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.
|
