SCHOOL OF BIOENGINEERING AND BIOSCIENCES

END TERM PRACTICAL

COURSE CODE: BTY400

COURSE TITLE: CAPSTONE PROJECT

COURSE INSTRUCTOR: DR. SHIKHA SUMAN

SUBMITTED BY: RETIK KOUL

REGISTRATION NO: 11908084

PROGRAMME: P131::B.TECH.
(BIOTECHNOLOGY)
 DATA SET FOR MICROARRAYS

A microarray database is a collection of microarray gene expression data. A microarray

database's primary functions are to store measurement data, manage a searchable index, and
make the data available to other programmes for analysis and interpretation (either directly, or
through user downloads).

Microarray datasets are made up of complex and high-dimensional samples and genes, and the
number of samples is often significantly lower than the number of genes. Gene selection is a
difficult process for microarray expression data analysis because of the data imbalance.

DIFFERENTIALLY EXPRESSED GENES

A gene is termed differentially expressed if there is a statistically significant difference or

change in read counts or expression levels/index between two experimental conditions.
Transcription is the examination of gene population expression or the variations in gene
population expression under different settings, situations, treatments, and stages. There are
several statistical approaches for analysing gene expression. To estimate the pattern of
differential gene expression, statistical distributions are applied. These genes are chosen based
on a combination of expression change threshold and score cut-off, which are typically
generated through statistical modelling.

MACHINE LEARNING

Machine learning in bioinformatics is the use of machine learning techniques to

bioinformatics, such as genomics, proteomics, microarrays, systems biology, evolution, and
text mining. Preceding to the advent of machine learning, bioinformatics algorithms had to be
manually programmed; this proved difficult for problems such as protein structure prediction.
Deep learning, for example, may learn aspects of data sets rather than needing the
programmer to describe them individually. The algorithm may be taught to combine low-level
characteristics into more abstract features, and so on. When properly trained, such
algorithms may generate
complex predictions thanks to their multi-layered strategy. In contrast to previous
computational biology approaches, which use existing datasets but do not enable the data to be
interpreted and analysed in unexpected ways, these methods allow the data to be interpreted
and analysed in unexpected ways. The amount and number of available biological datasets
have exploded in recent years.

INTERACTION NETWORK ANALYSIS

It is a method of representing systems as complex set of binary interactions between various

biological entities.

MICROARRAY

A microarray is a laboratory technique that detects the expression of thousands of genes

simultaneously. DNA microarrays are microscope slides that include thousands of small dots
in specific places, each of which has a recognised DNA sequence or gene. These slides are
frequently referred to as gene chips or DNA chips. The DNA molecules linked to each slide
serve as probes for detecting gene expression, which is also referred to as the transcriptome or
the collection of messenger RNA (mRNA) transcripts expressed by a group of genes.

NEXT GENERATION SEQUENCING

NGS is a massively parallel sequence alignment technology that provides ultra-high

throughput, scalability, and speed. The technology is used to determine the nucleotide order
in entire genomes or specific regions of DNA or RNA. NGS has transformed the biological
sciences, allowing labs to perform a wide range of applications and study biological systems
at a previously unimaginable level.

PROTEIN PROTEIN INTERACTION NETWORKING

An organism's PPI network serves as a skeleton for its signalling circuitry, which governs
cellular responsiveness to environmental and genetic inputs. Understanding this circuitry may
help anticipate gene activity and cellular behaviour in response to various inputs. On a
genome-wide scale, PPI networks recreate the plethora of physical interactions between
proteins.
 Systematic & Bibliometric Analysis of Stomach
Adenocarcinoma.

Abstract:

A bibliometric analysis may and should be done to recapitulate research on the prognosis of
stomach cancer. This bibliometric analysis examined research production connected to the
coronavirus disease (COVID-19) pandemic using the Web of Science database due to the
intense academic emphasis and pandemic concern throughout the world. Simultaneously, the
Journal of Medical Virology and CUREUS (Cureus Journal of Medical Science) were popular
publications. Other major terms highlighted included pandemic, pneumonia, epidemiology,
public health, outbreak, epidemic, China, infection, and therapy, in addition to COVID-19 and
the new coronavirus. To stay ahead of the virus and prevent it from spreading beyond the
scope of management, communication of disease presentation and transmission mechanisms
is still crucial. For the dataset resource, Web of Science was used. Using predetermined search
parameters, articles from the Web of Science Core Collection database that were published
between 2000 and 2020 were included. With parameters derived from included research,
bibliometric analysis was conducted using CiteSpace version 5.7.R1 and R software version
4.0.3. From 2000 to 2020, 1721 papers were included, with impressively growing patterns.
The top three institutions in terms of publications were SUN YAT SEN University, FUDAN
University, and NANJING MED University. Keywords having the highest citation bursts
between 2000 and 2020 were identified. The most recent increasing terms since 2017 were
"statistics," "resistance," "mortality," "lncrna," "diagnostic," "outcome," "migration,"
"promote," and "regulatory t cell." Several papers received the most citations, including Jemal
A. CA-CANCER J CLIN, Van Cutsem E. LANCET, and Japanese Gastric Cancer Association
GASTRIC CANCER. Conclusion: This bibliometric study yields a thought-provoking,
enlightening conclusion about the track of research progress in stomach cancer prognosis with
an outlook.

