1. Interrogation of cross talk between proteins and gene regulatory networks in
breast cancer
Chambers, Teressa Lee Hiren Karathia Sridhar Hannenhalli

2. Cross Talk of Protein and Gene Regulation??
HPRD
HPRD
Ligand
INTERACTION
Receptor
INTERACTION
PPI Interactions
PTM I A P
NETPATH S E E
Interact with other Protein molecules
Prot
ANNOTATION
Transport of Pn to Nucleus from Cytoplasm
Prot
Getting information of pathway events from literatures
Activation of TF TF
Regulation of Genes

3. View of EGFR Protein Signaling Pathways

4. View of EGFR Protein Signaling Pathways

5. View of EGFR Protein Signaling Pathways

6. NetPath
NetPath is a curated resource of signal transduction pathways in humans.
At present there are 20 pathways
10 – Immune signaling pathways
10 – Cancer Signaling pathways

7. TCGA data set
100 Normal
100 Benign Cancer

8. Protein Protein Interactions
Proteins
Proteins
Protein Protein Interactions
Interfacing TF
(ITF) ?? TF
Protein DNA Interactions
DNA (Genes)

9. Questions
How can we identify context specific ITFs?
What are correlation between ITFs centric protein and gene regulatory networks?
Which ITF centric paths and target genes are cancer specific?

10. Collected from Databases and Literatures
Pipeline
Protein paths (K = 2)
200 Samples
Parse XML (SBML)
STAT
RNA-Seq
Collected from Databases and Literatures
Target Genes
Proteins
Target Genes
Corr
STAT

11. Comparisons

12. Comparisons
Protein paths (K = 3)
STAT
STAT
Target Genes

13. All Protein paths (K <= 3)
STAT **
Target Genes

14. **
Protein paths (K = 1)
STAT **
Target Genes

15. Protein paths (K = 2)
STAT **
Target Genes

16. **
Protein paths (K = 1) **
Target Genes

17. **
Protein paths (K = 2)
Target Genes **

22. Validation of the analyses

23. Validating a candidate gene

24. Flow of whole experiment

25. THANK YOU

26. Molecular Cross Talk

27. RELATIONSHIPS OF ALL THE RESOURCES
Protein or gene centric functional information
i.e., HPRD
PUBMED
Interaction information
Annotation
Gene
regulation database
Gene locus
NetPath (Information of signaling pathways)
SNPs
Pathway Details
Biological scientists read full text papers from pubmed database
GenProt (Genomic information with SNPs)
Genomic Details
VALIDATION OF PATHWAY CANDIDATES
dbSNP

28. View of EGFR induced Signaling pathways

29. RELATIONSHIPS OF ALL THE RESOURCES
Protein centric functional annotations
i.e., HPRD
PUBMED
Interaction information
Manual
annotation
Gene
regulation database
Gene locus
NetPath (Information of signaling pathways)
SNPs
Pathway Details
Biological scientists read full text research papers from pubmed database.
GenProt (Genomic information with SNPs)
Genomic Details
VALIDATION OF PATHWAY CANDIDATES
dbSNP

30. Biological databases HPRD (Human Protein Reference Database)
PPD (Plasma Protein Database)
GenProt
NetPATH (Networks and PATHways)
Proteinpedia

31. HPRD (Human Protein Reference Database)
The HPRD is a protein information resource that provides extensive information pertaining to human proteins.
It includes information as follows:
Domain Architecture
Protein Function
Protein-protein Interaction
Post Translation Modification (PTMs)
Enzyme-substrate relationships
Sub cellular localization
Tissue Expression
Disease association
All this Information collected by Molecular Biologists from full text papers available in Pubmed Database

32. ARCHITECTURE OF HPRD

33. ARCHITECTURE OF HPRD

34. FRONT PAGE OF HPRD @ http://hprd.org

35. Queries in HPRD

36. RESULT PAGE OF QUERY

37. PAGE OF INDIVIDUAL PROTEIN ENTRY

38. Protein Sequence Information

39. Protein Interaction Information

40. Protein Post Translation Modification & Substrate information

41. GENPROT
Genprot is graphically viewer, which depicts human genomic sequence alongside its transcript and SNP (Single Nucleotide Polymorphism) if available on protein coding or non coding DNA sequences.

