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DataSource::listSources() - CORE/Cake/Model/Datasource/DataSource.php, line 110
Mysql::listSources() - CORE/Cake/Model/Datasource/Database/Mysql.php, line 219
Model::setSource() - CORE/Cake/Model/Model.php, line 1142
Model::getDataSource() - CORE/Cake/Model/Model.php, line 3551
Model::_findCount() - CORE/Cake/Model/Model.php, line 3066
Model::buildQuery() - CORE/Cake/Model/Model.php, line 2979
Model::find() - CORE/Cake/Model/Model.php, line 2914
TranscriptController::index() - APP/Controller/TranscriptController.php, line 502
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 490
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 191
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
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Cache::write() - CORE/Cake/Cache/Cache.php, line 323
DataSource::listSources() - CORE/Cake/Model/Datasource/DataSource.php, line 110
Mysql::listSources() - CORE/Cake/Model/Datasource/Database/Mysql.php, line 219
Model::setSource() - CORE/Cake/Model/Model.php, line 1142
Model::getDataSource() - CORE/Cake/Model/Model.php, line 3551
Model::_findCount() - CORE/Cake/Model/Model.php, line 3066
Model::buildQuery() - CORE/Cake/Model/Model.php, line 2979
Model::find() - CORE/Cake/Model/Model.php, line 2914
TranscriptController::index() - APP/Controller/TranscriptController.php, line 502
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 490
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 191
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108

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DataSource::listSources() - CORE/Cake/Model/Datasource/DataSource.php, line 110
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Model::setSource() - CORE/Cake/Model/Model.php, line 1142
Model::getDataSource() - CORE/Cake/Model/Model.php, line 3551
Model::_findCount() - CORE/Cake/Model/Model.php, line 3066
Model::buildQuery() - CORE/Cake/Model/Model.php, line 2979
Model::find() - CORE/Cake/Model/Model.php, line 2914
TranscriptController::index() - APP/Controller/TranscriptController.php, line 502
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 490
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 191
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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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. Expression Example (Links run searchs) Description 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	Description	Biotype	Tax ID	Location	# of Detections
ENSDART00000126697	gclc-201		protein_coding	7955	13:2261362-2296122	4
ENSDART00000126698	Metazoa_SRP.59-201		misc_RNA	7955	11:12374319-12374606	1
ENSDART00000126704	zgc:171570-202		protein_coding	7955	2:187800-195081	2
ENSDART00000126705	eif3ea-001		protein_coding	7955	16:38606804-38679176	0
ENSDART00000126708	rhoub-001		protein_coding	7955	15:9014506-9026084	2
ENSDART00000126709	U6.263-201		snRNA	7955	4:32344960-32345066	0
ENSDART00000126712	ccdc6b-202		protein_coding	7955	12:7575660-7605029	3
ENSDART00000126716	paics-004		protein_coding	7955	20:25719024-25727108	5
ENSDART00000126718	fam131a-201		protein_coding	7955	2:17178182-17199347	2
ENSDART00000126725	ppm1ba-002		protein_coding	7955	13:10563917-10597581	0
ENSDART00000126727	atg101-003		protein_coding	7955	10:32713636-32719899	0
ENSDART00000126730	GPR35 (3 of 3)-201		protein_coding	7955	22:3216653-3217558	2
ENSDART00000126736	kcnma1a-003		retained_intron	7955	13:16628690-16629816	0
ENSDART00000126737	BX957297.1-201		protein_coding	7955	7:38424470-38427354	3
ENSDART00000126739	tspan5a-202		protein_coding	7955	7:69363762-69399342	3
ENSDART00000126740	ftr22-001		protein_coding	7955	2:48046342-48049926	0
ENSDART00000126741	serf2-001		protein_coding	7955	7:30004374-30009784	6
ENSDART00000126743	U1.51-201		snRNA	7955	4:46643162-46643310	0
ENSDART00000126744	nrg3b-001		protein_coding	7955	12:29235796-29509736	2
ENSDART00000126746	cbsa-003		nonsense_mediated_decay	7955	1:28264830-28276504	0
ENSDART00000126749	si:ch73-281f12.3-001		unprocessed_pseudogene	7955	3:58643013-58651448	2
ENSDART00000126753	U6.121-201		snRNA	7955	4:32340198-32340304	0
ENSDART00000126755	AL928685.3-201		protein_coding	7955	22:6337325-6339366	2
ENSDART00000126759	cnih4-201		protein_coding	7955	16:2232276-2235182	3
ENSDART00000126761	PIP4K2C (2 of 2)-001		protein_coding	7955	11:2387491-2402926	0

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