Assignment 3 - bcb420-2023/Maryam_Hasanzadehkiabi GitHub Wiki

Time estimated: 2 h; taken 12 h; date started: 2023-04-03; date completed: 2023-04-09

Table of Contents

Link to assignment 3 : https://github.com/bcb420-2023/Maryam_Hasanzadehkiabi/tree/main/Assignment%203

Goal

Objects • Review assignment 2 • Gene Set Enrichment Analysis (GSEA) • Visualization by Cytoscape • Compilation • Remarks

Link to assignment 3

Goal

Genes expressions could be identified mainly in two ways, thresholded and non-thresholded. The main goal of this work is to perform non-thresholded analysis and compare the results with those resulted in thresholded analysis. Thresholded analysis was conducted using g:Profilre web tools in the assignment

  1. In this assignment, non-thresholded analysis would be performed using GSEA software and visualization would be conducted by Cytoscape software from Bader lab.

Review assignment 2

g:Profilre resulted in two separated pathways that were associated with the gene lists

up-regulated genes revealed 8 GO:BP pathways, and 3 Reactome pathways; while, down-regulated genes did not returned any results.

GSEA

Appropriate gmt file was selected from Bader lab collections i.e. Human/symbol/Human_GOBP_AllPathways_no_GO_iea_March_02_2023_symbol.gmt

GSEA desktop app version 4.3.2. was used.

Required Fields and Basic Fields were selected accordingly.

The results were put in the Result_data folder.

Cytoscape

The ouptputs of GSEA analysis were fed to Cytoscape to visualize the genes expressions.

My main issue was that the original dataset included 3 different groups who were treated by different agents. The primary investigators, studied the effect of inhibition of some signaling pathways in colon cancer. Two groups were very similar, therefore, I decided to use only two groups out of 3.

Also I had problem in running these appa inside R, specifically with MAC. That is why I did all analyses one time with MAC and one time with Windows. I included both versions on my GitHub.

After initial visualization I performed two ways annotation: AutoAnnotate and manually annotation using different criteria. Eventually I did a post analysis to discover the potential effects of drugs in this geneset.

The above figure is the network build using Human_DrugBank_all_symbol gmt file from Bader lab as signature gene set.

References:

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. doi: 10.1073/pnas.0506580102. Epub 2005 Sep 30. PMID: 16199517; PMCID: PMC1239896.

Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003 Jul;34(3):267-73. doi: 10.1038/ng1180. PMID: 12808457.

Cytoscape

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 13:11 (2498-504). 2003 Nov. PubMed ID: 14597658. Open in PubMed →

BiNGO Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21:16 (3448-9). 2005 Aug 15. PubMed ID: 15972284. Open in PubMed →

CyAnimator Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res, 4: (482). 2015. PubMed ID: 26937268. Open in PubMed →

CyTargetLinker Kutmon M, Ehrhart F, Willighagen EL, Evelo CT, Coort SL. CyTargetLinker app update: A flexible solution for network extension in Cytoscape. F1000Res, 7: (). 2018. PubMed ID: 31489175. Open in PubMed →

EnrichmentMap Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One, 5:11 (e13984). 2010 Nov 15. PubMed ID: 21085593. Open in PubMed →

EnrichmentMap Pipeline Collection Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. Nat Protoc, 14:2 (482-517). 2019 Feb. PubMed ID: 30664679. Open in PubMed →

GeneMANIA Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD. GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics, 26:22 (2927-8). 2010 Nov 15. PubMed ID: 20926419. Open in PubMed →

NetworkAnalyzer Assenov Y, Ramírez F, Schelhorn SE, Lengauer T, Albrecht M. Computing topological parameters of biological networks. Bioinformatics, 24:2 (282-4). 2008 Jan 15. PubMed ID: 18006545. Open in PubMed →

ReactomeFIPlugIn Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol, 11:5 (R53). 2010. PubMed ID: 20482850. Open in PubMed →

WikiPathways Kutmon M, Lotia S, Evelo CT, Pico AR. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000Res, 3: (152). 2014. PubMed ID: 25254103. Open in PubMed →

WordCloud Oesper L, Merico D, Isserlin R, Bader GD. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol Med, 6: (7). 2011 Apr 7. PubMed ID: 21473782. Open in PubMed →

clusterMaker2 Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics, 12: (436). 2011 Nov 9. PubMed ID: 22070249. Open in PubMed →

enhancedGraphics Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res, 3: (147). 2014. PubMed ID: 25285206. Open in PubMed →

stringApp Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. J Proteome Res, 18:2 (623-632). 2019 Feb 1. PubMed ID: 30450911. Open in PubMed →