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
ENSG00000138078	PREPL, KIAA0436	prolyl endopeptidase-like	protein_coding	9606	2:44316281-44361862	92
ENSG00000033011	ALG1, CDG1K, hMat-1, HMAT1, HMT-1, HMT1, Mat-1, MT-1	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	protein_coding	9606	16:5033702-5087379	51
ENSG00000083750	RRAGB, bA465E19.1, RAGB	Ras-related GTP binding B	protein_coding	9606	X:55717739-55758774	64
ENSG00000138658	ZGRF1, C4orf21, FLJ11331	zinc finger, GRF-type containing 1	protein_coding	9606	4:112539333-112636995	21
ENSG00000167916	KRT24, FLJ20261, K24, KA24, MGC138169, MGC138173	keratin 24	protein_coding	9606	17:40697991-40703750	1
ENSG00000139648	KRT71, HYPT13, K6IRS1, KB34, KRT6IRS, KRT6IRS1	keratin 71	protein_coding	9606	12:52543909-52553147	2
ENSG00000144015	TRIM43, TRIM43A	tripartite motif containing 43	protein_coding	9606	2:95592018-95599778	1
ENSG00000145863	GABRA6	gamma-aminobutyric acid (GABA) A receptor, alpha 6	protein_coding	9606	5:161547063-161702593	20
ENSG00000146049	KAAG1, RU2, RU2AS	kidney associated antigen 1	protein_coding	9606	6:24356903-24358284	1
ENSG00000148634	HERC4, DKFZP564G092, KIAA1593	HECT and RLD domain containing E3 ubiquitin protein ligase 4	protein_coding	9606	10:67921899-68075348	88

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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