Skip to content
Meizhen Zheng Lab edited this page May 28, 2025 · 21 revisions

This wiki aims to present our approaches to data processing, analysis, and visualization in the study of the roX2-RDD.

Tian, Simon Zhongyuan#*; Yang, Yang#; Ning, Duo#; Fang, Ke#; Jing, Kai; Huang, Guangyu; Xu, Yewen; Yin, Pengfei; Huang, Haibo; Chen, Gengzhan; Deng, Yuqing; Zhang, Shaohong; Zhang, Zhimin; Chen, Zhenxia; Gao, Tong; Chen, Wei; Li, Guoliang; Tian, Ruilin; Ruan, Yijun*; Li, Yiming*; Zheng, Meizhen*. 3D chromatin structures associated with ncRNA roX2 for hyperactivation and coactivation across the entire X chromosome. Science Advances, 2024, 10(30): eado5716.

Index

01. RDD and ChIA‐PET data processing

02. RNA‐seq data processing

03. Peak correlation

04. Loop correlation

05. Peak distribution of chromatin states and genomic locations

06. Chromosome‐wise binding and interaction enrichment

07. roX2 mediated chromatin interaction networks of wild type and heat shock S2 cell

08. Identification and Analysis of Active and Inactive Domains

09. Definition of roX2 enriched boots

10. roX2 boots boundaries enrichment profiles of beaf, H3K27ac and H3K27me3 signals

11. Features active inactive domains and roX2 boots

12. Domain to domain interactions displayed by heatmap

13. Tornado plots of peak region signal enrichment of roX2 RDD in wild type and heat shock S2 cells

14. Peak aggregation plot

15. Loop aggregation plot

16. Four types of roX2 associated genes

17. Aggregation plots of four types of genes against various factors

18. Gene expression of the 4 types of genes between S2 and Kc167 cells and within wilt‐type heat shock and recovery S2 cells

19. Relationship between intra‐gene and inter‐gene

20. Behaviors of the 24 boot‐disappeared genes on intra‐gene and inter‐gene

21. Gene expression in different cells of Aging Fly Cell Atlas

22. Kc167 and S2 cell loops aggregation at 4 types of gene

23. Extract coordinates from high resolution imaging Data

24. Using GMM Method Automatically Cluster The X Chromosome High‐Resolution Imaging Data

25. Minimum distance of cluster‐center to cluster‐center

26. Spatial density of image dots of clusters

27. Domain type classification

28. Determine the number of centroid for each roX2 photo cluster

29. Determine the number of centroid for each H3K27me3 photo cluster

30. Motif analysis on roX2 peak and loop anchor

31. Analysis of roX2 interacting proteins via Mass Spectrometry (MS)

32. roX2 dynamics in embryonic cells based on imaging data

33. roX2 dynamics in embryonic cells based on omics data

Software used in this work

Clone this wiki locally