 'Placenta',
(int) 112 => '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) 33,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000370542' => array(
'start' => '87331668',
'end' => '87345408',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LMO4-002'
),
'ENST00000370544' => array(
'start' => '87328468',
'end' => '87348923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LMO4-001'
),
'ENST00000489303' => array(
'start' => '87331781',
'end' => '87345015',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LMO4-004'
),
'ENST00000495705' => array(
'start' => '87329099',
'end' => '87339632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LMO4-003'
),
'ENST00000362448' => array(
'start' => '87453240',
'end' => '87453373',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP52-201'
),
'ENST00000408295' => array(
'start' => '87151298',
'end' => '87151445',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL139139.1-201'
),
'ENST00000437598' => array(
'start' => '87899909',
'end' => '87905714',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-1027O11.1-001'
),
'ENST00000452509' => array(
'start' => '87353524',
'end' => '87371655',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01364-001'
),
'ENST00000461990' => array(
'start' => '87129870',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-002'
),
'ENST00000467438' => array(
'start' => '87131975',
'end' => '87134595',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-004'
),
'ENST00000469312' => array(
'start' => '87129765',
'end' => '87168505',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-009'
),
'ENST00000471417' => array(
'start' => '87129854',
'end' => '87134469',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-006'
),
'ENST00000476432' => array(
'start' => '87131969',
'end' => '87134131',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-007'
),
'ENST00000484933' => array(
'start' => '87132003',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-005'
),
'ENST00000490006' => array(
'start' => '87129774',
'end' => '87169198',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-001'
),
'ENST00000587165' => array(
'start' => '87132055',
'end' => '87162137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-010'
),
'ENST00000589455' => array(
'start' => '87132055',
'end' => '87134192',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-008'
),
'ENST00000590653' => array(
'start' => '87131955',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-003'
),
'ENST00000619924' => array(
'start' => '87132002',
'end' => '87133035',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-201'
),
'ENST00000370548' => array(
'start' => '86993009',
'end' => '87169204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RP5-1052I5.2-001'
),
'ENST00000603130' => array(
'start' => '88313153',
'end' => '88313302',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTA-21C21.1-001'
),
'ENST00000623157' => array(
'start' => '87805286',
'end' => '87808372',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-60A14.1-001'
),
'ENSMUST00000120539' => array(
'start' => '144188530',
'end' => '144205220',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-001'
),
'ENSMUST00000121112' => array(
'start' => '144188632',
'end' => '144202332',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-003'
),
'ENSMUST00000121796' => array(
'start' => '144188530',
'end' => '144202317',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-002'
),
'ENSMUST00000124891' => array(
'start' => '144201623',
'end' => '144202300',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-006'
),
'ENSMUST00000134961' => array(
'start' => '144200783',
'end' => '144205180',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-004'
),
'ENSMUST00000148128' => array(
'start' => '144189062',
'end' => '144194818',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-005'
),
'ENSMUST00000158226' => array(
'start' => '143674943',
'end' => '143675067',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24728-201'
),
'ENSDART00000076997' => array(
'start' => '25668492',
'end' => '25687604',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lmo4b-001'
),
'ENSDART00000148748' => array(
'start' => '25669249',
'end' => '25687626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lmo4b-002'
),
'ENSDART00000156456' => array(
'start' => '25526811',
'end' => '25551593',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch211-132f21.1-001'
),
'ENSDART00000119643' => array(
'start' => '215250',
'end' => '215378',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.580-201'
)
),
'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_0007N8_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N8_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007N8_0005' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007N8_0001' => array(
