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
ENSG00000007038	PRSS21, ESP-1, ESP1, TEST1, TESTISIN	protease, serine, 21 (testisin)	protein_coding	9606	16:2817180-2826304	70
ENSG00000006282	SPATA20, FLJ21347, SSP411, Tisp78	spermatogenesis associated 20	protein_coding	9606	17:50543058-50555852	128
ENSG00000007312	CD79B, AGM6, B29, IGB	CD79b molecule, immunoglobulin-associated beta	protein_coding	9606	17:63928740-63932354	74
ENSG00000007376	RPUSD1, C16orf40, MGC19600, RLUCL	RNA pseudouridylate synthase domain containing 1	protein_coding	9606	16:784974-788397	75
ENSG00000007520	TSR3, C16orf42, MGC24381	TSR3, 20S rRNA accumulation, homolog (S. cerevisiae)	protein_coding	9606	16:1349240-1351911	54
ENSG00000006025	OSBPL7, MGC71150, ORP7	oxysterol binding protein-like 7	protein_coding	9606	17:47807372-47821834	55
ENSG00000004777	ARHGAP33, FLJ39019, NOMA-GAP, SNX26, TCGAP	Rho GTPase activating protein 33	protein_coding	9606	19:35774532-35788822	56
ENSG00000004779	NDUFAB1, ACP, FASN2A, SDAP	NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa	protein_coding	9606	16:23581002-23596356	52
ENSG00000008517	IL32, IL-32alpha, IL-32beta, IL-32delta, IL-32gamma, NK4, TAIF, TAIFa, TAIFb, TAIFc, TAIFd	interleukin 32	protein_coding	9606	16:3065297-3082192	121
ENSG00000008405	CRY1, PHLL1	cryptochrome circadian clock 1	protein_coding	9606	12:106991364-107093829	50

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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