ANGIOGENES

Expression	Example (Links run searchs)	Description
This is a cheat-sheet for the advanced search. A more comprehensive explanation can be found on the help page . The advance search was designed in response to the high expression specificity of lncRNAs. We hope users will recognize its utility as queries are are only limited by ones imagination and the RAM memory of the server.
No tag.	MALAT1	When no tag is specified the query is treated as an accession or gene name. Wildcards are supported.
SPECIFIC:(condition)	SPECIFIC:"HAoEC--Heart--Normal"	Returns sequences specific (i.e. not expressed elsewhere.) to the specified condition. See "Supported Conditions" on the Help page for a list of searchable values.
ENRICHED:(condition)	ENRICHED:"HAoEC--Heart--Normal"	Returns sequences with higher than average expression in the given condition. See "Supported Conditions" on the Help page for a list of searchable values.
EXPRESSED:(condition)	EXPRESSED:"HAoEC--Heart--Normal"	Returns transcripts expressed in the given condition. See "Supported Conditions" on the Help page for a list of searchable values.
HOMOLOGS:(Gene Accession)	HOMOLOGS:ENSG00000003436	Returns homologs of searched genes. For a BLAST/BLAT search see Finding Homologs
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. For detail, please refer to C-It-Loci database: http://c-it-loci.uni-frankfurt.de
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:7955 and BIOTYPE:lincRNA	Returns accessions existing between two query sets.
or	BIOTYPE:lincRNA or BIOTYPE:antisense	Returns accessions existing in either of two query sets.
not	POS:9606:1:814880-3069309 and not POS:9606:1:1714880-2169309	Returns accessions not in the query.
()	BIOTYPE:lincRNA and (TAXID:9606 or TAXID:10090)	Increases the precedence of a query.
*	gata*	Specifies where to use wildcards in query. Note: wildcards are only supported for tagless searches.
More Examples
Behavior	Query	Explination
Return all lncRNAs	BIOTYPE:lincRNA or BIOTYPE:processed_transcript or BIOTYPE:3prime_overlapping_ncrna or BIOTYPE:antisense or BIOTYPE:non_coding or BIOTYPE:retained_intron or BIOTYPE:sense_intronic or BIOTYPE:sense_overlapping	Using the "or" operator, link all sub-types of lncRNA. See Ensembl's documentation for a description of each biotype.
Return lincRNAs falling within Conserved Gene Pairs (CGPs)	BIOTYPE:lincRNA and REGIONTYPE:CGP	One lncRNA characteristic is a lack of sequence conservation. Therefore, by using conserved gene pairs or other highly conserved regions, one can quickly find syntetic regions to hunt for related lncRNAs.

Accession	Name(s)	Description	Biotype	Tax ID	Position	# of Detections
ENSG00000162576	MXRA8, DKFZp586E2023	matrix-remodelling associated 8	protein_coding	9606	1:1352689-1361777	80
ENSG00000162585	C1orf86, C1orf86, FAAP20, FLJ31031, FP7162	chromosome 1 open reading frame 86	protein_coding	9606	1:2184461-2212720	118
ENSG00000169717	ACTRT2, Arp-T2, ARPM2, ARPT2, FLJ25424, HARPM2	actin-related protein T2	protein_coding	9606	1:3021483-3022903	1
ENSG00000169962	TAS1R3, T1R3, TR3	taste receptor, type 1, member 3	protein_coding	9606	1:1331314-1335306	0
ENSG00000169972	PUSL1, FLJ90811	pseudouridylate synthase-like 1	protein_coding	9606	1:1308567-1311677	1
ENSG00000175756	AURKAIP1, AIP, AKIP, FLJ20608, MRP-S38, MRPS38	aurora kinase A interacting protein 1	protein_coding	9606	1:1373730-1375495	98
ENSG00000176022	B3GALT6, beta3GalT6, EDSP2, SEMDJL1	UDP-Gal:betaGal beta 1,3-galactosyltransferase polypeptide 6	protein_coding	9606	1:1232265-1235041	44
ENSG00000177133	LINC00982, FLJ42875	long intergenic non-protein coding RNA 982	antisense	9606	1:3059615-3068437	4
ENSG00000177757	FAM87B, FLJ40008	family with sequence similarity 87, member B	lincRNA	9606	1:817371-819837	30
ENSG00000179403	VWA1, FLJ22215, VWA-1, WARP	von Willebrand factor A domain containing 1	protein_coding	9606	1:1434861-1442882	101

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

Loading