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
ENSG00000100565	LRRC74A, C14orf166B, LRRC74	leucine rich repeat containing 74A	protein_coding	9606	14:76826372-76870302	7
ENSG00000196700	ZNF512B, GM632, KIAA1196, MGC149845, MGC149846	zinc finger protein 512B	protein_coding	9606	20:63956702-64048758	44
ENSG00000104499	GML, LY6DL	glycosylphosphatidylinositol anchored molecule like	protein_coding	9606	8:142834247-142916506	2
ENSG00000105388	CEACAM5, CD66e, CEA	carcinoembryonic antigen-related cell adhesion molecule 5	protein_coding	9606	19:41576273-41729798	2
ENSG00000107872	FBXL15, Fbl15, FBXO37, JET, MGC11279, PSD	F-box and leucine-rich repeat protein 15	protein_coding	9606	10:102419189-102423136	41
ENSG00000225569	CCT4P2	chaperonin containing TCP1, subunit 4 (delta) pseudogene 2	processed_pseudogene	9606	X:65270913-65273019	3
ENSG00000242715	CCDC169, C13orf38, LOC728591, RP11-251J8.1	coiled-coil domain containing 169	protein_coding	9606	13:36222008-36297840	59
ENSG00000122180	MYOG, bHLHc3, myf-4, MYF4	myogenin (myogenic factor 4)	protein_coding	9606	1:203083132-203086036	2
ENSG00000123358	NR4A1, 139145, GFRP1, HMR, N10, NAK-1, NAK1, NGFIB, NP10, NUR77, TR3	nuclear receptor subfamily 4, group A, member 1	protein_coding	9606	12:52022832-52059507	81
ENSG00000124900	TRIM51, SPRYD5, TRIM51A	tripartite motif-containing 51	protein_coding	9606	11:55883297-55891810	1

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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