Institute of Cardiovascular Regeneration Webtool Repository

CIL_00013G_0001 (Click to Hide/Show)

Source ID	Type	Tax ID	Position
ENSDARG00000063911-ENSDARG00000063912	CGP	7955	MT:9052-10520
Gene	Transcript	Position	Biotype
ENSDARG00000063910 (mt-atp8) ATP synthase 8, mitochondrial	ENSDART00000093611 (mt-atp8-201)	8894-9058	protein_coding
ENSDARG00000063911 (mt-atp6) ATP synthase 6, mitochondrial	ENSDART00000093612 (mt-atp6-201)	9052-9735	protein_coding
ENSDARG00000063912 (mt-co3) cytochrome c oxidase III, mitochondrial	ENSDART00000093613 (mt-co3-201)	9735-10520	protein_coding

CIL_00013G_0002 (Click to Hide/Show)

Notice (8): Undefined index: CIL_00013G_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_00013G_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_00013G_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSDARG00000063910' => 'ATP synthase 8, mitochondrial',
		'ENSDARG00000063911' => 'ATP synthase 6, mitochondrial',
		'ENSDARG00000063912' => 'cytochrome c oxidase III, mitochondrial',
		'ENSDARG00000081758' => null,
		'ENSG00000198899' => 'mitochondrially encoded ATP synthase 6',
		'ENSG00000198938' => 'mitochondrially encoded cytochrome c oxidase III',
		'ENSG00000228253' => 'mitochondrially encoded ATP synthase 8',
		'ENSMUSG00000064356' => 'mitochondrially encoded ATP synthase 8',
		'ENSMUSG00000064357' => 'mitochondrially encoded ATP synthase 6',
		'ENSMUSG00000064358' => 'mitochondrially encoded cytochrome c oxidase III'
	),
	'gene_name_arr' => array(
		'ENSDARG00000063910' => 'mt-atp8',
		'ENSDARG00000063911' => 'mt-atp6',
		'ENSDARG00000063912' => 'mt-co3',
		'ENSDARG00000081758' => 'AC024175.12',
		'ENSG00000198899' => 'MT-ATP6',
		'ENSG00000198938' => 'MT-CO3',
		'ENSG00000228253' => 'MT-ATP8',
		'ENSMUSG00000064356' => 'mt-Atp8',
		'ENSMUSG00000064357' => 'mt-Atp6',
		'ENSMUSG00000064358' => 'mt-Co3'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 4 => 'Brain',
		(int) 7 => 'Breast',
		(int) 9 => 'Colon',
		(int) 11 => 'Heart',
		(int) 14 => 'Kidney',
		(int) 19 => 'Liver',
		(int) 23 => 'Lung',
		(int) 25 => 'Muscle',
		(int) 27 => 'Ovary',
		(int) 30 => 'Placenta',
		(int) 31 => '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) 10,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENSDART00000093611' => array(
			'start' => '8894',
			'end' => '9058',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-atp8-201'
		),
		'ENSDART00000093612' => array(
			'start' => '9052',
			'end' => '9735',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-atp6-201'
		),
		'ENSDART00000093613' => array(
			'start' => '9735',
			'end' => '10520',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-co3-201'
		),
		'ENSDART00000116044' => array(
			'start' => '10520',
			'end' => '10589',
			'transcript_biotype' => 'Mt_tRNA',
			'transcript_name' => 'AC024175.12-201'
		),
		'ENST00000361899' => array(
			'start' => '8527',
			'end' => '9207',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'MT-ATP6-201'
		),
		'ENST00000362079' => array(
			'start' => '9207',
			'end' => '9990',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'MT-CO3-201'
		),
		'ENST00000361851' => array(
			'start' => '8366',
			'end' => '8572',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'MT-ATP8-201'
		),
		'ENSMUST00000082407' => array(
			'start' => '7766',
			'end' => '7969',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-Atp8-201'
		),
		'ENSMUST00000082408' => array(
			'start' => '7927',
			'end' => '8607',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-Atp6-201'
		),
		'ENSMUST00000082409' => array(
			'start' => '8607',
			'end' => '9390',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-Co3-201'
		)
	),
