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
ENSG00000004059	ARF5	ADP-ribosylation factor 5	protein_coding	9606	7:127588345-127591705	67
ENSG00000173153	ESRRA, ERR1, ERRa, ERRalpha, ESRL1, NR3B1	estrogen-related receptor alpha	protein_coding	9606	11:64305572-64316743	29
ENSG00000004478	FKBP4, FKBP51, FKBP52, FKBP59, HBI, Hsp56, p52, PPIase	FK506 binding protein 4, 59kDa	protein_coding	9606	12:2794953-2805423	43
ENSG00000003137	CYP26B1, CYP26A2, P450RAI-2, P450RAI2, RHFCA	cytochrome P450, family 26, subfamily B, polypeptide 1	protein_coding	9606	2:72129238-72148038	57
ENSG00000001036	FUCA2, 229950, dJ20N2.5, MGC1314	fucosidase, alpha-L- 2, plasma	protein_coding	9606	6:143494811-143511690	44
ENSG00000003249	DBNDD1, FLJ12582, MGC3101	dysbindin (dystrobrevin binding protein 1) domain containing 1	protein_coding	9606	16:90004865-90020128	43
ENSG00000002587	HS3ST1, 3OST, 3OST1	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein_coding	9606	4:11393150-11429765	52
ENSG00000001630	CYP51A1, CP51, CYP51, CYPL1, LDM, P450-14DM, P450L1	cytochrome P450, family 51, subfamily A, polypeptide 1	protein_coding	9606	7:92112151-92142952	43
ENSG00000003989	SLC7A2, ATRC2, CAT-2, CAT2, HCAT2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein_coding	9606	8:17497088-17570573	63
ENSG00000004776	HSPB6, FLJ32389, HEL55, Hsp20, PPP1R91	heat shock protein, alpha-crystallin-related, B6	protein_coding	9606	19:35754568-35758079	51

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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