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
ENSG00000127529	OR7C2, CIT-HSP-87M17, OR19-18, OR7C3	olfactory receptor, family 7, subfamily C, member 2	protein_coding	9606	19:14941489-14942448	1
ENSG00000132879	FBXO44, FBG3, FBX30, Fbx44, FBX6A, Fbxo6a, MGC14140	F-box protein 44	protein_coding	9606	1:11654375-11663327	93
ENSG00000130159	ECSIT, SITPEC	ECSIT signalling integrator	protein_coding	9606	19:11505916-11529174	91
ENSG00000169951	ZNF764, MGC13138	zinc finger protein 764	protein_coding	9606	16:30553764-30558498	21
ENSG00000131652	THOC6, BBIS, fSAP35, MGC2655, WDR58	THO complex 6 homolog (Drosophila)	protein_coding	9606	16:3024027-3027755	64
ENSG00000135063	FAM189A2, C9orf61, X123	family with sequence similarity 189, member A2	protein_coding	9606	9:69324572-69392455	61
ENSG00000135443	KRT85, ECTD4, Hb-5, HB5, hHb5, K85, KRTHB5	keratin 85	protein_coding	9606	12:52360006-52367481	2
ENSG00000120235	IFNA6, IFN-alphaK	interferon, alpha 6	protein_coding	9606	9:21349835-21351378	1
ENSG00000204540	PSORS1C1, C6orf16, SEEK1	psoriasis susceptibility 1 candidate 1	protein_coding	9606	6:31114750-31140092	61
ENSG00000138031	ADCY3, AC3, KIAA0511	adenylate cyclase 3	protein_coding	9606	2:24819169-24919839	54

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

Loading