Methods

Datasets and Annotation

Mapping the Chimeric Transcripts by the RNA-Seq Paired Reads

Chimeras with the Hi-C points

High-throughput chromosome conformation capture (Hi-C) is a method to identify chromatin interactions across an entire genome. Hi-C experiments aim to measure the frequencies of contacts between all pairs of loci in the genome. So Hi-C quantifies interactions between all possible pairs of fragments simultaneously. The ChiTaRS database provides evidence of Hi-C points in the chimeras.

The ChiTaRS database includes Hi-C chromatin contact maps from public datasets for four organisms, namely, human, mouse, fruit fly, and yeast. We have included nearly 5,600 chimeras, spanning across 14 cell lines and tissue samples. The following Hi-C resources were used in the ChiTaRS database:

Organism GEO link Library/cell line .hic file(,s)
Human GSE63525 GM12878 [GSE63525 GM12878 dilution combined], [GM12878 combined in situ from Cell 2014]
Human GSE63525 HUVEC [GSE63525 HUVEC combined], [HUVEC 1in situ combined]
Human GSE63525 NHEK [NHEK combined], [NHEK 1in situ combined]
Human GSE63525 HMEC [HMEC combined], [HMEC 1in situ combined]
Human GSE63525 K562 [K562 combined], [K562 in situ combined]
Human GSE63525 KBM7 [KBM7 combined], [KBM7 in situ combined]
Human GSE63525 IMR90 [IMR90 combined], [IMR90 1in situ combined]
Human - HeLa [HeLa in situ combined]
Mouse GSE71831 Patski [Patski], [PNAS 2016 Patski combined]
Mouse GSE96692 C57BL/6 [GSM2544836_No_Tx]
Mouse GSE96692 C57BL/6 [GSM2544837_TAC]
Mouse GSE96692 C57BL/6 [GSM2544839_Tx_Cre-plus]
Mouse GSE119171 F123 [GSE119171_JL]
Mouse GSE63525 CH12-LX [GSE63525_CH12-LX]
Fly GSE89244 Kc167 [GSM2362844_CP190_HiChIP], [CP190_HiChIP]
Fly GSE89112 Kc167 [GSE89112_Kc167combined], [GSE89112_Kc167combined]
Yeast SRP053245 SRR1791297 [SRR1791297]
Yeast SRP053245 SRR1791299 [SRR1791299]

Visualization of Chimeras by SpliceGraphs

Identification Chimeric Proteins by the Mass-Spectrometry Experiments

References

  1. Li, X. et. al. (2009) Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes. J Mol Evol. 68(1):56-65.
  2. Kim, P. et. al. (2010) ChimerDB 2.0-a knowledgebase for fusion genes updated. Nucleic Acids Res. 38(Database issue): D81-5.
  3. Guido Lab. GEM Tool and Library.
  4. Rogers, M.F. et. al. (2012) SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol. 13(1): R4.
  5. Tress, M.L. et. al. (2008) Proteomics studies confirm the presence of alternative protein isoforms on a large scale Genome Biol. 9(11): R162.