'genes_in_region' => array(
'ENSG00000143013' => array(
[maximum depth reached]
),
'ENSG00000224235' => array(
[maximum depth reached]
),
'ENSG00000227290' => array(
[maximum depth reached]
),
'ENSG00000267561' => array(
[maximum depth reached]
),
'ENSG00000279778' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Heart',
(int) 30 => 'Kidney',
(int) 31 => 'Liver',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Brain',
(int) 36 => 'Breast',
(int) 37 => 'Heart',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Brain',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Lung',
(int) 45 => 'Testis',
(int) 46 => 'Adipose',
(int) 47 => 'Adrenal',
(int) 48 => 'Breast',
(int) 49 => 'Colon',
(int) 50 => 'Heart',
(int) 51 => 'Lung',
(int) 52 => 'Placenta',
(int) 53 => 'Colon',
(int) 54 => 'Heart',
(int) 55 => 'Liver',
(int) 56 => 'Placenta',
(int) 57 => 'Adipose',
(int) 58 => 'Adrenal',
(int) 59 => 'Bladder',
(int) 60 => 'Brain',
(int) 61 => 'Breast',
(int) 62 => 'Colon',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Lung',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis'
)
),
'CIL_0007N8_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000028266' => 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 => 'Breast',
(int) 16 => 'Heart',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Bladder',
(int) 24 => 'Brain',
(int) 25 => 'Breast',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Breast',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta'
)
),
'CIL_0007N8_0005' => array(
'genes_in_region' => array(
'ENSDARG00000054749' => array(
[maximum depth reached]
),
'ENSDARG00000096974' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Muscle',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000143013' => 'LIM domain only 4',
'ENSG00000199318' => 'RNA, 5S ribosomal pseudogene 52',
'ENSG00000221222' => null,
'ENSG00000224235' => null,
'ENSG00000227290' => 'long intergenic non-protein coding RNA 1364',
'ENSG00000267272' => 'long intergenic non-protein coding RNA 1140',
'ENSG00000267561' => 'Heparan sulfate 2-O-sulfotransferase 1 {ECO:0000313|Ensembl:ENSP00000467253}',
'ENSG00000270507' => null,
'ENSG00000279778' => null,
'ENSMUSG00000028266' => 'LIM domain only 4',
'ENSMUSG00000088851' => 'predicted gene, 24728',
'ENSDARG00000054749' => 'LIM domain only 4b',
'ENSDARG00000096974' => 'si:ch211-132f21.1',
'ENSDARG00000084243' => '5S ribosomal RNA'
)
$gene_name_arr = array(
'ENSG00000143013' => 'LMO4',
'ENSG00000199318' => 'RNA5SP52',
'ENSG00000221222' => 'AL139139.1',
'ENSG00000224235' => 'RP5-1027O11.1',
'ENSG00000227290' => 'LINC01364',
'ENSG00000267272' => 'LINC01140',
'ENSG00000267561' => 'RP5-1052I5.2',
'ENSG00000270507' => 'CTA-21C21.1',
'ENSG00000279778' => 'RP11-60A14.1',
'ENSMUSG00000028266' => 'Lmo4',
'ENSMUSG00000088851' => 'Gm24728',
'ENSDARG00000054749' => 'lmo4b',
'ENSDARG00000096974' => 'si:ch211-132f21.1',
'ENSDARG00000084243' => '5S_rRNA'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0001',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '87150228',
'seq_end' => '88462394',
'region_length' => '1312166',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0002',
'tax_id' => '10090',
'chromosome' => '3',
'seq_start' => '143101318',
'seq_end' => '144382743',
'region_length' => '1281425',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0003',
'tax_id' => '7955',
'chromosome' => '2',
'seq_start' => '23139057',
'seq_end' => '23139286',
'region_length' => '229',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0004',
'tax_id' => '7955',
'chromosome' => '5',
'seq_start' => '34574816',
'seq_end' => '34575288',
'region_length' => '472',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0005',
'tax_id' => '7955',
'chromosome' => '6',
'seq_start' => '25381261',
'seq_end' => '25718815',
'region_length' => '337554',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 5 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0006',
'tax_id' => '7955',
'chromosome' => '8',
'seq_start' => '55027279',
'seq_end' => '55027446',
'region_length' => '167',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
),
(int) 6 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0007',
'tax_id' => '7955',
'chromosome' => 'Zv9_scaffold3471',
'seq_start' => '185031',
'seq_end' => '588459',
'region_length' => '403428',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 17 => 'Brain',
(int) 29 => 'Breast',
(int) 38 => 'Colon',
(int) 46 => 'Heart',
(int) 60 => 'Kidney',
(int) 68 => 'Liver',
(int) 75 => 'Lung',
(int) 84 => 'Muscle',
(int) 93 => 'Ovary',
(int) 102 => 'Placenta',
(int) 112 => '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) 33
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000370542' => array(
'start' => '87331668',
'end' => '87345408',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LMO4-002'
),
