SUBMITTED TO THE FACULTY OF SCIENCE

PANJAB UNIVERSITY, CHANDIGARH

IN PARTIAL FULFILLMENT OF
DEGREE OF MASTERS OF SCIENCE IN
SYSTEMS BIOLOGY AND BIOINFORMATICS

PRESENTED BY
DIKSHA MARWAHA
1) Why an individual gene or group of oncogenes responsible
for colorectal neoplasia develop secondry tumor?
2) How differential gene expression profiles are correlated
with metastasis in other organ?
3) How biological process annotation & functional
enrichment analysis of oncogenes would be helpful in
development of biomarkers for dignosis of neoplasia?
 Genomic alterations lead to cancer complexity and form a major hurdle for a

comprehensive understanding of the molecular mechanisms underlying

oncogenesis .
 The study of colorectal neoplasia-associated differential genes expression in
kidney neoplasia from a systems biological point of view show that if any cancer
gene that show overexpression or underexpression in other organ and can lead
to development of secondary cancer, can be used as a genetic biomarker for
early molecular diagnosis of cancer stage i:e neoplasia.
 Neoplasia is the development of a tumor that occurs due to series of
changes in the biology of the cell, with progressive loss of the controls that
limit cell division.
 Analysis of differential gene expression profiles in neoplasms or cancers to
identify biomarkers are directly correlated with metastasis.
1. canEVOLVE
2. FIDEA (Functional Interpretation of Differential Expression
Analysis)
3. g:Profiler
4. STRING (Search Tool for the Retrieval of Interacting
Genes/Proteins)
5. DISEASECONNECT
6. MALACARDS
7. COLORECTAL CANCER GENE DATABASE (CoReCG)
8. RENAL CANCER GENE DATABASE (RCGD)
 • Colorectal and kidney neoplasm genes from disease -connect database &
1
Malacards

• Information of genes from COLORECTAL CANCER GENE DATABASE

2 (CoReCG) & RENAL CANCER GENE DATABASE (RCDB)

• Differential gene expression of neoplasm gene list from each dataset in

3 canEVOLVE tool .

• The upregulated and downregulated genes with logFC values in microsoft

4 excel for both colorectal and kidney neoplasia seperately.

• The common upregulated genes in both colorectal and kidney neoplasia and
5 similarly observe common fordownregulated gene .

• Gene annotation for similar upregulated resulting genes in FIDEA

6 (Functional Interpretation of Differential Expression Analysis .
 • Biological process gene annotation and network of genes in g:Profiler.
7

• Interaction & biological enriched pathways of common upregulated genes in

8 STRING database.

• Conclude expression of colorectal neoplasia gene in kidney neoplasia from topmost

9 biological process annotation.
The diseases Renal Carcinoma and colorectal cancer were searched in Disease-connect database

OMIM genes of Renal Cell Carcinoma and its related disease Colorectal Cancer were retrieved
 Phenotype neoplasm search result for colorectal

Phenotype neoplasm search result for kidney

Search the colorectal cancer and in MalaCards database

Comborbidity disease renal/kidney neoplasm in

relation to colorectal cancer.
Genes related to colorectal cancer (CRC)

Genes related to kidney cancer.

Gene interaction network in STRING software which show genes as nodes and their interaction
with edges connecting genes
Differential gene expression analysis from canEVOLVE tool GEO series GSE5364 was selected with 18 samples of
colon cancer

Result of output genes/probeset of series of colorectal cancer with statistical values .positive values
are upregulated genes and negative values were downregulated genes.
Upregulated and downregulated gene list of colorectal neoplasia in upregulated and downregulated gene list of kidney
MS excel neoplasia in MS excel

2D graph plotted for gene symbol at horizontal axis 2D graph showing differentially expressed genes for
and logFC at vertical axis showing differentially kidney cancer /neoplasia with gene symbol plotted at
expressed genes for colorectal neoplasia horizontal axis and logFC at vertical axis
 Result of common upregulated genes in both
colorectal and kidney neoplasia

Result of plotted comparison graph for 3 common

upregulated genes showing close expression patterns
between genes in both the phenotypes
 Brown solid line showed that for gene list either text gene or file of other
format were accepted ,p –value can be either 0.05 or 0.1.submit option was
to view and analyse the results

Results for gene annotation was retrieved by selecting

option “ start analysis”.
These are results of cellular component and molecular function gene
ontology in FIDEA tool for query upregulated genes.

Word cloud analysis of gene ontology biological process

 Interactive table analysis of gene ontology biological process.

Genes are result of analysis of biological process

annotation with less p- value that might be involved in
metastasis of kidney neoplasia
GENE ONTOLOGY biological process from tool
g:Profiler with query genes (APC,ATM,DICER1)
GENE ONTOLOGY biological process result for three
upregulated genes with p values and term ID
Significantly enriched biological network of upregulated Violet arrow towards yellow node show
genes. Red dotted box with inside yellow nodes the selected significant biological processes between DICER1
ones that were significant enriched nodes(genes) between and APC and red dotted box with black nodes
ATM and APC genes. between ATM DICER1
 Nodes genes network analysis result.
The annotated upregulated genes
searched in STRING Database

Fig 30 Biological process functional enrichment of resulting upregulated genes on basis of false discovery rate.
Selection of any biological process contribute to count
of genes involved by red color nodes or any other
color
Analysis result of final upregulated genes on basis of
biological process annotation.

Result of biological process annotation for ATM gene

 Plotted graph result for ATM gene on basis of
biological process annotation and false discovery rate.
From this study ,we predicted that colorectal cancer gene APC and kidney cancer
gene DICER1 did not interact in functionally enriched biological network but
common gene found in both the carcinomas i:e ATM showed much interactions
with APC gene in network and were found significant in biological process “mitotic
spindle cell cycle assembly checkpoint” during their annotation with false discovery
rate 0.0132<0.05 these genes were of mutant type.
 It revealed that ATM (Ataxia telangiectasia mutated; Serine/threonine protein
kinase which activates checkpoint signaling upon double strand breaks (DSBs),
thereby act as DNA damage sensor from (STRING)) ,Due to mutation in this gene,
alteration in biological function “mitotic spindle assembly checkpoint”occurs and it
would not activate checkpoint signaling and lead to uncontrolled division of cells
and metastasis of kidney neoplasia or develop secondry tumor. The 3D structure of
ATM gene is unknown and its role is still uncertain and can experimentally
validated in kidney cancer.
In Systems biology approach, the ATM gene predicted that might be
involved in metastasis of kidney neoplasia can be used as genetic marker for
earlier molecular diagnosis of earlier cancer stage like dysplasia or
neoplasia.Result of work done for hypothesis confirmed moderate risk of
secondry tumor.

This study can further be used to validate the role of ATM gene in kidney
cancer from experimental studies through microarray analysis.
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