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
ENSG00000009780	FAM76A, MGC34648	family with sequence similarity 76, member A	protein_coding	9606	1:27725979-27763122	82
ENSG00000008394	MGST1, GST12, MGST, MGST-I	microsomal glutathione S-transferase 1	protein_coding	9606	12:16347142-16609259	61
ENSG00000008282	SYPL1, H-SP1, SYPL	synaptophysin-like 1	protein_coding	9606	7:106090503-106112576	55
ENSG00000010017	RANBP9, BPM-L, BPM90, RanBP7, RANBPM	RAN binding protein 9	protein_coding	9606	6:13621498-13711564	64
ENSG00000008323	PLEKHG6, FLJ10665, MyoGEF	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein_coding	9606	12:6310436-6328506	65
ENSG00000008324	SS18L2, KIAA-iso	synovial sarcoma translocation gene on chromosome 18-like 2	protein_coding	9606	3:42581840-42595114	17
ENSG00000048707	VPS13D, FLJ10619, KIAA0453	vacuolar protein sorting 13 homolog D (S. cerevisiae)	protein_coding	9606	1:12230067-12512047	90
ENSG00000011105	TSPAN9, NET-5, NET5, PP1057	tetraspanin 9	protein_coding	9606	12:3077355-3286564	74
ENSG00000011485	PPP5C, PP5, PPP5, PPT	protein phosphatase 5, catalytic subunit	protein_coding	9606	19:46346994-46392981	78
ENSG00000013588	GPRC5A, GPCR5A, RAI3, RAIG1	G protein-coupled receptor, class C, group 5, member A	protein_coding	9606	12:12890782-12917937	72

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

Loading