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Project Title and Overview

Genome-wide analysis of H3K27me3 distribution and its functional correlation with 3D genome architecture in human cells

Translational Epigenomics in 3D Genome Architecture

Work done at Papantonis lab, Universitätsmedizin Göttingen

Integration of Micro-C & RNA-Seq to understand loop dynamics under PRC2 inhibition.

Background

To be updated

Data

Chapters

• Chapter.1 - Architectural changes

Micro-C and Loop Analysis

• QC & .pairs file generation - documentation
• Loop calling via Mustache, Cooltools-dots, Peakachu
• TAD calling - RobusTAD & Arrowhead
• A/B compartment analysis - Cooltools eigs-cis, Calder2
• Stripes - Stripenn, Stripecaller
• Differential analysis - diffDomain

RNA-Seq Analysis

Gene body analysis - DESeq2
Intron & Exon - iRNASeq
GO & Genomic coordinates - clusterProfiler, GSEA.py & TxDb

ML Modeling

Logistic Regression & Gradient Boost Model

Contact

aman.nalakath@tum.de or amanshamil@protonmail.com

to-dos

HiGlass server for visualizing loops -

to be added…