	'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_00013G_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_00013G_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00013G_0001' => array(
		'genes_in_region' => array(
			'ENSDARG00000063910' => array(
				[maximum depth reached]
			),
			'ENSDARG00000063911' => array(
				[maximum depth reached]
			),
			'ENSDARG00000063912' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Heart',
			(int) 1 => 'Kidney',
			(int) 2 => 'Brain',
			(int) 3 => 'Heart',
			(int) 4 => 'Kidney',
			(int) 5 => 'Liver',
			(int) 6 => 'Muscle',
			(int) 7 => 'Brain',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle'
		)
	),
	'CIL_00013G_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000064356' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000064357' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000064358' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Kidney',
			(int) 6 => 'Liver',
			(int) 7 => 'Lung',
			(int) 8 => 'Ovary',
			(int) 9 => 'Placenta',
			(int) 10 => 'Testis',
			(int) 11 => 'Adipose',
			(int) 12 => 'Adrenal',
			(int) 13 => 'Breast',
			(int) 14 => 'Colon',
			(int) 15 => 'Kidney',
			(int) 16 => 'Liver',
			(int) 17 => 'Lung',
			(int) 18 => 'Ovary',
			(int) 19 => 'Ovary'
		)
	)
)
$gene_desc_arr = array(
	'ENSDARG00000063910' => 'ATP synthase 8, mitochondrial',
	'ENSDARG00000063911' => 'ATP synthase 6, mitochondrial',
	'ENSDARG00000063912' => 'cytochrome c oxidase III, mitochondrial',
	'ENSDARG00000081758' => null,
	'ENSG00000198899' => 'mitochondrially encoded ATP synthase 6',
	'ENSG00000198938' => 'mitochondrially encoded cytochrome c oxidase III',
	'ENSG00000228253' => 'mitochondrially encoded ATP synthase 8',
	'ENSMUSG00000064356' => 'mitochondrially encoded ATP synthase 8',
	'ENSMUSG00000064357' => 'mitochondrially encoded ATP synthase 6',
	'ENSMUSG00000064358' => 'mitochondrially encoded cytochrome c oxidase III'
)
$gene_name_arr = array(
	'ENSDARG00000063910' => 'mt-atp8',
	'ENSDARG00000063911' => 'mt-atp6',
	'ENSDARG00000063912' => 'mt-co3',
	'ENSDARG00000081758' => 'AC024175.12',
	'ENSG00000198899' => 'MT-ATP6',
	'ENSG00000198938' => 'MT-CO3',
	'ENSG00000228253' => 'MT-ATP8',
	'ENSMUSG00000064356' => 'mt-Atp8',
	'ENSMUSG00000064357' => 'mt-Atp6',
	'ENSMUSG00000064358' => 'mt-Co3'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00013G_0001',
			'tax_id' => '7955',
			'chromosome' => 'MT',
			'seq_start' => '9052',
			'seq_end' => '10520',
			'region_length' => '1468',
			'region_type' => 'CGP',
			'el_id' => 'ENSDARG00000063911-ENSDARG00000063912'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00013G_0002',
			'tax_id' => '9606',
			'chromosome' => 'MT',
			'seq_start' => '8527',
			'seq_end' => '9990',
			'region_length' => '1463',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000198899-ENSG00000198938'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00013G_0003',
			'tax_id' => '10090',
			'chromosome' => 'MT',
			'seq_start' => '7927',
			'seq_end' => '9390',
			'region_length' => '1463',
			'region_type' => 'CGP',
			'el_id' => 'ENSMUSG00000064357-ENSMUSG00000064358'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 4 => 'Brain',
	(int) 7 => 'Breast',
	(int) 9 => 'Colon',
	(int) 11 => 'Heart',
	(int) 14 => 'Kidney',
	(int) 19 => 'Liver',
	(int) 23 => 'Lung',
	(int) 25 => 'Muscle',
	(int) 27 => 'Ovary',
	(int) 30 => 'Placenta',
	(int) 31 => '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) 10
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENSDART00000093611' => array(
		'start' => '8894',
		'end' => '9058',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-atp8-201'
	),
	'ENSDART00000093612' => array(
