Alternative for BGI WEGO

Question

[Amk]

Hi Friends,

Do any one have a suggestion on the alternative for the BGI WEGO? As it is not updated since 2009. My goal is to compare GO terms of two species.

Thank you.

Amk

[lakhujanivijay]

This is an update that I wanted to share. It seems that the wego wesite got a makeover recently and appears quite better

Just have a look http://wego.genomics.org.cn/

Though I am still struggling to get a good quality bar plot in png format.

Answer 1

[Ying W]

you could try using DAVID but i am not too sure how common web based GO enrichment tools are nowadays. There was a post made a couple years ago but some of those links are dead: How Can I Compare Enriched/Depleted Go Terms Between Genelists?

Gene Ontology website used to curate a list of tools but they removed it after warning that it was out of date for a while. An archived list of resources can be found here: https://web.archive.org/web/20140625053522/http://geneontology.org/GO.tools.shtml

Here is another archived list of tools: https://web.archive.org/web/20141002022923/http://neurolex.org/wiki/Category:Resource:Gene_Ontology_Tools

[Amk]

Hi Ying,

Thank you for the suggestion. Links found to be useful. As you said we can't rely on any of the tool as the updation is quite far away for those tools.

Thank you.
Amk

Answer 2

[liketree36]

If you want an alternative for WEGO, PloGO is deserved to look into, I think. :) http://onlinelibrary.wiley.com/doi/10.1002/pmic.201100445/abstract

It's an R package tool. Here's an introduction of the paper.

This R package contains tools for plotting gene ontology information in a similar fashion to the WEGO web gene ontology plotting tool Ye et al. (2006). However it was designed to incorporate information about abundance in addition to the gene ontology annotation, as well as handle multiple les and allow for a small selection of gene ontology categories of interest.

[lakhujanivijay]

I am not able to search it in bioconductor package repo

Neither, I could install it.

> biocLite("plogo")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'plogo'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/src/contrib:

Could this be a proxy issue?

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7600)

Matrix products: default

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252    LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base