Keywords: Covid-19, gastric cancer, bibliometric analysis, prognosis, journal, Web of

Science
 LITRATURE REVIEW OF RESEARCH PAPERS (2022)
NAME OF THE AUTHORS BIOMARKERS PUBLICATION METHODS USED
PAPER THEY DATE
PROPOSED
Ferroptosis‐related Ruoxi Xiao, NOX4, CHAC1 13 January 2022 The Cancer Genome
gene NOX4, Shasha Wang, and HIF1A Atlas (TCGA)
CHAC1 and Jing Guo, Shihai
HIF1A are valid Liu, Aiping Ding,
biomarkers for Gongjun Wang,
stomach Wenqian Li, Yuqi
adenocarcinoma. Zhang, Xiaoqian
Bian, Shufen
Zhao, Wensheng
Qiu.

Identification of Hao Qian, TGF-β, FoxO and 16 May 2022 The Cancer Genome
miRNA biomarkers Nanxue Cui, Qiao miRNA Atlas (TCGA)
for stomach Zhou, Shihai
adenocarcinoma. Zhang.
Development of Min Fu, TMB, STAD 23 March 2022 The Cancer Genome
Tumor Mutation Yongbiao Huang, Atlas (TCGA) and
Burden-Related Xiaohong Peng, the Gene Expression
Prognostic Model Xiaoyu Li, Na Omnibus (GEO)
and Novel Luo, Wenjun
Biomarker Zhu,
Identification in Feng Yang, Ziqi
Stomach Chen,
Adenocarcinoma. Shengling Ma,
Yuanyuan Zhang,
Qianxia Li
and
Guangyuan Hu.

Ferroptosis-related Dandan Zhu, SLC1A5, 19 March 2022 gene ontology (GO)

gene SLC1A5 is a Sifan Wu, Yafang lncRNA, miRNA and Kyoto
novel prognostic Li, Yu Zhang, encyclopaedia of
biomarker and Jierong Chen, genes and genomes
correlates with Jianhong Ma, (KEGG)
immune infiltrates Lixue Cao, Zejian
in stomach Lyu & Tieying
adenocarcinoma. Hou.
Discovery of Ji Chen, Yang COL10A1, CST1, 11 April 2022 The Cancer Genome
Stomach Hao, Tianjun ESM1, HOXC11 Atlas (TCGA)
Adenocarcinoma Wang, Daiyun and HOXC9,
Biomarkers by Huang, Xin Liu. GAD1, HOXA11
Consensus Scoring and PRKCG
of Random
Sampling and
Machine Learning
Modeling.
Comprehensive Zhengguang EDNRA, 21 April 2022 Receiver Operating
analysis of Wang, Kangchun Endothelin Characteristic (ROC)
expression Wang, Xue Yu, Receptor Type A and Endothelin
signature and Moye Chen, Yaqi Receptor Type A
immune Du. (EDNRA)
microenvironment
signature of
biomarker
Endothelin
Receptor Type A in
stomach
adenocarcinoma.

Assessment of Mingyu Zhu, POLE and 2 May 2022 POLE/POLD1 mutat

POLE and POLD1 Haiyan Cui, Lu POLD1 ions and clinical
mutations as Zhang, Kuo Zhao, characteristics
prognosis and Xiaochen Jia,
immunotherapy Hao Jin.
biomarkers for
stomach
adenocarcinoma
GGT5 Is an Yong Huang, CTLA4, GGT5 26 Feb 2022 Gene Set
Independent HaiLang Zhou, Enrichment Analysis
Prognostic Junwei Zou, (GSEA)
Biomarker in Dong Wang.
Stomach
Adenocarcinoma.