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
ENSG00000078808	SDF4, Cab45, SDF-4	stromal cell derived factor 4	protein_coding	9606	1:1216908-1232031	60
ENSG00000107404	DVL1, DVL, DVL1L1, DVL1P1	dishevelled segment polarity protein 1	protein_coding	9606	1:1335276-1349350	84
ENSG00000116151	MORN1, FLJ13941	MORN repeat containing 1	protein_coding	9606	1:2321253-2391707	82
ENSG00000127054	CPSF3L, CPSF73L, FLJ20542, hsa-mir-6727, INT11, INTS11, RC-68, RC68	cleavage and polyadenylation specific factor 3-like	protein_coding	9606	1:1311585-1324691	54
ENSG00000131584	ACAP3, CENTB5, KIAA1716	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	protein_coding	9606	1:1292376-1309609	25
ENSG00000131591	C1orf159, FLJ20584	chromosome 1 open reading frame 159	protein_coding	9606	1:1081818-1116361	95
ENSG00000142606	MMEL1, MELL1, MMEL2, NEP2, NEPII, NL1, NL2, SEP	membrane metallo-endopeptidase-like 1	protein_coding	9606	1:2590639-2632990	30
ENSG00000142611	PRDM16, CMD1LL, KIAA1675, LVNC8, MEL1, MGC166915, PFM13	PR domain containing 16	protein_coding	9606	1:3069168-3438621	55
ENSG00000149527	PLCH2, KIAA0450, PLC-eta2, PLCeta2, PLCL4, RP3-395M20.1	phospholipase C, eta 2	protein_coding	9606	1:2425980-2505530	60
ENSG00000157870	FAM213B, C1orf93, MGC26818	family with sequence similarity 213, member B	protein_coding	9606	1:2586491-2591469	84

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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