		'start' => '9052',
		'end' => '9735',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-atp6-201'
	),
	'ENSDART00000093613' => array(
		'start' => '9735',
		'end' => '10520',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-co3-201'
	),
	'ENSDART00000116044' => array(
		'start' => '10520',
		'end' => '10589',
		'transcript_biotype' => 'Mt_tRNA',
		'transcript_name' => 'AC024175.12-201'
	),
	'ENST00000361899' => array(
		'start' => '8527',
		'end' => '9207',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'MT-ATP6-201'
	),
	'ENST00000362079' => array(
		'start' => '9207',
		'end' => '9990',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'MT-CO3-201'
	),
	'ENST00000361851' => array(
		'start' => '8366',
		'end' => '8572',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'MT-ATP8-201'
	),
	'ENSMUST00000082407' => array(
		'start' => '7766',
		'end' => '7969',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-Atp8-201'
	),
	'ENSMUST00000082408' => array(
		'start' => '7927',
		'end' => '8607',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-Atp6-201'
	),
	'ENSMUST00000082409' => array(
		'start' => '8607',
		'end' => '9390',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-Co3-201'
	)
)
$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_00013G_0001' => array(
		'genes_in_region' => array(
			'ENSDARG00000063910' => array(
				[maximum depth reached]
			),
			'ENSDARG00000063911' => array(
				[maximum depth reached]
			),
			'ENSDARG00000063912' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Heart',
			(int) 1 => 'Kidney',
			(int) 2 => 'Brain',
			(int) 3 => 'Heart',
			(int) 4 => 'Kidney',
			(int) 5 => 'Liver',
			(int) 6 => 'Muscle',
			(int) 7 => 'Brain',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle'
		)
	),
	'CIL_00013G_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000064356' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000064357' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000064358' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Kidney',
			(int) 6 => 'Liver',
			(int) 7 => 'Lung',
			(int) 8 => 'Ovary',
			(int) 9 => 'Placenta',
			(int) 10 => 'Testis',
			(int) 11 => 'Adipose',
			(int) 12 => 'Adrenal',
			(int) 13 => 'Breast',
			(int) 14 => 'Colon',
			(int) 15 => 'Kidney',
			(int) 16 => 'Liver',
			(int) 17 => 'Lung',
			(int) 18 => 'Ovary',
			(int) 19 => 'Ovary'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00013G_0002',
		'tax_id' => '9606',
		'chromosome' => 'MT',
		'seq_start' => '8527',
		'seq_end' => '9990',
		'region_length' => '1463',
		'region_type' => 'CGP',
		'el_id' => 'ENSG00000198899-ENSG00000198938'
	)
)
$gene_el = array(
	'ENSDART00000093613' => array(
		'Brain' => array(
			'average_FPKM' => '9637.060',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '1261.900',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '2686.317',
			'stddev_FPKM' => '1995.03'
		),
		'Liver' => array(
			'average_FPKM' => '592.049',
			'stddev_FPKM' => '0.00'
		),
		'Muscle' => array(
			'average_FPKM' => '6483.380',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSDARG00000063912'
$is_first = false
$tran_el = array(
	'Brain' => array(
		'average_FPKM' => '9637.060',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '1261.900',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '2686.317',
		'stddev_FPKM' => '1995.03'
	),
	'Liver' => array(
		'average_FPKM' => '592.049',
		'stddev_FPKM' => '0.00'
	),
	'Muscle' => array(
		'average_FPKM' => '6483.380',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENSDART00000093613'
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_00013G_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_00013G_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSDARG00000063910' => 'ATP synthase 8, mitochondrial',
