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
ENSDART00000033078	pds5a-201	protein_coding	7955	1:22632560-22679781	0
ENSDART00000033090	SPEF1-001	protein_coding	7955	13:24549224-24557672	0
ENSDART00000033093	lad1-001	protein_coding	7955	23:5754000-5785481	4
ENSDART00000033103	gatad2ab-001	protein_coding	7955	22:18294688-18358178	3
ENSDART00000033118	fga-001	protein_coding	7955	1:9381989-9387428	1
ENSDART00000033121	morn3-201	protein_coding	7955	10:42098309-42111424	2
ENSDART00000033132	fam126a-001	protein_coding	7955	19:2672019-2734038	4
ENSDART00000033152	rab35b-001	protein_coding	7955	8:3590287-3616166	6
ENSDART00000033188	btg1-001	protein_coding	7955	4:16547197-16556109	6
ENSDART00000033211	zgc:66448-001	protein_coding	7955	16:25192312-25200440	4
ENSDART00000033237	wdr45b-201	protein_coding	7955	12:269291-273331	5
ENSDART00000033248	fam107b-003	protein_coding	7955	18:12307979-12326374	5
ENSDART00000033263	ankrd49-201	protein_coding	7955	15:2887692-2894167	2
ENSDART00000033294	wdr13-001	protein_coding	7955	8:6877286-6899642	2
ENSDART00000033316	vangl2-201	protein_coding	7955	7:5206015-5253407	0
ENSDART00000033325	slc25a24-001	protein_coding	7955	20:34751037-34767357	3
ENSDART00000033332	si:ch211-246m6.5-001	protein_coding	7955	22:14198546-14222701	2
ENSDART00000033361	ttyh3b-001	protein_coding	7955	1:11094744-11163553	2
ENSDART00000033362	gatad2b-001	protein_coding	7955	19:42116521-42139107	0
ENSDART00000033363	col11a2-201	protein_coding	7955	19:7262385-7306215	1
ENSDART00000033380	zgc:92326-201	protein_coding	7955	15:30973828-31186924	2
ENSDART00000033386	ocstamp-001	protein_coding	7955	8:28686682-28694086	2
ENSDART00000033394	pfkpa-001	protein_coding	7955	24:3931994-3972265	5
ENSDART00000033404	CABZ01062778.1-201	protein_coding	7955	20:6198019-6214134	1
ENSDART00000033405	tcirg1a-201	protein_coding	7955	1:44171306-44197988	2
ENSDART00000033411	trappc4-001	protein_coding	7955	15:9339106-9345899	4
ENSDART00000033429	npbwr2a-001	protein_coding	7955	23:30901428-30919328	0
ENSDART00000033436	cep135-001	protein_coding	7955	20:25812628-25836225	4
ENSDART00000033479	si:ch211-129c21.1-201	protein_coding	7955	22:22291748-22315783	1
ENSDART00000033491	spryd4-001	protein_coding	7955	8:21127037-21130677	4
ENSDART00000033494	klf6a-201	protein_coding	7955	24:4109840-4117085	2
ENSDART00000033514	psen1-201	protein_coding	7955	17:51117190-51133475	2
ENSDART00000033528	tnfaip3-201	protein_coding	7955	13:1051036-1078837	1
ENSDART00000033545	ndor1-201	protein_coding	7955	5:31890085-31898585	3
ENSDART00000033566	smad1-001	protein_coding	7955	1:35165017-35196915	5
ENSDART00000033574	slc24a5-001	protein_coding	7955	18:5532057-5546139	1
ENSDART00000033588	BX248324.1-201	pseudogene	7955	20:30130679-30132431	0
ENSDART00000033591	cd276-201	protein_coding	7955	18:50460911-50527452	0
ENSDART00000033610	tnnt3b-201	protein_coding	7955	7:39175230-39189342	0
ENSDART00000033617	stil-001	protein_coding	7955	22:15933735-15946255	5
ENSDART00000033621	tm9sf1-201	protein_coding	7955	24:11749800-11767971	0
ENSDART00000033630	OSBP2 (1 of 2)-001	protein_coding	7955	5:24067950-24208605	2
ENSDART00000033657	grm6b-001	protein_coding	7955	11:25396425-25441517	2
ENSDART00000033663	rps21-001	protein_coding	7955	23:9285466-9293608	6
ENSDART00000033669	lipt1-001	protein_coding	7955	1:45230904-45232209	3
ENSDART00000033691	pth2-001	protein_coding	7955	17:33542683-33546512	0
ENSDART00000033701	sema3ga-003	protein_coding	7955	8:25631160-25671827	0
ENSDART00000033702	comtb-001	protein_coding	7955	11:25382316-25393826	2
ENSDART00000033706	syne3-201	protein_coding	7955	17:15891162-15955847	0
ENSDART00000033713	arpc1b-001	protein_coding	7955	3:40667153-40678754	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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