1. Pathway Informatics December 5, 2018 Ansuman Chattopadhyay, PhD
Asst Director, Molecular Biology information service
Health sciences library system
University of pittsburgh

2. http://hsls.libguides.com/pathwayinformatics Workshop Page

3. Biological Pathway Map

4. Software
Learn How to …
Find Statistically Overrepresented Attribute Linked to Differentially Expressed Genes: IPA, DAVID, Reactome
Identify correlated studies from public gene expression repository (GEO):
BaseSpace Correlation Engine (Nextbio)

5. RNA-Seq Software @ HSLS MolBio
Enrichment Analysis
Deferentially Expressed Genes
CLC Genomics
Work Bench
Ingenuity
Pathway Analysis
Functions
Diseases
Pathways
RNA-Seq
Reads
Key Pathway Advisor
Upstream Regulators
Any Organism
Volcano Plot
PCA Plot
Venn
Diagram
Heat Map
Illumina BaseSpace
Correlation Engine
Correlated Expression Studies
CLC BioMedical
Work Bench
Variant Detection
Ingenuity
Variant Analysis
Human, Mouse and Rat
Variant Annotation
and Prioritization
RNA-Seq Analysis
Down Stream Analysis

6. RNA-seq Study

9. NCBI SRA
Untreated Vs DEX

10. RNA-Seq Workshop FASTq Reads CLC Genomics WorkBench
RNA-Seq Analysis Pipeline
Dex vs UNT DEG

12. FDR p-value <0.05 Number of genes: 1161 Suggested Number of Genes:
Dex vs. Unt CLCGx DEG Output
FDR p-value <0.05
Number of genes:
1161
Suggested Number
of Genes:
Between 5% to 10%
of the background

13. GraphPad Statistics Guide :

14. Data Formatting

15. Software Registration

16. Data Formatting
IPA
One Excel spread sheet
Row one: Column Headers

17. Correlation Engine Data Formatting One Excel spread sheet
Column A should be gene names
Column A Header: Gene

18. Reactome Data Formatting
Save Excel Spread Sheet in a tab delimited text
Column A header: #Gene; Column B header : # FoldChange etc

19. Pathway Drawing ePath3D

20. Seminal Paper

21. Input Datasets
Gene List
DEG with expression FC

22. Databases to Search Gene Ontology (GO)
Broad Molecular Signature Database (mSigdb)
Reactome Pathway
WikiPathway
Ingenuity Pathway database
Metacore GeneGO
Gene List
Pathway Database
Signaling
Metabolic

23. https://journals. plos. org/ploscompbiol/article. id=10. 1371/journal

24. Figure 1. Overview of existing pathway analysis methods using gene expression data as an example.
NIH-DAVID
GSEA
IPA
Khatri P, Sirota M, Butte AJ (2012) Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. PLOS Computational Biology 8(2): e

25. DAVID Bioinformatics Resources

26. DAVID Tools Functional Annotation Clustering Chart – Term centric
Table – Gene centric

27. DAVID

28. NIH DAVID

30. IPA

31. Correlation Engine

36. Correlation Engine

37. Pathway analysis in non human, mouse and rat

38. Protein-Protein Interaction Database
Pathway Informatics
List of Genes
Protein-Protein Interaction Database
Pathway Map

39. PPI Databases
BioGRID
STRING

40. Thank you! Any questions?
Ansuman Chattopadhyay