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
ENSG00000157873	TNFRSF14, ATAR, CD270, HVEA, HVEM, LIGHTR, TR2	tumor necrosis factor receptor superfamily, member 14	protein_coding	9606	1:2555639-2565382	70
ENSG00000157881	PANK4, FLJ10782	pantothenate kinase 4	protein_coding	9606	1:2508533-2526600	58
ENSG00000157911	PEX10, NALD, PBD6A, PBD6B, RNF69	peroxisomal biogenesis factor 10	protein_coding	9606	1:2403964-2413797	8
ENSG00000157916	RER1	retention in endoplasmic reticulum sorting receptor 1	protein_coding	9606	1:2391775-2405444	68
ENSG00000157933	SKI, SGS, SKV	SKI proto-oncogene	protein_coding	9606	1:2228695-2310119	40
ENSG00000160072	ATAD3B, AAA-TOB3, KIAA1273, TOB3	ATPase family, AAA domain containing 3B	protein_coding	9606	1:1471769-1497848	114
ENSG00000160075	SSU72, HSPC182, PNAS-120	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	protein_coding	9606	1:1541673-1574869	78
ENSG00000160087	UBE2J2, NCUBE-2, NCUBE2, PRO2121, Ubc6p	ubiquitin-conjugating enzyme E2, J2	protein_coding	9606	1:1253909-1273885	91
ENSG00000162571	TTLL10, FLJ36119, TTLL5	tubulin tyrosine ligase-like family, member 10	protein_coding	9606	1:1173884-1197935	21
ENSG00000162572	SCNN1D, dNaCh, ENaCd, ENaCdelta, SCNED	sodium channel, non-voltage-gated 1, delta subunit	protein_coding	9606	1:1280436-1292029	65

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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