Institute of Cardiovascular Regeneration Webtool Repository

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

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Expression	Example	Description
No tag.	CIL_000001	When no tag is specified the query is treated as an accession or gene name
SPECIFIC:(tissue)	SPECIFIC:Heart	Returns transcripts detected in only one type of tissue.
ENRICHED:(tissue)	ENRICHED:Heart	Returns transcripts which have increased expression in the given tissue.
EXPRESSED:(tissue)	EXPRESSED:Heart	Returns transcripts expressed in the given tissue type.
FPKMGT:(FPKM) or FPKMGT:(FPKM):(tissue)	FPKMGT:5 or FPKMGT:5:Heart	Returns transcripts with expression greater than the given FPKM. If a tissue is passed this will return transcripts with expression greater than the given FPKM in the given tissue.
FPKMLT:(FPKM) or FPKMLT:(FPKM):(tissue)	FPKMLT:5 or FPKMLT:5:Heart	Returns transcripts with expression less than the given FPKM. If a tissue is passed this will return transcripts with expression less than the given FPKM in the given tissue.
POS:(tax_id):(chromosome):(start)-(end)	POS:9606:1:914880-969309	Returns regions, genes, or transcripts falling withing the given position.
BIOTYPE:(biotype)	BIOTYPE:lincRNA	Returns regions, genes, or transcripts which contain a transcript annotated as the given biotype.
REGIONTYPE:(CGP\|UCNEbase\|VISTA)	REGIONTYPE:UCNEbase	Returns regions which contain the given region type. If searching for genes or transcripts, genes and transcripts contained within the given region type will be returned.
TAXID:(7955\|9606\|10090)	TAXID:7955	Returns regions, genes, or transcripts associated with the given taxonomy. Taxonomy IDs (TAXID) are: 7955 (zebrafish), 9606 (human), and 10090 (mouse).
GO:(GO term accession)	GO:0005515	Returns regions, genes, or transcripts which contain an annotation of the given Gene Ontology (GO) term.
Boolean Operators
and	TAXID:7655 and TAXID:10090	Returns accessions existing between two query sets.
or	BIOTYPE:lincRNA or BIOTYPE:antisense	Returns accessions existing in either of two query sets.
not	not TAXID:9606	Returns accessions not in the query.
()	BIOTYPE:lincRNA and (TAXID:7955 and TAXID:10090 and not TAXID:9606) or (TAXID:9606 and TAXID:7955 and not TAXID:10090)	Increases the precedence of a query.
*	gata*	Specifies where to use wildcards in query. Note: wildcards are only supported for tagless searches.

C-It-Loci Accession	Region Type	# of Unique Species with Region	# of Genes in Region
CIL_00000B	CGP	2	9606: 4 10090: 2
CIL_00000C	CGP	3	7955: 2 9606: 6 10090: 4
CIL_00000D	CGP	2	9606: 3 10090: 2
CIL_00000E	CGP	2	9606: 3 10090: 3
CIL_00000F	CGP	2	9606: 2 10090: 2
CIL_00000G	CGP	2	9606: 2 10090: 2
CIL_00000H	CGP	2	9606: 4 10090: 2
CIL_00000I	CGP	2	9606: 3 10090: 2
CIL_00000J	CGP	2	9606: 2 10090: 2
CIL_00000K	CGP	2	7955: 2 9606: 2

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