Hello, I am using DAVID for the first time and struggling to understand it. I want to do a quick pathway analysis, but I am unsure how to use DAVID and how to report the results. I would really appreciate some help.
- I have a whole bunch of genes, some upregulated and some downregulated. Should I put them into the gene list together or apart?
- If I use the functional categories option, and click the "chart" button, what does this output mean? If I do this, the top hit is "disulfide bond", would it be correct to say that "the unregulated genes show enrichment for disulfide bonds"?
- If that is not correct, do I need to use the "functional annotation clustering" to analyze enrichment? My top cluster contains "disulfide bond", but also "glycoprotein" and "signal". How can I report this result?
My samples are mRNA sequenced human tissue
Thank you :):)
1 answer
You can choose whether to input all genes together or to analyse them separately. In each case, the meaning is different. If you input all together, then you just get a general feeling of 'dys-regulation'. If you think about it, it is quite reasonable to assume that, in a given pathway, some genes may be up- and down-regulated.
Functional annotation clustering will perform enrichment and then perform a second step whereby it clusters the enriched terms into cluster groups, and then ranks them by the score.
Functional Annotation Chart will just perform the enrichment step and output all terms. You can filter the list by p-value.
If you are comfortable in R, I have provided a tutorial to plot the results of DAVID (this will be a Bioconductor package once I get time): Clustering of DAVID gene enrichment results from gene expression studies
Also in R, the KEGGprofile package can also do pathway enrichment.
Kevin
Log in to answer this question.
-
Visualizing Upregulated and Downregulated Genes in GO and KEGG Pathway Analyses
written by roxana •
-
0 enriched terms found (Gene Ontology Analysis)
written by tsomakiank •
-
Identification of transcription factors from a list of DEGs
written by navamikrishna99 •
-
Differential expression analysis
written by Anupama •
-
DAVID enrichment analysis
written by barix •
-
How can I use DAVID Database on comparing proteomic IDs from wild type and knockout strains on upre…
written by tpm •
-
Pathway analysis and Gene enrichment Analysis Queries
written by bioinforesearchquestions
-
Identify Transcription factor from a list of genes
written by Natasha •
-
Blog: DAVID gene annotation functional classificaion an visualisation
written by rajasekargutha •
-
The way to get the all p-value of functionally annotated categories from DAVID?
written by kim •
