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
ENSG00000013583	HEBP1, HBP, HEBP	heme binding protein 1	protein_coding	9606	12:12974864-13000273	50
ENSG00000014919	COX15, CEMCOX2	cytochrome c oxidase assembly homolog 15 (yeast)	protein_coding	9606	10:99711844-99732100	63
ENSG00000015532	XYLT2, PXYLT2, XT-II, XT2, xylT-II	xylosyltransferase II	protein_coding	9606	17:50346092-50363138	71
ENSG00000017797	RALBP1, RIP, RIP1, RLIP1, RLIP76	ralA binding protein 1	protein_coding	9606	18:9475009-9538116	64
ENSG00000019505	SYT13, KIAA1427	synaptotagmin XIII	protein_coding	9606	11:45240301-45286319	24
ENSG00000019549	SNAI2, SLUG, SLUGH, SLUGH1, SNAIL2, WS2D	snail family zinc finger 2	protein_coding	9606	8:48917690-48921740	46
ENSG00000078668	VDAC3, HD-VDAC3, VDAC-3	voltage-dependent anion channel 3	protein_coding	9606	8:42391624-42405897	49
ENSG00000022277	RTFDC1, C20orf43, CDAO5, HSPC164, SHUJUN-3	replication termination factor 2 domain containing 1	protein_coding	9606	20:56468585-56519449	91
ENSG00000023516	AKAP11, AKAP-11, AKAP220, DKFZp781I12161, FLJ11304, KIAA0629, PPP1R44, PRKA11	A kinase (PRKA) anchor protein 11	protein_coding	9606	13:42272153-42323267	41
ENSG00000007541	PIGQ, c407A10.1, GPI1, hGPI1	phosphatidylinositol glycan anchor biosynthesis, class Q	protein_coding	9606	16:566995-584136	103

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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