API:

Using aGEM Web Services for building workflows...

E-mail: VisualOmics @ cnb.csic.es

Some opf the aGEM platform features are available directly through a different series of Web Services. If you are developing your own application and think the integration with aGEM is possible, please contact us to get directions on how to proceed.
A number of BioMOBY Web Services have been built and can be accessed from the INB Platform. Some of these services try to simulate an aGEM functionality, while others acts as linkers to concatenate services in different workflows.

-getAnatComponentsFromGene

Returns the anatomic components and Theiler stages where a gene is expressed together with some additional annotations such as expression level & pattern. All these data and annotations come from EMAGE, GXD and GENSAT databases without preprocessing.

-getGenesFromAnatComponent

Returns the genes whose expression has been observed for a given anatomic component together with some additional annotations such as expression level & pattern. All these data and annotations come from EMAGE, GXD and GENSAT databases without preprocessing.

-getExpressionStatisticsFromGenes

Returns some statistics computed from a set of genes concerning to the set of anatomic structures where these genes are expressed. This statistics include the average expression level & pattern. All this information is comes from EMAGE, GXD and GENSAT databases and it has been processed to obtain the average expression level.

-getExpressionStatisticsFromStructures

Returns some statistics computed from a set of anatomic structures concerning to the set of genes that are expressed in these anatomic structures. This statistics include the average expression level & pattern. All this information is comes from EMAGE, GXD and GENSAT databases and it has been processed to obtain the average expression level.

-parseExpressionStatistics

Allows filtering only those statistics that comply with the requisites imposed by the user in terms of expression level, expression pattern, anatomic structure and gene.

-parseExpressedGenes

From the statistics, it returns only the set of genes.

-parseAnatomicalStructures

From the statistics, it retunrs only the set of anatomic structures.

-parseExpressionLevel

From the statistics, it returns only the set of expression levels.

-parseExpressionPattern

From the statistics, it retuns only the set of expression patterns.
workflow
workflow

Current Workflows:

The main core of these workflows consists on (1) finding the set of genes expressed in an anatomic component (MGI IDs), (2) translating these MGI IDs into the EMBL IDs and (3) retrieving the nucleotide sequence from EMBL or GenBank databases. From the set of nucleotide sequences a broad set of analyses can be done. Some of them are described below:

Building a phylogenetic tree

From the set of nucleotide sequences corresponding to the genes expressed in a given anatomic component, the workflow computes the multiple alignment among these, estimates phylogenies by maximum likelihood and finally displays the phylogenetic tree.

Finding the consensus sequence

From the set of nucleotide sequences corresponding to the genes expressed in a given anatomic component, the workflow computes the multiple alignments among these and creates the consensus sequence from multiple alignments.
workflow

Finding possible transcription factors for each sequence

This workflow scans the set of nucleotide sequences corresponding to the genes expressed in a given anatomic component for transcription factors using the Transfac database as a reference.

Finding high frequency of CG dinucleotides

This workflow scans the set of nucleotide sequences corresponding to the genes expressed in a given anatomic component for higher than expected frequencies of the dinucleotide CG. Detection of regions of genomic sequences that are rich in the CpG pattern is important because such regions are resistant to methylation and tend to be associated with genes which are frequently switched on.
workflow
workflow

Finding potential tandem repeats

This workflow scans the set of nucleotide sequences corresponding to the genes expressed in a given anatomic component for potential tandem repeats.

Technical Underpinnings:

Find more detailshere...

Version History:

Find more detailshere...
aGEM perl library