		'ENSDARG00000063911' => 'ATP synthase 6, mitochondrial',
		'ENSDARG00000063912' => 'cytochrome c oxidase III, mitochondrial',
		'ENSDARG00000081758' => null,
		'ENSG00000198899' => 'mitochondrially encoded ATP synthase 6',
		'ENSG00000198938' => 'mitochondrially encoded cytochrome c oxidase III',
		'ENSG00000228253' => 'mitochondrially encoded ATP synthase 8',
		'ENSMUSG00000064356' => 'mitochondrially encoded ATP synthase 8',
		'ENSMUSG00000064357' => 'mitochondrially encoded ATP synthase 6',
		'ENSMUSG00000064358' => 'mitochondrially encoded cytochrome c oxidase III'
	),
	'gene_name_arr' => array(
		'ENSDARG00000063910' => 'mt-atp8',
		'ENSDARG00000063911' => 'mt-atp6',
		'ENSDARG00000063912' => 'mt-co3',
		'ENSDARG00000081758' => 'AC024175.12',
		'ENSG00000198899' => 'MT-ATP6',
		'ENSG00000198938' => 'MT-CO3',
		'ENSG00000228253' => 'MT-ATP8',
		'ENSMUSG00000064356' => 'mt-Atp8',
		'ENSMUSG00000064357' => 'mt-Atp6',
		'ENSMUSG00000064358' => 'mt-Co3'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 4 => 'Brain',
		(int) 7 => 'Breast',
		(int) 9 => 'Colon',
		(int) 11 => 'Heart',
		(int) 14 => 'Kidney',
		(int) 19 => 'Liver',
		(int) 23 => 'Lung',
		(int) 25 => 'Muscle',
		(int) 27 => 'Ovary',
		(int) 30 => 'Placenta',
		(int) 31 => '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) 10,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENSDART00000093611' => array(
			'start' => '8894',
			'end' => '9058',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-atp8-201'
		),
		'ENSDART00000093612' => array(
			'start' => '9052',
			'end' => '9735',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-atp6-201'
		),
		'ENSDART00000093613' => array(
			'start' => '9735',
			'end' => '10520',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-co3-201'
		),
		'ENSDART00000116044' => array(
			'start' => '10520',
			'end' => '10589',
			'transcript_biotype' => 'Mt_tRNA',
			'transcript_name' => 'AC024175.12-201'
		),
		'ENST00000361899' => array(
			'start' => '8527',
			'end' => '9207',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'MT-ATP6-201'
		),
		'ENST00000362079' => array(
			'start' => '9207',
			'end' => '9990',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'MT-CO3-201'
		),
		'ENST00000361851' => array(
			'start' => '8366',
			'end' => '8572',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'MT-ATP8-201'
		),
		'ENSMUST00000082407' => array(
			'start' => '7766',
			'end' => '7969',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-Atp8-201'
		),
		'ENSMUST00000082408' => array(
			'start' => '7927',
			'end' => '8607',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-Atp6-201'
		),
		'ENSMUST00000082409' => array(
			'start' => '8607',
			'end' => '9390',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'mt-Co3-201'
		)
	),
	'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_00013G_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_00013G_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00013G_0001' => array(
		'genes_in_region' => array(
			'ENSDARG00000063910' => array(
				[maximum depth reached]
			),
			'ENSDARG00000063911' => array(
				[maximum depth reached]
			),
			'ENSDARG00000063912' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Heart',
			(int) 1 => 'Kidney',
			(int) 2 => 'Brain',
			(int) 3 => 'Heart',
			(int) 4 => 'Kidney',
			(int) 5 => 'Liver',
			(int) 6 => 'Muscle',
			(int) 7 => 'Brain',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle'
		)
	),
