Cancer Genes Expression analysis | GEPIA2 | DEG Survival Analysis| Lecture 420 | Dr. Muhammad Naveed

Cancer Gene Expression Profiling iterative analysis (GEPIA2):
GEPIA2 weblink: gepia2.cancer-p...
Single Gene Analysis: gepia2.cancer-p...
Differential Expression Analysis: gepia2.cancer-p...
Expression DIY: gepia2.cancer-p...
Survival Analysis: gepia2.cancer-p...
Isoform Details: gepia2.cancer-p...
Correlation Analysis: gepia2.cancer-p...
Examples for GEPIA2 Usage: gepia2.cancer-p...#e3
Introduction:
Statement: All the datasets on the server are computed by a standard pipeline and are compatible with each other. Use the Google Chrome browser for best visualization quality.
GEPIA2 is a web server for analyzing the RNA sequencing expression data of 9,736 tumors and 8,587 normal samples from the TCGA and the GTEx projects, using a standard processing pipeline.
Differential Expression Analysis
This feature allows users to apply custom statistical methods and thresholds on a given dataset to dynamically obtain differentially expressed genes and their chromosomal distribution.
Parameters
Dataset: Select a cancer type of interest.
Chromosome Distribution: Select “Over-expressed”, “Under-expressed” or “Both” for chromosomal distribution plots.
Differential thresholds: [See detail of differential analysis methods here]
Differential Methods: Select a method for differential analysis.
|log2FC| Cutoff: Set custom fold-change threshold.
q-value Cutoff: Set custom q-value threshold.
Percentage Cutoff: Set custom percentage threshold.
For the ANOVA and LIMMA options, genes with higher |log2FC| values and lower q values than pre-set thresholds are considered differentially expressed genes.
For the Top 10 option, genes with higher log2FC values and higher percentage value than the thresholds are considered over-expressed genes; thus, only over-expressed genes will be presented in the list and the chromosomal plot.
DIY Expression
GEPIA plots expression profiles of a given gene according to selected datasets and statistical methods by cancer types or pathological stages. The details are shown below:
Gene Expression Profile
GEPIA generates dot plots profiling gene expression across multiple cancer types and paired normal samples, with each dot representing a distinct tumor or normal sample.
Differential thresholds: [See detail of differential analysis methods here]
Differential Methods: Statistical methods used for differential gene expression analysis.
|log2FC| Cutoff: Set custom fold-change threshold.
q-value Cutoff: Set custom q-value threshold.
Percentage Cutoff: Set custom percentage threshold.
Box Plots
GEPIA generates box plots with jitter for comparing expression in several cancer types (For best visual quality, we recommend 1-4 cancer types).
Survival Analysis
GEPIA performs overall survival (OS) or disease free survival (DFS, also called relapse-free survival and RFS) analysis based on gene expression. GEPIA uses Log-rank test, a.k.a the Mantel-Cox test, for hypothesis test. Cohorts thresholds can be adjusted, and gene-pairs can be used. The cox proportional hazard ratio and the 95% confidence interval information can also be included in the survival plot. Genes most associated with patient survival can be searched.
About Dr. Muhammad Naveed
(HoD, Biotechnology, University of Central Punjab, Lahore)
With distinction, Dr. Muhammad Naveed obtained a Ph.D. degree in Biotechnology (Genomics & Bioinformatics) from Quaid-e-Azam University, Islamabad. He has won Ph.D. indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research at the University of Ghent, Belgium. HEC awarded him the best Ph.D. (IRSIP) Scholar of the Year in 2013 & QAU honored him as a “Distinguished Alumni” in 2017. He is doing research projects in Bioinformatics, Molecular Biotechnology, Nano-informatics and vaccine designing, and Drug designing against infectious diseases. He has supervised 90 MSc. and 80 MPhil. & 02 Ph.D. students. He has published 162 Research articles with 1246 impact factors, 7060 citations, 01 book, 06 book chapters, and filed 05 Patents. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).
Contact links:
1. Official website: ucp.edu.pk/mem...
2. Facebook: / drmuhammadnaveed22
3. LinkedIn: www.linkedin.c...
4. Instagram: / prof.dr.naveed
5. Google Scholar: scholar.google...
6. ResearchGate: www.researchga...
7. Twitter: / naveedqau
#geneexpression #cancer #GEPIA2 #tumors #bioinformatics #drmuhammadnaveed

[@zombie8122]

Can we check protein expression through this software

[@madhuripagare7523]

Sir, how to meta analysis for gene?

[@BIOTECH-63100]

Please Alzheimer's disease sy relate hai koi website to wo bi guide kr dy

[@bioworld7565]

Sir effect of various drugs on animal modela ka koi software hai toh plz bataye

[@Prof.Dr.MuhammadNaveed]

sure use toxpred