Cancer Immune response and Immunotherapy analysis | TIMER 2:0 | Lecture 421 | Dr. Muhammad Naveed

TIMER analyzes the immune infiltrates across diverse cancer types:
TIMER 2:0 weblink: timer.cistrome.org/
Immune Gene Analysis:
Instruction: Gene module allows users to select any gene of interest and visualize the correlation of its expression with immune infiltration level in diverse cancer types. Once your interested gene and immune infiltrates submitted, a heatmap with numbers will show the purity-adjusted spearman's rho across various cancer types. When you click your interested cell on the heatmap, a scatter plot will pop out to present the relationship between infiltrates estimation value and gene expression. Tumor purity is a major confounding factor in this analysis, since most immune cell types are negatively correlated with tumor purity. Therefore, we recommend users to select the “Purity Adjustment” option, which will use the partial Spearman’s correlation to perform this association analysis. Specially, for methods like EPIC and quanTIseq, which provide cell fractions referred to total cells, tumor purity and immune infiltration are necessarily negatively correlated, hence there is no need to adjust purity for the asscociation analysis using the estimations from EPIC and quanTIseq.
2. Mutant Gene Analysis:
Instruction: Mutation module allows users to analyze and visualize the effect of gene mutations on immune cell infiltration across multiple cancer types and immune cell types simultaneously. User can input a gene by either manually typing the gene name or selecting from a list of commonly mutated genes ordered by mutation frequency. Given the input gene, TIMER2.0 displays a bar plot showing mutation frequency of the gene for each TCGA cancer type. When the user specifies the immune cell type and clicks submit, TIMER2.0 presents a heatmap table of the log-fold changes of immune infiltration level between tumors with the input gene mutated and tumors without. User can click an entry on the heatmap to see violin plots of immune infiltration distribution in the mutant vs wildtype tumors.
3. sCNA analysis
Instruction: sCNA Module allows a user to compare immune infiltration distribution by the sCNA status of a gene across TCGA cancer types. GISTIC2.0 (25) estimates the sCNA information from copy number segmentation profiles at the gene level, including “deep deletion”, “arm-level deletion”, “diploid/normal”, “arm-level gain”, and “high amplification” defined by GISTIC2.0. Given the input gene, TIMER2.0 displays a stacked bar plot showing the relative proportion of different sCNA states of the gene for all TCGA cancer types. TIMER2.0 requires the user to specify a “deep deletion” or “high amplification” alteration status of the gene to compare with the “diploid/normal” status. When a user submits a query, TIMER2.0 draws a heatmap table for the log-fold changes of immune infiltration levels between the specified alteration group and the normal one. With a click on an entry of the table, the user can view the immune infiltration distribution between different sCNA status of the gene on a violin plot for pairwise comparisons of normal group with each alteration group.
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 172 Research articles with 1246 impact factors, 8060 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/member/dr-muhammad...
2. Facebook: / drmuhammadnaveed22
3. LinkedIn: www.linkedin.com/in/dr-muhamm...
4. Instagram: / prof.dr.naveed
5. Google Scholar: scholar.google.com/citations?...
6. ResearchGate: www.researchgate.net/profile/...
7. Twitter: / naveedqau
#geneexpression #cancer #timer #tumors #bioinformatics #drmuhammadnaveed

[@arpitajena8866]

Sir, pls make some video related to bioinformatic tools in antibiotic resistance

[@starlightmadhu]

very informative sir💯

[@Prof.Dr.MuhammadNaveed]

glad its help you

[@Uthman_Humzah]

assalamu alaikum Dear Sir, I want to get some information about taking getting admission in undergraduate program in BS biotechnology, BS Bioinformatics and BS Biomedical Engineering. I got 1052 in FSc pre medical and 1068 in matric. I have taken MDCAT two times and now i am appearing for MDCAT for third time. Kindly guide me about these fields. Also give me information about Pharmacy and DVM.i would be very thankful to you

[@mahrukhzahid4611]

Drawback:They are giving limited cancers

[@lifesciencedecoded]

Sir jese humne docking kar li, ab hume redocking karna hai kon saa software best rahega? Please bata dijiye aapne hamesha help ki h......

[@lifesciencedecoded]

Sir which software is used to predict the anti-cancer compound ?

[@ZafarAli-lj5yn]

YoYou might be check chembl or pubchem

[@lifesciencedecoded]

Thank you bro