Pack: Genotype to Pathway

Description:

This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

Example ids from the Mouse430_2 affymetrix array are as follows (newline separated):

1447227_at
1440624_at
1436240_at
1454904_at
1435665_at
1418148_at
1429831_at

Description:

This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype.

Example input for this workflow is given below (as newline separated values).

qtl_pathways:

path:mmu04060
path:mmu04370
path:mmu04510
path:mmu04060
path:mmu04670
path:mmu00040
path:mmu00150
path:mmu00500
path:mmu00860

microarray_pathways:

path:mmu04060
path:mmu04370
path:mmu00040
path:mmu00150
path:mmu00500
path:mmu00860

Description:

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.

Description:

This file contains all genes identified in the Tir1 QTL region.
Each gene is (if available) associated with an Entrez, UniProt, External Gene Id, Affymetrix probeset identifers (mouse_430_A chip), and Ensembl identifers for genes and their transcripts.

Description:

This file contains a list of KEGG pathway identifiers, derived from a list of Ensembl genes found to be located with a given QTL/chromosomal region in the mouse. These genes are located in the Tir1 QTL.

Description:

This file contains a list of KEGG pathway descriptions, identified from genes found within the Tir1 QTL region (for African Trypanosomiasis). Each pathway may contain multiple genes from within the QTL region.

Description:

This file contains a list of all genes found within the Tir1 QTL region. These are represented as KEGG gene identifiers. Each gene is listed in tab deliminated format along with all KEGG pathway ids in which the gene is involved. These are given as KEGG pathway identifiers. Each gene may be included in zero or more pathways, with multiple instances of the same pathway being included in the file (due to multiple genes included in a single pathway).

Description:

This file contains the version of the KEGG pathway database used in the analysis of the Tir1 QTL region

Description:

This file contains a list of KEGG gene identifiers, cross-referenced to UniProt and Entrez identifiers. The UniProt and Entrez ids were obtained from BioMart for genes located in the Tir1 QTL region.

Description:

This file contains a list of KEGG gene descriptions, for each KEGG gene identified within the Tir1 QTL region.

Description:

The release of the Ensembl database used to identify genes in Tir1 QTL region.

Description:

This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 7 differentially expressed genes

Description:

This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 3 differentially expressed genes

Description:

This spreadsheet contains information about the re-sequencing of the daxx gene, identified as a candidate QTg for the African Trypanosomiasis resiatance phenotype. This file is related to the paper: http://www.ncbi.nlm.nih.gov/pubmed/17709344

Description:

This table contains a list of articles used to construct a list of issues with regards to the lack of systematic and explicit data analyses conducted in bioinformatcis. Each author list is linked directly to their publication within PubMed.

Description:

This file contains the results of re-sequencing the Daxx gene

Description:

This protocol provides details on how to identify candidate genes from the returned workflow results.

Description:

This PDF is my personal copy of the NAR publication.