Pack: A workflow approach to mine pathway databases provides novel biological insight into the genetics of metabolomics data

Description:

The purpose of the workflow is to determine all the genes operating in BioCyc pathways that the input metabolite participates in. The overall idea is to generate a set of genes that potentially influence the levels of a metabolite due to the common pathways that they share.

Description:

The purpose of this workflow is to determine all the enzymes/genes that participate in a radius of 2 reaction steps around a given metabolite. Broadly, the scheme involves the following steps:

1. determine all the reactions that the given metabolite participates in
2. determine all the compounds that participate in these reactions
3. filter certain compounds like H2O, ATP etc to avoid non-specific connections
4. determine all the reactions that the compounds passing through step 3 participate in
5. determine the enzymes that drive the reactions from step 4
6. determine genes corresponding to the enzymes in step 5
7. store the entrez gene ids as a text file

Description:

The purpose of the workflow is to determine SNPs in the vicinity of the genes and create a SNP set for a given set of genes. The user has the freedom to choose the flanking width around the gene for determining the SNPs. The input is in the form of entrez gene ids. Biomart services are used to determine the chromosome and position of the gene as well as determining Affy gene chip 6k ids. The final report is stored as a tab-delimited text file with Affy 6 gene chip ids for the SNP and Kegg info for the gene that it is associated with.

Description:

The purpose of the workflow is to determine all the genes operating in the pathways that the input metabolite participates in. The overall idea is to generate a set of genes that potentially influence the levels of a metabolite due to the common pathways that they share.

Description:

The purpose of this workflow is to determine all the enzymes/genes that participate in a radius of 2 reaction steps around a given metabolite. Broadly, the scheme involves the following steps:

1. determine all the reactions that the given metabolite participates in
2. determine all the compounds that participate in these reactions
3. filter certain compounds like H2O, ATP etc to avoid non-specific connections
4. determine all the reactions that the compounds passing through step 3 participate in
5. determine the enzymes that drive the reactions from step 4
6. determine genes corresponding to the enzymes in step 5
7. store the entrez gene ids as a text file