Gene Ontology (GO) Enrichment Analysis in Novel Transcriptomes using BiNGO!!

A greater hurdle while dealing with differentially expressed transcripts in novel organisms is the Gene Ontology (GO) enrichment analysis and their visual interpretation.

To date there are several open-source applications available to extract GO terms corresponding to protein/nucleotide sequences (A detailed list can be accessed here, However, the best I have experienced for the De novo transcripts is InterProScan), and to perform enrichment analysis (A detailed list is here). Most of these enrichment tools work like a charm for model organisms, but only handful of them support the incorporation of custom annotations. One such tool is BiNGO (Biological Networks Gene Ontology tool), an open-source Java plug-in of Cytoscape. BiNGO can be used either on a list of genes, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy.

In order to use BiNGO for novel organisms, one need to provide a custom annotation file (CAF). In principle, CAF contains the gene/transcript and GO relationship, with one relationship per line, eg.

XLOC_000001=0005515
XLOC_000001=0008270
XLOC_000001=0016491

XLOC_000002=0055114
XLOC_000003=0016491
.
.
XLOC_999999=9999999

The left value is the transcript name and right value is the GO category (without the prefix, ‘GO:’) obtained using InterProScan or synonymous tool.

The first line of GAF should always be:

(species=Custom_species)(type=Biological Process)(curator=GO)

You can choose to change species name from “Custom_species” to something else. Once the building of GAF (GAF.txt) is complete for all the annotated transcripts. It can be used in place of “Select organism/annotation” by choosing “Custom” option. (As shown in the figure below)

Additionally, one can also choose to switch to a newer ontology (obo) file downloaded from geneontology.org download page. After providing gene list of interest and choosing the appropriate options, hit the “Start BiNGO” button to start the analysis.

Cytoscape together with BiNGO offers several downstream network grooming options, which you may find useful. For more on this, visit BiNGO and Cytoscape user guides. Hope this helps in your endeavor.

Your eLearning Directory of Bioinformatics Essentials!

In the previous section we discussed “What makes you a Good Bioinformatician?” and concluded that one requires to take a slice from the three major pillars of bioinformatics i.e. biology, mathematics and computer sciences. It is required to gain expertise in any of the two, and learn the fundamentals of the third one. We also discussed that there are range of options that one can opt for, from amongst the three. Here, I have hand-picked a list of online resources that can provide a PRIMER on some of these options.

Note: This page will update time to time! You might want to save this page for the current listings or Bookmark it for further updates in this catalogue.

Biology

Mathematics

Computer Sciences

Cross Platform Courses

This catalog is intentionally kept smaller, in spite of dozens of other publicly available courses. The intention is NOT to trigger a Decision Fatigue, a very common fallacy arose when mind is subjected to multiple options (as very well described by Rolf Debelli), but to facilitate the selection.

If you want to give a try 🙂 visit: http://www.coursera.org http://ocw.mit.edu/courses http://nptel.iitm.ac.in/ http://videolectures.net/ If you find any alternative and better course for the given topics, please care to use the following comment box. I will update this list whenever possible.