'ENST00000370544' => array(
'start' => '87328468',
'end' => '87348923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LMO4-001'
),
'ENST00000489303' => array(
'start' => '87331781',
'end' => '87345015',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LMO4-004'
),
'ENST00000495705' => array(
'start' => '87329099',
'end' => '87339632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LMO4-003'
),
'ENST00000362448' => array(
'start' => '87453240',
'end' => '87453373',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP52-201'
),
'ENST00000408295' => array(
'start' => '87151298',
'end' => '87151445',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL139139.1-201'
),
'ENST00000437598' => array(
'start' => '87899909',
'end' => '87905714',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP5-1027O11.1-001'
),
'ENST00000452509' => array(
'start' => '87353524',
'end' => '87371655',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01364-001'
),
'ENST00000461990' => array(
'start' => '87129870',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-002'
),
'ENST00000467438' => array(
'start' => '87131975',
'end' => '87134595',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-004'
),
'ENST00000469312' => array(
'start' => '87129765',
'end' => '87168505',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-009'
),
'ENST00000471417' => array(
'start' => '87129854',
'end' => '87134469',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-006'
),
'ENST00000476432' => array(
'start' => '87131969',
'end' => '87134131',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-007'
),
'ENST00000484933' => array(
'start' => '87132003',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-005'
),
'ENST00000490006' => array(
'start' => '87129774',
'end' => '87169198',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-001'
),
'ENST00000587165' => array(
'start' => '87132055',
'end' => '87162137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-010'
),
'ENST00000589455' => array(
'start' => '87132055',
'end' => '87134192',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-008'
),
'ENST00000590653' => array(
'start' => '87131955',
'end' => '87136669',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-003'
),
'ENST00000619924' => array(
'start' => '87132002',
'end' => '87133035',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC01140-201'
),
'ENST00000370548' => array(
'start' => '86993009',
'end' => '87169204',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RP5-1052I5.2-001'
),
'ENST00000603130' => array(
'start' => '88313153',
'end' => '88313302',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTA-21C21.1-001'
),
'ENST00000623157' => array(
'start' => '87805286',
'end' => '87808372',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-60A14.1-001'
),
'ENSMUST00000120539' => array(
'start' => '144188530',
'end' => '144205220',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-001'
),
'ENSMUST00000121112' => array(
'start' => '144188632',
'end' => '144202332',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-003'
),
'ENSMUST00000121796' => array(
'start' => '144188530',
'end' => '144202317',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lmo4-002'
),
'ENSMUST00000124891' => array(
'start' => '144201623',
'end' => '144202300',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-006'
),
'ENSMUST00000134961' => array(
'start' => '144200783',
'end' => '144205180',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-004'
),
'ENSMUST00000148128' => array(
'start' => '144189062',
'end' => '144194818',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Lmo4-005'
),
'ENSMUST00000158226' => array(
'start' => '143674943',
'end' => '143675067',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24728-201'
),
'ENSDART00000076997' => array(
'start' => '25668492',
'end' => '25687604',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lmo4b-001'
),
'ENSDART00000148748' => array(
'start' => '25669249',
'end' => '25687626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lmo4b-002'
),
'ENSDART00000156456' => array(
'start' => '25526811',
'end' => '25551593',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch211-132f21.1-001'
),
'ENSDART00000119643' => array(
'start' => '215250',
'end' => '215378',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.580-201'
)
)
$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_0007N8_0001' => array(
'genes_in_region' => array(
'ENSG00000143013' => array(
[maximum depth reached]
),
'ENSG00000224235' => array(
[maximum depth reached]
),
'ENSG00000227290' => array(
[maximum depth reached]
),
'ENSG00000267561' => array(
[maximum depth reached]
),
'ENSG00000279778' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Heart',
(int) 30 => 'Kidney',
(int) 31 => 'Liver',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Brain',
