ANGIOGENES

Warning (512): _cake_core_ cache was unable to write 'cake_dev_eng' to File cache [CORE/Cake/Cache/Cache.php, line 323]

Code Context

                ),
                E_USER_WARNING
            );

$key = 'cake_dev_eng'
$value = array(
	'LC_MESSAGES' => array()
)
$config = '_cake_core_'
$settings = array(
	'prefix' => '*****',
	'engine' => 'File',
	'path' => '/var/www/angiogenes/app/tmp/cache/persistent/',
	'serialize' => true,
	'duration' => (int) 10,
	'lock' => true,
	'isWindows' => false,
	'mask' => (int) 436,
	'probability' => (int) 100,
	'groups' => array()
)
$success = false

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

Warning (512): _cake_model_ cache was unable to write 'default_angiogenes_list' to File cache [CORE/Cake/Cache/Cache.php, line 323]

Code Context

                ),
                E_USER_WARNING
            );

$key = 'default_angiogenes_list'
$value = null
$config = '_cake_model_'
$settings = array(
	'prefix' => '*****',
	'engine' => 'File',
	'path' => '/var/www/angiogenes/app/tmp/cache/models/',
	'serialize' => true,
	'duration' => (int) 10,
	'lock' => true,
	'isWindows' => false,
	'mask' => (int) 436,
	'probability' => (int) 100,
	'groups' => array()
)
$success = false

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

Warning (512): _cake_model_ cache was unable to write 'default_angiogenes_list' to File cache [CORE/Cake/Cache/Cache.php, line 323]

Code Context

                ),
                E_USER_WARNING
            );

$key = 'default_angiogenes_list'
$value = array(
	(int) 0 => 'diffexp',
	(int) 1 => 'experiment',
	(int) 2 => 'expressed_transcripts',
	(int) 3 => 'genes',
	(int) 4 => 'go_annotations',
	(int) 5 => 'homologues',
	(int) 6 => 'repeats',
	(int) 7 => 'study',
	(int) 8 => 'synonyms',
	(int) 9 => 'transcripts'
)
$config = '_cake_model_'
$settings = array(
	'prefix' => '*****',
	'engine' => 'File',
	'path' => '/var/www/angiogenes/app/tmp/cache/models/',
	'serialize' => true,
	'duration' => (int) 10,
	'lock' => true,
	'isWindows' => false,
	'mask' => (int) 436,
	'probability' => (int) 100,
	'groups' => array()
)
$success = false

