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Mysql::listSources() - CORE/Cake/Model/Datasource/Database/Mysql.php, line 219
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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
ENSDART00000127144	cacna2d2a-201		protein_coding	7955	6:53503063-53879179	2
ENSDART00000127145	ptprdb-002		protein_coding	7955	1:18512260-18540953	0
ENSDART00000127150	arhgef39-201		protein_coding	7955	4:12414356-12478379	1
ENSDART00000127151	dnmt3bb.2-002		processed_transcript	7955	23:17057434-17058251	1
ENSDART00000127152	dre-mir-430a-4.4-201		miRNA	7955	4:28740933-28741014	0
ENSDART00000127153	dhx37-201		protein_coding	7955	8:4460113-4516894	6
ENSDART00000127154	toporsa-002		protein_coding	7955	1:25411446-25413393	1
ENSDART00000127155	pik3c3-002		nonsense_mediated_decay	7955	7:24322099-24350530	1
ENSDART00000127157	hlfa-201		protein_coding	7955	3:11618818-11657952	6
ENSDART00000127161	si:ch1073-303k11.2-201		protein_coding	7955	14:1100761-1101483	0
ENSDART00000127162	BX470211.1-201		protein_coding	7955	7:22431271-22442080	6
ENSDART00000127166	dre-mir-430a-2.8-201		miRNA	7955	4:28748544-28748625	0
ENSDART00000127167	fam217b-201		protein_coding	7955	23:12217089-12223438	2
ENSDART00000127173	clu-001		protein_coding	7955	20:39357729-39371108	2
ENSDART00000127174	hnrnpa1b-002		nonsense_mediated_decay	7955	23:36208858-36211615	6
ENSDART00000127176	chrna4a-201		protein_coding	7955	6:58514189-58527543	0
ENSDART00000127177	MRPL52-201		protein_coding	7955	7:23843537-23846005	6
ENSDART00000127180	5S_rRNA.622-201		rRNA	7955	KN150251.1:23641-23758	2
ENSDART00000127182	arl2bp-001		protein_coding	7955	18:18881559-18886242	2
ENSDART00000127183	U1.58-201		snRNA	7955	4:46641858-46642021	1
ENSDART00000127184	bsnb-201		protein_coding	7955	11:37172497-37184992	0
ENSDART00000127188	pola1-001		protein_coding	7955	24:23695675-23787351	3
ENSDART00000127192	ccdc187-003		protein_coding	7955	23:30090316-30114584	0
ENSDART00000127195	5S_rRNA.563-201		rRNA	7955	13:43951244-43951347	0
ENSDART00000127196	CR931792.1-201		miRNA	7955	13:38359487-38359571	0

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