42. Genprot main interface

43. Integration of HPRD in GENPROT

44. PATH FOR KNOWLEDGE DISCOVERY
Data
(Biological Data)
Information
Knowledge
OLAP
OLTP
Obtained Raw DATA
From DATABASE
(Biological Database)
Storing Information in
DATABASE
(Biological Database)
Storing Knowledge in
Knowledge Base
(Biological
Data Warehouse)
Data Manipulation
Data Mining

45. DATA MINING APPROACH ON HPRD
Biological Data
(Interpreted by Biologist)
Biologial meaningful Information
Knowledge discovered (Data mining process)
OLAP
OLTP
Obtained Raw DATA
From DATABASE
(Pubmed)
Storing Information in
DATABASE
(HPRD)
Storing Knowledge in
Knowledge Base
(Biological
Data Warehouse)
Data Interpretation
Data Mining

46. HPRD report on Chromosome dimension

47. HPRD Report on Disease dimension

48. HPRD report based on Localization dimension

49. PTM event distribution

50. HPRD report on Protein and cDNA length

51. HPRD report based on Protein expression in Tissues

52. HPRD report based on Protein expression in Tissues

53. RELATIONSHIPS OF ALL THE RESOURCES
HPRD or
PPD
PUBMED
Interaction information
Annotation
Gene
regulation database
Gene locus
NetPath (Information of signaling pathways)
SNPs
Pathway Details
Biological scientists read full text papers from pubmed database
GenProt (Genomic information with SNPs)
Genomic Details
VALIDATION OF PATHWAY CANDIDATES
dbSNP

54. POSSIBLE APPLICATIONS OF HPRD IN MOLECULAR BIOLOGY
1. Comparative interactome analysis between
human and other species by using data
mining and wet laboratory approach
2. Design the strategy for validating the
protein-protein interactions.

55. Example of comparative interactome analysis
25,464
24,587
105
Human
Worm
ORTHOLOGS ANALYSIS 42
21 PPI out of 36 found to be with high confidence 36 63
Fly
5,625
Human: 25,464 PPI (HPRD)
9 out of these 21 PPI was taken for validation done by Coimmunoprecipitation experiment
C.elegans: 5,625 PPI (Li et al., 2004)
CO-IMMUNOPRECIPITATION (CO-IP) EXPERIMENT
S.cerevisiae: 15,675 PPI (MIPS & DIP)
D.melanogaster: 20,439 PPI (Glot et al., 2003)

56. Objectives for validating biomolecules
Specific objective - 1:
Analysis of protein complexes of adapter proteins that are not well characterized in EGFR1 pathway.
Experiment techniques: Protein digestion & Mass Spectroscopy
Specific objective - 2:
Validating the interactions/interactors of EGFR1 pathway molecules
identified through large-scale yeast 2-hybrid (Y2H) screens through
biochemical and functional assays.
Experiment techniques: Co-IP and Western Blotting

57. Human ProteinPedia
Human Proteinpedia is a community portal for sharing and integration of human protein data.
Human Proteinpedia is information source of
Protein-Protein interactions
Tissue expression
Expression in Cell line
Subcellular Localization
Enzyme Substrate relationships
All together are obtained from number of experiment evidences. For example
1. Co-immunoprecipitation Western Blotting.
2. Mass spectroscopy Yeast 2 Hybrid experiments.
3. Fluorescence based experiments
4. Immunohistochemistry
5. Protein peptide Microarray

58. Human Proteinpedia

59. QUERING IN HUMAN PROTEINPEDIA

60. Results of Query

61. Results

62. Mass spectroscopy results

63. Mass spectroscopy peaks

64. CONCLUSION
HPRD is a knowledgebase of Human Proteins that can assist the biomedical community in discovering genomic, transcriptomic and proteomic information together in an integrated view in terms of sequence, function and protein interactions, which provides facilities to a scientist to differentiate between ordered and disordered states of human cells.

65. CAREER PATH EDUCATION B.Sc (Biochemistry) M.Sc (Biomedical Technology)
M.Sc (Bioinformatics)
Joined as Research Scientist at
Institute of Bioinformatics
Worked for developing and designing
HPRD, NetPath & Genprot.

66. Dept. of Biomathematics and Bioinformatics Under the supervision of
HPRD development team
Joined as Ph.D student
funded by
AGAUR in
Dept. of Biomathematics and Bioinformatics
at UDL
Under the supervision of
Dr. Rui Alves

67. “MOLTES GRACIES”