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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
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
16. Four types of roX2 associated genes
17. Aggregation plots of four types of genes against various factors
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
Data processing and analyzing method for article roX2-RDD