Case Study: Unsupervised Analysis of Gene Expression data.

Data from http://www.ncbi.nlm.nih.gov/pubmed/19361613

Microarray Gene Expression Data: Confirmed Pathogological diagnosis on late-onset Alzheimer Disease (188 controls, 176 cases)

Unsupervised Method to Identify Important Genes applied to Gene Expression in Alzheimer Disease

(data from: http://www.ncbi.nlm.nih.gov/pubmed/19361613)

MV

Genes that define the gene expression specificity of patients

Uniformly distributed (“random”) genes

Viral titer linked genes

VTMV

Genes that define the gene expression specificity of patients

Uniformly distributed (“random”) genes

Viral titer linked genes

VT

Schematic representation of the algorithms main idea

Ttest values for AD/control differentiation: by individual network modules (clusters)Co-expressionnetworkmethodscanbesuccessfullyappliedtomechanismsofcomplex diseases,suchasAlzheimer'sdiseaseanddiabetes.Wedevelopedanovel co-expression network approach thatisrobustunderaseriesoftestsforvalida@ngsta@s@callysignificantnetworkmodules.AsetofgeneexpressiondataofAlzheimer's disease producedco-expressionnetworkmodules(clusters)thatareassociatedwiththedisease.

Ttest%values%for%AD/control%%differen5a5on:%by%individual%network%modules%(clusters)%

Co-Expression Network of Genes and its Modules

Cluster 40 (highest peak) identified from unsupervised analysis is used for further analysis Network Modules (Clusters) with high T-test values for differentiation between Alzheimer and control patients

Theintegra@onapproachcanbeillustratedbyanalysisoftheAlzheimergeneexpressionmicroarraydata(butequallycanbeappliedtootherhighthroughputdata).Theapproachgeneratesanetworkofgeneco-expression,andselectsthenetworkmodules(clustersofco-expression)thatdifferen@atebetweenADandcontrolpa@ents.Severalnetworkco-expressionmodules(clusters40,44,and47below--188genestogether)arehighlydifferen@a@ng:

DAVID Functional Annotation Chart: detected enriched classes of genes Enrichment Score:1.3= non log scale of 0.05- so interest is in higher than 1.3, only one group of genes were significant by enrichment

% is Number of genes involved in given term is divided by the total number of user's input genes, i.e., percentage of user's input gene hitting a given term.

Annota8on Term # mapped genes P-value Benjamini

ZincFingerRegions:C2H2-type9 10 9.80E-05 3.10E-02

ZincFingerRegions:C2H2-type11 9 9.90E-05 1.60E-02

ZincFingerRegions:C2H2-type8 10 2.10E-04 2.20E-02

KRAB(Krueppel-associatedbox) 9 2.30E-04 1.80E-02

ZincFingerRegion:C2H2-type10 9 2.40E-04 1.50E-02

ZincFingerRegion:C2H2-type12 8 2.50E-04 1.30E-02

KRAB(Krueppel-associatedbox) 9 4.20E-04 7.60E-02

ZincFingerRegion:C2H2-type6 10 6.70E-04 3E-02

KRAB-Zinc Finger Protein’s could play a crucial role in Alzheimers, as its has been associated with the onset of

the disease.

Shulman JM, Chibnik LB, Aubin C, Schneider JA, Bennett DA, De Jager PL. Intermediate Phenotypes Identify Divergent Pathways to

Alzheimer’s Disease. Domschke K, ed. PLoS ONE. 2010;5(6):e11244. doi:10.1371/journal.pone.0011244.

C2H2 Zinc Fingers function in a variety of ways, including: DNA-binding domains Protein-Protein

Interactions Regulation of gene expression in the central nervous system Important role in brain development

Gower-Winter SD, Levenson CW. Zinc in the central nervous system: From molecules to behavior. BioFactors (Oxford, England).

2012;38(3):186-193. doi:10.1002/biof.1012.

Coexpressed KRAB-Zinc Finger C2H2 genes are associated with Alzheimer disease

Summary:

Further literature review can lead to better biological interpretation. At the same time, understanding what role these genes play in Alzheimers in this specific example can remain challenging and requires further studies.

Aims: Unsupervised Method (clustering) between those with late-onset Alzheimer’s disease and control

Results: Cluster 40 identified 138 unique genes whose expression clustering demonstrated link with Alzheimers disease

Using Gene Ontology (Panther), DAVID, and KEGG , numerous genes and pathways were associated with Alzheimer’s disease, specific mention of Zinc Finger (C2H2 KRAB - Krueppel associated box) gene enrichment is interesting.

A Microarray Gene Expression Data: Confirmed Pathological diagnosis on late-onset Alzheimer Disease (188 controls, 176 cases)