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Cache::write() - CORE/Cake/Cache/Cache.php, line 323
I18n::translate() - CORE/Cake/I18n/I18n.php, line 237
__d - CORE/Cake/basics.php, line 617
Cache::write() - CORE/Cake/Cache/Cache.php, line 321
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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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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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 236
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
ENSDART00000127023	CABZ01071909.1-201		protein_coding	7955	4:72468478-72477950	3
ENSDART00000127024	U6.274-201		snRNA	7955	4:48287208-48287314	0
ENSDART00000127029	si:ch211-220i18.4-201		protein_coding	7955	23:9973771-9990159	2
ENSDART00000127033	ppp1r3ab-001		protein_coding	7955	25:21689625-21698382	2
ENSDART00000127034	si:dkey-257e4.2-201		protein_coding	7955	4:53436894-53470761	1
ENSDART00000127037	si:ch73-96b22.1-001		protein_coding	7955	23:925807-960724	3
ENSDART00000127042	zgc:154164-201		protein_coding	7955	7:6231968-6232548	1
ENSDART00000127043	ythdf2-001		protein_coding	7955	17:27390955-27402356	5
ENSDART00000127044	armc1-201		protein_coding	7955	24:24556606-24579059	4
ENSDART00000127046	cdh15-201		protein_coding	7955	7:55797111-55844052	1
ENSDART00000127047	tusc5a-001		protein_coding	7955	15:24909880-24934561	2
ENSDART00000127049	il1fma-001		protein_coding	7955	11:29718638-29724970	2
ENSDART00000127050	nrxn3b-203		protein_coding	7955	20:5518645-5921039	1
ENSDART00000127051	KBTBD13 (2 of 3)-201		protein_coding	7955	12:30167987-30169381	0
ENSDART00000127053	kdm5c-001		protein_coding	7955	8:36951125-36994173	6
ENSDART00000127054	C11orf24-201		protein_coding	7955	25:10681255-10694595	5
ENSDART00000127058	acbd3-201		protein_coding	7955	20:30799689-30817648	0
ENSDART00000127062	egr3-001		protein_coding	7955	8:50738574-50744862	4
ENSDART00000127063	FAM183B-201		protein_coding	7955	6:34154021-34157654	2
ENSDART00000127064	si:dkeyp-104f11.7-201		protein_coding	7955	20:47293760-47300242	2
ENSDART00000127065	si:ch211-135n15.1-201		protein_coding	7955	16:42573257-42575077	2
ENSDART00000127069	si:ch211-215m21.14-201		protein_coding	7955	20:42956444-42960432	0
ENSDART00000127072	tmem107l-001		protein_coding	7955	23:28556239-28560612	2
ENSDART00000127073	LRRC75B (2 of 2)-201		protein_coding	7955	10:41746654-41813830	2
ENSDART00000127075	ugt1b1-001		protein_coding	7955	11:30073932-30081871	2

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[main] - [internal], line ??