	'CIL_00013G_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000064356' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000064357' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000064358' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Kidney',
			(int) 6 => 'Liver',
			(int) 7 => 'Lung',
			(int) 8 => 'Ovary',
			(int) 9 => 'Placenta',
			(int) 10 => 'Testis',
			(int) 11 => 'Adipose',
			(int) 12 => 'Adrenal',
			(int) 13 => 'Breast',
			(int) 14 => 'Colon',
			(int) 15 => 'Kidney',
			(int) 16 => 'Liver',
			(int) 17 => 'Lung',
			(int) 18 => 'Ovary',
			(int) 19 => 'Ovary'
		)
	)
)
$gene_desc_arr = array(
	'ENSDARG00000063910' => 'ATP synthase 8, mitochondrial',
	'ENSDARG00000063911' => 'ATP synthase 6, mitochondrial',
	'ENSDARG00000063912' => 'cytochrome c oxidase III, mitochondrial',
	'ENSDARG00000081758' => null,
	'ENSG00000198899' => 'mitochondrially encoded ATP synthase 6',
	'ENSG00000198938' => 'mitochondrially encoded cytochrome c oxidase III',
	'ENSG00000228253' => 'mitochondrially encoded ATP synthase 8',
	'ENSMUSG00000064356' => 'mitochondrially encoded ATP synthase 8',
	'ENSMUSG00000064357' => 'mitochondrially encoded ATP synthase 6',
	'ENSMUSG00000064358' => 'mitochondrially encoded cytochrome c oxidase III'
)
$gene_name_arr = array(
	'ENSDARG00000063910' => 'mt-atp8',
	'ENSDARG00000063911' => 'mt-atp6',
	'ENSDARG00000063912' => 'mt-co3',
	'ENSDARG00000081758' => 'AC024175.12',
	'ENSG00000198899' => 'MT-ATP6',
	'ENSG00000198938' => 'MT-CO3',
	'ENSG00000228253' => 'MT-ATP8',
	'ENSMUSG00000064356' => 'mt-Atp8',
	'ENSMUSG00000064357' => 'mt-Atp6',
	'ENSMUSG00000064358' => 'mt-Co3'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00013G_0001',
			'tax_id' => '7955',
			'chromosome' => 'MT',
			'seq_start' => '9052',
			'seq_end' => '10520',
			'region_length' => '1468',
			'region_type' => 'CGP',
			'el_id' => 'ENSDARG00000063911-ENSDARG00000063912'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00013G_0002',
			'tax_id' => '9606',
			'chromosome' => 'MT',
			'seq_start' => '8527',
			'seq_end' => '9990',
			'region_length' => '1463',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000198899-ENSG00000198938'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00013G_0003',
			'tax_id' => '10090',
			'chromosome' => 'MT',
			'seq_start' => '7927',
			'seq_end' => '9390',
			'region_length' => '1463',
			'region_type' => 'CGP',
			'el_id' => 'ENSMUSG00000064357-ENSMUSG00000064358'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 4 => 'Brain',
	(int) 7 => 'Breast',
	(int) 9 => 'Colon',
	(int) 11 => 'Heart',
	(int) 14 => 'Kidney',
	(int) 19 => 'Liver',
	(int) 23 => 'Lung',
	(int) 25 => 'Muscle',
	(int) 27 => 'Ovary',
	(int) 30 => 'Placenta',
	(int) 31 => '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) 10
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENSDART00000093611' => array(
		'start' => '8894',
		'end' => '9058',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-atp8-201'
	),
	'ENSDART00000093612' => array(
		'start' => '9052',
		'end' => '9735',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-atp6-201'
	),
	'ENSDART00000093613' => array(
		'start' => '9735',
		'end' => '10520',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-co3-201'
	),
	'ENSDART00000116044' => array(
		'start' => '10520',
		'end' => '10589',
		'transcript_biotype' => 'Mt_tRNA',
		'transcript_name' => 'AC024175.12-201'
	),
	'ENST00000361899' => array(
		'start' => '8527',
		'end' => '9207',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'MT-ATP6-201'
	),
	'ENST00000362079' => array(
		'start' => '9207',
		'end' => '9990',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'MT-CO3-201'
	),
	'ENST00000361851' => array(
		'start' => '8366',
		'end' => '8572',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'MT-ATP8-201'