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

Download

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	Biotype	Tax ID	Location	# of Detections
ENSDART00000032374	xkr8.2-001	unprocessed_pseudogene	7955	19:25472589-25476654	2
ENSDART00000032389	plekhf2-001	protein_coding	7955	16:40475841-40509072	2
ENSDART00000032390	gtf2h1-001	protein_coding	7955	25:3071111-3091371	3
ENSDART00000032392	dhdhl-001	protein_coding	7955	18:1077870-1084699	5
ENSDART00000032393	ginm1-001	protein_coding	7955	20:23955925-23961708	6
ENSDART00000032407	prf1.6-001	protein_coding	7955	8:29661295-29668068	4
ENSDART00000032410	gpr132a-001	protein_coding	7955	17:39812560-39813501	1
ENSDART00000032459	aqp1a.1-201	protein_coding	7955	2:2895633-2907365	6
ENSDART00000032460	med21-001	protein_coding	7955	4:1908149-1910242	6
ENSDART00000032474	pabpc1b-001	protein_coding	7955	19:12202416-12226237	2
ENSDART00000032481	ckma-001	protein_coding	7955	5:36231926-36237693	3
ENSDART00000032494	ttc26-001	protein_coding	7955	6:7531322-7554180	2
ENSDART00000032498	tspan36-001	protein_coding	7955	8:29717388-29725719	6
ENSDART00000032502	nebl-001	protein_coding	7955	2:21418523-21424633	2
ENSDART00000032527	cav3-001	protein_coding	7955	6:41998530-42006244	2
ENSDART00000032540	usp14-201	protein_coding	7955	2:2948672-2971360	6
ENSDART00000032547	lect2l-001	protein_coding	7955	14:36545210-36546752	2
ENSDART00000032552	taf5l-001	protein_coding	7955	1:53252091-53259096	2
ENSDART00000032603	tspo-001	protein_coding	7955	6:40580683-40585717	6
ENSDART00000032695	asic4a-201	protein_coding	7955	9:11063764-11257161	2
ENSDART00000032702	sst1.2-001	protein_coding	7955	15:36257986-36262308	2
ENSDART00000032722	pigm-201	protein_coding	7955	24:42180468-42187198	4
ENSDART00000032744	rpl10-002	protein_coding	7955	23:19786214-19789478	4
ENSDART00000032757	ncf4-201	protein_coding	7955	22:29255705-29302852	2
ENSDART00000032770	ell-001	protein_coding	7955	22:20822602-20899592	0
ENSDART00000032778	rnf144b-201	protein_coding	7955	16:43464814-43488697	4
ENSDART00000032788	rdh8a-001	protein_coding	7955	3:53432982-53467519	6
ENSDART00000032805	gxylt1b-001	protein_coding	7955	4:13893924-13903339	3
ENSDART00000032808	BX004816.2-201	protein_coding	7955	3:254567-256534	2
ENSDART00000032821	cyth1b-001	protein_coding	7955	12:34018456-34091972	3
ENSDART00000032827	zgc:162964-001	protein_coding	7955	17:33422958-33434079	2
ENSDART00000032841	DCHS2-202	protein_coding	7955	1:24902969-24957735	2
ENSDART00000032844	plekha6-001	protein_coding	7955	11:23089972-23205768	3
ENSDART00000032857	mapk11-001	protein_coding	7955	4:5498382-5513867	2
ENSDART00000032861	ankrd52a-001	protein_coding	7955	23:32435554-32464211	1
ENSDART00000032877	ino80e-201	protein_coding	7955	16:10522678-10531587	5
ENSDART00000032880	rpa1-001	protein_coding	7955	15:26565463-26606113	6
ENSDART00000032899	clpxa-201	protein_coding	7955	7:13422418-13444542	5
ENSDART00000032909	kat5b-201	protein_coding	7955	5:66054184-66070395	5
ENSDART00000032963	apoob-001	protein_coding	7955	24:21833056-21844232	3
ENSDART00000032967	notch2-201	protein_coding	7955	8:19579628-19586762	2
ENSDART00000032975	heatr5a-201	protein_coding	7955	17:28611441-28651901	2
ENSDART00000032978	nsl1-001	protein_coding	7955	20:37911466-37918060	6
ENSDART00000032982	slc5a8l-001	protein_coding	7955	6:49064636-49079610	2
ENSDART00000032992	arsh-001	protein_coding	7955	9:56225934-56244631	2
ENSDART00000032996	ppdpfa-001	protein_coding	7955	8:23192081-23194796	3
ENSDART00000033018	pi4k2b-201	protein_coding	7955	1:14572167-14598717	4
ENSDART00000033024	tmem41ab-001	protein_coding	7955	1:29618212-29634105	3
ENSDART00000033037	col9a2-201	protein_coding	7955	19:38834939-38880432	0
ENSDART00000033053	dennd5b-201	protein_coding	7955	4:16660566-16717965	3

Warning (512): _cake_core_ cache was unable to write 'file_map' to File cache [CORE/Cake/Cache/Cache.php, line 323]

Code Context

                ),
                E_USER_WARNING
            );