(int) 36 => 'Breast',
(int) 37 => 'Heart',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Brain',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Lung',
(int) 45 => 'Testis',
(int) 46 => 'Adipose',
(int) 47 => 'Adrenal',
(int) 48 => 'Breast',
(int) 49 => 'Colon',
(int) 50 => 'Heart',
(int) 51 => 'Lung',
(int) 52 => 'Placenta',
(int) 53 => 'Colon',
(int) 54 => 'Heart',
(int) 55 => 'Liver',
(int) 56 => 'Placenta',
(int) 57 => 'Adipose',
(int) 58 => 'Adrenal',
(int) 59 => 'Bladder',
(int) 60 => 'Brain',
(int) 61 => 'Breast',
(int) 62 => 'Colon',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Lung',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis'
)
),
'CIL_0007N8_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000028266' => 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 => 'Breast',
(int) 16 => 'Heart',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Bladder',
(int) 24 => 'Brain',
(int) 25 => 'Breast',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Breast',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta'
)
),
'CIL_0007N8_0005' => array(
'genes_in_region' => array(
'ENSDARG00000054749' => array(
[maximum depth reached]
),
'ENSDARG00000096974' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Muscle',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007N8_0003',
'tax_id' => '7955',
'chromosome' => '2',
'seq_start' => '23139057',
'seq_end' => '23139286',
'region_length' => '229',
'region_type' => 'UCNEbase',
'el_id' => 'LMO4'
)
)
$gene_el = array(
'ENSMUST00000120539' => array(
'Adipose' => array(
'average_FPKM' => '19.553',
'stddev_FPKM' => '7.55'
),
'Adrenal' => array(
'average_FPKM' => '35.040',
'stddev_FPKM' => '6.58'
),
'Bladder' => array(
'average_FPKM' => '54.415',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '19.649',
'stddev_FPKM' => '6.43'
),
'Breast' => array(
'average_FPKM' => '15.750',
'stddev_FPKM' => '5.84'
),
'Colon' => array(
'average_FPKM' => '11.277',
'stddev_FPKM' => '1.47'
),
'Heart' => array(
'average_FPKM' => '3.536',
'stddev_FPKM' => '1.00'
),
'Kidney' => array(
'average_FPKM' => '13.602',
'stddev_FPKM' => '4.02'
),
'Liver' => array(
'average_FPKM' => '5.800',
'stddev_FPKM' => '5.18'
),
'Lung' => array(
'average_FPKM' => '12.496',
'stddev_FPKM' => '1.22'
),
'Muscle' => array(
'average_FPKM' => '5.350',
'stddev_FPKM' => '1.42'
),
'Ovary' => array(
'average_FPKM' => '19.151',
'stddev_FPKM' => '6.16'
),
'Placenta' => array(
'average_FPKM' => '4.006',
'stddev_FPKM' => '3.38'
),
'Testis' => array(
'average_FPKM' => '1.431',
'stddev_FPKM' => '0.76'
)
),
'ENSMUST00000121112' => array(
'Brain' => array(
'average_FPKM' => '6.490',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '13.199',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3.361',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '5.887',
'stddev_FPKM' => '0.73'
),
'Muscle' => array(
'average_FPKM' => '3.039',
'stddev_FPKM' => '0.45'
),
'Ovary' => array(
'average_FPKM' => '3.776',
'stddev_FPKM' => '2.06'
),
'Placenta' => array(
'average_FPKM' => '1.043',
'stddev_FPKM' => '0.17'
)
),
'ENSMUST00000121796' => array(
'Adipose' => array(
'average_FPKM' => '48.538',
'stddev_FPKM' => '22.92'
),
'Adrenal' => array(
'average_FPKM' => '46.103',
'stddev_FPKM' => '9.65'
),
'Bladder' => array(
'average_FPKM' => '57.334',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '16.284',
'stddev_FPKM' => '8.05'
),
'Breast' => array(
'average_FPKM' => '35.879',
'stddev_FPKM' => '5.57'
),
'Colon' => array(
'average_FPKM' => '13.500',
'stddev_FPKM' => '3.35'
),
'Heart' => array(
'average_FPKM' => '12.799',
'stddev_FPKM' => '2.44'
),
'Kidney' => array(
'average_FPKM' => '40.969',
'stddev_FPKM' => '4.19'
),
'Liver' => array(
'average_FPKM' => '6.121',
'stddev_FPKM' => '1.39'
),
'Lung' => array(
'average_FPKM' => '30.711',
'stddev_FPKM' => '5.64'
),
'Muscle' => array(
'average_FPKM' => '3.325',
'stddev_FPKM' => '1.92'
),
'Ovary' => array(
'average_FPKM' => '24.258',
'stddev_FPKM' => '6.42'
),
'Placenta' => array(
'average_FPKM' => '4.531',
'stddev_FPKM' => '1.97'
),
'Testis' => array(
'average_FPKM' => '4.126',
'stddev_FPKM' => '1.88'
)
),
'ENSMUST00000124891' => array(),
'ENSMUST00000134961' => array(),
'ENSMUST00000148128' => array(
'Breast' => array(
'average_FPKM' => '10.593',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '12.248',
'stddev_FPKM' => '0.15'
),
'Placenta' => array(
'average_FPKM' => '3.990',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000028266'
$is_first = false
$tran_el = array(
'Breast' => array(
'average_FPKM' => '10.593',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '12.248',
'stddev_FPKM' => '0.15'
),
'Placenta' => array(
'average_FPKM' => '3.990',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000148128'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
(LMO4)