1. Project2 Daotai Nie, PhD Hongwei Dong PhD Wenjun Zhang PhD
Ann Kirchmaier PhD
Jixin Ding PhD
Xiangqi Meng PhD

2. Total patients:119
Ctr: 70
NAFLD: 49

3. Results
190 genes (after removal of bottom 25% of low expression genes, performing logistic normalization, set FDR cutoff value to 0.05, run linear regression to identify the top genes with significant association with high fat level in liver tissue)
Name
GENE_SYMBOL FC
beta_estimate
pvalue
adjusted_pvalue
GAS6
2.62E-07
C9orf125
3.36E-07
1.26E-07
KDELR3
3.41E-07
IGHA1
4.93E-07
TSPYL5
6.20E-07
OLFM2
1.08E-06
RET
1.48E-06
1.89E-06
ARSF
1.78E-06
IGKC
3.60E-06
MAMDC4
3.21E-06
3.76E-06
FLJ30901
3.11E-06
3.96E-06

4. 91 genes IPA Pathway Analysis (p=0
91 genes IPA Pathway Analysis (p=0.05) ready molecules across observations with p=0.001 to (110 mapped IDs, 80 unmapped IDs) for All Pathways
Entrez Gene Name
FDR
Location
Type(s)
Biomarker Application(s)
IGH
immunoglobulin heavy locus
0.010
Other
other
diagnosis,prognosis
IGHA1
immunoglobulin heavy constant alpha 1
0.014
Extracellular Space
IGHG1
immunoglobulin heavy constant gamma 1 (G1m marker)
0.012
peptidase
IGLL1/IGLL5
immunoglobulin lambda like polypeptide 1
0.006
Plasma Membrane

5. IPA Biomarker selection
Symbol
Entrez Gene Name
FDR
Expected
Location
Type(s)
Biomarker Application(s)
CAMK1
calcium/calmodulin dependent protein kinase I
0.044 Up
Cytoplasm
kinase
PLCB1
phospholipase C beta 1
0.042
enzyme
PLCH2
phospholipase C eta 2
0.008
PRKCE
protein kinase C epsilon
0.016
disease progression

6. Organ System + Hepatoma Overlapping Canonical Pathways
67 genes IPA Pathway Analysis (p=0.05) for Hepatoma Cell Line & Organ Systems

7. Tissue Development Pathway/Growth of Epithelial Tissues

9. ID
Name
GENE_SYMBOL FC
beta_estimate
pvalue
adjusted_pvalue
3320
GAS6
2.62E-07
42396
C9orf125
1.26E-07
30877
3.36E-07
32794
OLFM2
1.08E-06
2654
RET
1.48E-06
21190
ARSF
1.78E-06
26093
C15orf52
4.59E-06
22960
SATB2
1.30E-05
11791
HPS5
1.08E-05
44682
DERL3
1.19E-05
10297
1.07E-05
5506
CNTN3
1.45E-05

10. Future Directions
Validate, Validate, Validate in the independent Cohort
Figure out what these genes do.
Development of Assay system

11. Acknowledgements: The BigTAP Workshop Team Min Zhang, MD, PhD
Department of Statistics
Wanqing Liu, PhD
Department of Medicinal Chemistry and Molecular Pharmacology
Purdue University Center for Cancer Research
Peter Pascuzzi, PhD
Purdue University Libraries
James C. Fleet, PhD
Department of Nutrition Science
Doug Crabill, Ph.D
Min Ren
Department of Statistics
Chen Chen