$key = 'file_map'
$value = array(
	'Configure' => '/var/www/angiogenes/lib/Cake/Core/Configure.php',
	'Hash' => '/var/www/angiogenes/lib/Cake/Utility/Hash.php',
	'Cache' => '/var/www/angiogenes/lib/Cake/Cache/Cache.php',
	'FileEngine' => '/var/www/angiogenes/lib/Cake/Cache/Engine/FileEngine.php',
	'CacheEngine' => '/var/www/angiogenes/lib/Cake/Cache/CacheEngine.php',
	'Inflector' => '/var/www/angiogenes/lib/Cake/Utility/Inflector.php',
	'ErrorHandler' => '/var/www/angiogenes/lib/Cake/Error/ErrorHandler.php',
	'CakePlugin' => '/var/www/angiogenes/lib/Cake/Core/CakePlugin.php',
	'CakeLog' => '/var/www/angiogenes/lib/Cake/Log/CakeLog.php',
	'LogEngineCollection' => '/var/www/angiogenes/lib/Cake/Log/LogEngineCollection.php',
	'ObjectCollection' => '/var/www/angiogenes/lib/Cake/Utility/ObjectCollection.php',
	'FileLog' => '/var/www/angiogenes/lib/Cake/Log/Engine/FileLog.php',
	'BaseLog' => '/var/www/angiogenes/lib/Cake/Log/Engine/BaseLog.php',
	'CakeLogInterface' => '/var/www/angiogenes/lib/Cake/Log/CakeLogInterface.php',
	'Debugger' => '/var/www/angiogenes/lib/Cake/Utility/Debugger.php',
	'String' => '/var/www/angiogenes/lib/Cake/Utility/String.php',
	'Dispatcher' => '/var/www/angiogenes/lib/Cake/Routing/Dispatcher.php',
	'CakeEventListener' => '/var/www/angiogenes/lib/Cake/Event/CakeEventListener.php',
	'CakeRequest' => '/var/www/angiogenes/lib/Cake/Network/CakeRequest.php',
	'CakeResponse' => '/var/www/angiogenes/lib/Cake/Network/CakeResponse.php',
	'CakeEvent' => '/var/www/angiogenes/lib/Cake/Event/CakeEvent.php',
	'CakeEventManager' => '/var/www/angiogenes/lib/Cake/Event/CakeEventManager.php',
	'AssetDispatcher' => '/var/www/angiogenes/lib/Cake/Routing/Filter/AssetDispatcher.php',
	'DispatcherFilter' => '/var/www/angiogenes/lib/Cake/Routing/DispatcherFilter.php',
	'CacheDispatcher' => '/var/www/angiogenes/lib/Cake/Routing/Filter/CacheDispatcher.php',
	'Router' => '/var/www/angiogenes/lib/Cake/Routing/Router.php',
	'CakeRoute' => '/var/www/angiogenes/lib/Cake/Routing/Route/CakeRoute.php',
	'PluginShortRoute' => '/var/www/angiogenes/lib/Cake/Routing/Route/PluginShortRoute.php',
	'TranscriptController' => '/var/www/angiogenes/app/Controller/TranscriptController.php',
	'AppController' => '/var/www/angiogenes/app/Controller/AppController.php',
	'Controller' => '/var/www/angiogenes/lib/Cake/Controller/Controller.php',
	'Object' => '/var/www/angiogenes/lib/Cake/Core/Object.php',
	'ComponentCollection' => '/var/www/angiogenes/lib/Cake/Controller/ComponentCollection.php',
	'SessionComponent' => '/var/www/angiogenes/lib/Cake/Controller/Component/SessionComponent.php',
	'Component' => '/var/www/angiogenes/lib/Cake/Controller/Component.php',
	'RequestHandlerComponent' => '/var/www/angiogenes/lib/Cake/Controller/Component/RequestHandlerComponent.php',
	'ClassRegistry' => '/var/www/angiogenes/lib/Cake/Utility/ClassRegistry.php',
	'Transcript' => '/var/www/angiogenes/app/Model/Transcript.php',
	'AppModel' => '/var/www/angiogenes/app/Model/AppModel.php',
	'Model' => '/var/www/angiogenes/lib/Cake/Model/Model.php',
	'BehaviorCollection' => '/var/www/angiogenes/lib/Cake/Model/BehaviorCollection.php',
	'ConnectionManager' => '/var/www/angiogenes/lib/Cake/Model/ConnectionManager.php',
	'Mysql' => '/var/www/angiogenes/lib/Cake/Model/Datasource/Database/Mysql.php',
	'DboSource' => '/var/www/angiogenes/lib/Cake/Model/Datasource/DboSource.php',
	'DataSource' => '/var/www/angiogenes/lib/Cake/Model/Datasource/DataSource.php',
	'I18n' => '/var/www/angiogenes/lib/Cake/I18n/I18n.php',
	'L10n' => '/var/www/angiogenes/lib/Cake/I18n/L10n.php',
	'CakeSession' => '/var/www/angiogenes/lib/Cake/Model/Datasource/CakeSession.php',
	'Set' => '/var/www/angiogenes/lib/Cake/Utility/Set.php',
	'View' => '/var/www/angiogenes/lib/Cake/View/View.php',
	'HelperCollection' => '/var/www/angiogenes/lib/Cake/View/HelperCollection.php',
	'ViewBlock' => '/var/www/angiogenes/lib/Cake/View/ViewBlock.php',
	'HtmlHelper' => '/var/www/angiogenes/lib/Cake/View/Helper/HtmlHelper.php',
	'AppHelper' => '/var/www/angiogenes/app/View/Helper/AppHelper.php',
	'Helper' => '/var/www/angiogenes/lib/Cake/View/Helper.php',
	'FormHelper' => '/var/www/angiogenes/lib/Cake/View/Helper/FormHelper.php',
	'SessionHelper' => '/var/www/angiogenes/lib/Cake/View/Helper/SessionHelper.php'
)
$config = '_cake_core_'
$settings = array(
	'prefix' => '*****',
	'engine' => 'File',
	'path' => '/var/www/angiogenes/app/tmp/cache/persistent/',
	'serialize' => true,
	'duration' => (int) 10,
	'lock' => true,
	'isWindows' => false,
	'mask' => (int) 436,
	'probability' => (int) 100,
	'groups' => array()
)
$success = false

