Version: 3.44

Date: 2007/03/01

Query Transcripts

The queries below are in categories according to finding transcripts/genes by names or identifiers, expression, transcriptional regulation, presence on an array, chromosomal location and annotation.

The queries use associations or annotations for DoTS transcripts, such as text matching against their gene names or expression in particular tissues, e.g., pancreas. A DoTS Transcript (DT.) is a consensus sequence generated by the assembly of ESTs and mRNAs. Since more than one transcript (alternative forms) can be derived from a gene, it is possible to have more than one DT associated with a particular gene.

The results of queries are stored in the "My Transcripts" history page (see button above), and can be revisited at a later time.
Using the history page, you can also build complex queries by combining the queries listed below.

Find a transcript or gene

Queries in this section return one or a number of transcripts based on an identifier or a text search. The IDs can be linked to a sequence (EST or mRNA) included in a DoTS transcript.

Type Description Species History
Gene Name - Text Search 

Performs a text search against gene names or symbols.

Hs Mm
Accession or RefSeq 

This query returns DoTS transcripts (EST and RNA assemblies) that contain a specific mRNA or EST sequence. It should return at most one DoTS transcript, because a single sequence can belong to at most one DoTS transcript.

Hs Mm
I.M.A.G.E. clone 

This query returns DoTS transcripts that contain ESTs generated from a specified I.M.A.G.E. clone identifier.

Hs Mm
Entrez gene ID 

This query returns DoTS transcripts that correspond to a given Entrez Gene identifier.

Hs Mm
MGI Gene ID 

This query returns DoTS transcripts that correspond to a MGI gene identifier.

Mm
Find transcripts or genes expressed in pancreatic tissues

Queries in this section return transcripts based on evidence of their expression in pancreatic tissues.

Type Description Species History
Transcription Factor Expression 

This query returns a list of human transcription factors found to be expressed in a fetal or adult tissue by semi-quantitative RT-PCR results.

Hs
Q value tissue expression 

This query returns a list of DoTS transcripts with Q values within a specified range. The lower the Q value for a DoTS transcript, the more specific its expression in that tissue, in this case, pancreas or islet.

Hs Mm
Up regulated Expression 

This query returns a list of genes whose expression was found to be up regulated compared to a reference or control condition using PaGE differential expression analysis.

Hs Mm
Down regulated Expression 

This query returns a list of genes whose expression was found to be down regulated compared to a reference or control condition using PaGE differential expression analysis.

Hs Mm
Gene Expression - Text Search 

This form allows text searching for gene names to retrieve their expression profiles in expression studies.

Hs Mm
EST expression profile 

This query returns a list of DoTS transcripts whose expression is predicted to be biased towards a specified tissue or organ type.

Hs Mm
dbEST library 

This query returns a list of DoTS transcripts that contain a certain number of input sequences from a given dbEST library.

Hs Mm
Find transcripts or genes by transcriptional regulation

The Query in this section returns all transcripts or genes regulated by a transcription factor expressed in the pancreas

Type Description Species History
Predicted Transcription Factor Target Genes 

This query returns a list of predicted transcription factor target genes based upon a particular transcription factor. The transcription factors available for this query are expressed in pancreatic tissues.

Hs Mm
Transcription Factor Target Genes identified by genome-wide location analysis (ChIP-on-Chip) 

This query returns a list of transcription factor target genes identified by genome-wide location analysis

Hs
Find transcripts or genes on a Chip

Queries in this section return transcripts or genes associated with a particular platform, i.e, PancChips or PromoterChips.

Type Description Species History
Element ID on a PancChip 

This query returns the DoTS transcripts that correspond to an element (spot) on a PancChip. Enter a feature location element ID, e.g., 1.1.7.3.1.13 and select a version of the PancChip. The query will return the DoTS transcript(s) that contain the ESTs associated with the cDNA clone for that element.

Hs Mm
Inclusion on a PancChip 

This query returns a list of DoTS transcripts that correspond to a given version of a PancChip.

Hs Mm
RefSeq Associated with an Element on a Promoter Chip 

This query returns genes associated with predicted promoter elements for a given RefSeq on a Mouse Promoter Chip, e.g., NM_008386

Mm
Gene corresponding to a mouse PromoterChip element 

This query returns a gene associated with a predicted promoter element on a Mouse PromoterChip, based upon a mouse PromoterChip element Id, e.g., P101647.

Mm
Entrez Gene associated with an element on a Promoter Chip 

This query returns genes associated with predicted promoter elements for a given Entrez Gene Identifier on a Mouse Promoter Chip.

Mm
Find transcripts by chromosomal location

Queries in this section select transcripts by their chromosomal location.

Type Description Species History
Diabetes Candidate Region 

This query returns a list of DoTS transcripts that align within a diabetes candidate region (Idd region) on a particular chromosome.

Hs Mm
BLAT-based chromosomal location 

This query returns a list of DoTS transcripts based upon their chromosomal location and alignment to the human or mouse genomes using BLAT.

Hs Mm
Find transcripts by annotation

Queries in this section find genes by their annotation.

Type Description Species History
Gene trap insertions 

This query returns a list of DoTS transcripts that represent genes for which gene trap insertion cell lines have been generated using mouse embryonic stem cells.

Mm
GO functional classifications 

This query retrieves a list of all genes/transcripts that have been assigned to a user-specified GO molecular function category.

Mm
Predicted signal peptide 

This query returns a list of transcripts whose protein translation contains a signal peptide predicted by SignalP.

Hs Mm
Predicted transmembrane domains 

This query returns a list of transcripts whose protein translation contains the specified number of transmembrane domains predicted by the chosen algorithm.

Hs Mm