	),
	'ENSMUST00000082407' => array(
		'start' => '7766',
		'end' => '7969',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-Atp8-201'
	),
	'ENSMUST00000082408' => array(
		'start' => '7927',
		'end' => '8607',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-Atp6-201'
	),
	'ENSMUST00000082409' => array(
		'start' => '8607',
		'end' => '9390',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'mt-Co3-201'
	)
)
$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_00013G_0001' => array(
		'genes_in_region' => array(
			'ENSDARG00000063910' => array(
				[maximum depth reached]
			),
			'ENSDARG00000063911' => array(
				[maximum depth reached]
			),
			'ENSDARG00000063912' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Heart',
			(int) 1 => 'Kidney',
			(int) 2 => 'Brain',
			(int) 3 => 'Heart',
			(int) 4 => 'Kidney',
			(int) 5 => 'Liver',
			(int) 6 => 'Muscle',
			(int) 7 => 'Brain',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle'
		)
	),
	'CIL_00013G_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000064356' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000064357' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000064358' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Kidney',
			(int) 6 => 'Liver',
			(int) 7 => 'Lung',
			(int) 8 => 'Ovary',
			(int) 9 => 'Placenta',
			(int) 10 => 'Testis',
			(int) 11 => 'Adipose',
			(int) 12 => 'Adrenal',
			(int) 13 => 'Breast',
			(int) 14 => 'Colon',
			(int) 15 => 'Kidney',
			(int) 16 => 'Liver',
			(int) 17 => 'Lung',
			(int) 18 => 'Ovary',
			(int) 19 => 'Ovary'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00013G_0002',
		'tax_id' => '9606',
		'chromosome' => 'MT',
		'seq_start' => '8527',
		'seq_end' => '9990',
		'region_length' => '1463',
		'region_type' => 'CGP',
		'el_id' => 'ENSG00000198899-ENSG00000198938'
	)
)
$gene_el = array(
	'ENSDART00000093613' => array(
		'Brain' => array(
			'average_FPKM' => '9637.060',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '1261.900',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '2686.317',
			'stddev_FPKM' => '1995.03'
		),
		'Liver' => array(
			'average_FPKM' => '592.049',
			'stddev_FPKM' => '0.00'
		),
		'Muscle' => array(
			'average_FPKM' => '6483.380',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSDARG00000063912'
$is_first = false
$tran_el = array(
	'Brain' => array(
		'average_FPKM' => '9637.060',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '1261.900',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '2686.317',
		'stddev_FPKM' => '1995.03'
	),
	'Liver' => array(
		'average_FPKM' => '592.049',
		'stddev_FPKM' => '0.00'
	),
	'Muscle' => array(
		'average_FPKM' => '6483.380',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENSDART00000093613'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108

Source ID		Type	Tax ID	Position
ENSG00000198899-ENSG00000198938		CGP	9606	MT:8527-9990
Gene		Transcript	Position	Biotype

CIL_00013G_0003 (Click to Hide/Show)

Source ID	Type	Tax ID	Position
ENSMUSG00000064357-ENSMUSG00000064358	CGP	10090	MT:7927-9390
Gene	Transcript	Position	Biotype
ENSMUSG00000064356 (mt-Atp8) mitochondrially encoded ATP synthase 8	ENSMUST00000082407 (mt-Atp8-201)	7766-7969	protein_coding
ENSMUSG00000064357 (mt-Atp6) mitochondrially encoded ATP synthase 6	ENSMUST00000082408 (mt-Atp6-201)	7927-8607	protein_coding
ENSMUSG00000064358 (mt-Co3) mitochondrially encoded cytochrome c oxidase III	ENSMUST00000082409 (mt-Co3-201)	8607-9390	protein_coding

C-It-Loci: A knowledge database for tissue-enriched loci.

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Region Summary

Expression Patterns

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