Cache::write() - CORE/Cake/Cache/Cache.php, line 323
App::shutdown() - CORE/Cake/Core/App.php, line 899
[main] - [internal], line ??

Warning (512): _cake_core_ cache was unable to write 'method_cache' to File cache [CORE/Cake/Cache/Cache.php, line 323]

Code Context

                ),
                E_USER_WARNING
            );

$key = 'method_cache'
$value = array(
	(int) 0 => false,
	'name' => array(
		'8e3e6ac3f0ef6fb8bcf1424a6423ed87' => '`angiogenes`',
		'47eb7bb09414c64f779510914712b6ee' => '`count`',
		'f2816a5be27cbf774db1203e73495133' => '`transcripts`',
		'8c6497837140572ea11ac9f79b9f25eb' => '`Transcript`'
	),
	'fields' => array(
		'f70aa2bc429854f4a00d220b8ccffb66' => array(
			(int) 0 => 'COUNT(*) AS `count`'
		)
	)
)
$config = '_cake_core_'
$settings = array(
	'prefix' => '*****',
	'engine' => 'File',
	'path' => '/var/www/angiogenes/app/tmp/cache/persistent/',
	'serialize' => true,
	'duration' => (int) 10,
	'lock' => true,
	'isWindows' => false,
	'mask' => (int) 436,
	'probability' => (int) 100,
	'groups' => array()
)
$success = false

Cache::write() - CORE/Cake/Cache/Cache.php, line 323
DboSource::__destruct() - CORE/Cake/Model/Datasource/DboSource.php, line 3539
[main] - [internal], line ??

ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt

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