hg_apopPath: Apoptosis sub-pathway dataset
In SimRVSequences: Simulate Genetic Sequence Data for Pedigrees

Description Usage Format Details References

This data set catalogs combined exon segments from the 25 genes that have the highest interaction with the TNFSF10 gene, a known member of the human apoptosis pathway.

1	hg_apopPath

A data set with 253 rows and 5 variables:

chrom: Numeric. The chromosome number.
exonStart: Numeric. The position of the first base pair.
exonStop: Numeric. The position of the last base pair.
NCBIref: Character. The NCBI reference sequence accession number of the gene(s) in which the exon(s) reside.
gene: Character. The name of the gene.

The hg_apopPath data set catalogs the positions of exons residing in the 25 genes that have the highest interaction with the TNFSF10 gene. The data contained in the hg_apopPath data set was collected from the hg 38 reference genome with the UCSC Genome Browser. The 25 genes that have the highest interaction with the TNFSF10 gene were identified by the UCSC Genome Browser's Gene Interaction Tool. In hg_apopPath overlapping exons have been combined into a single observation. When exons from genes with different NCBI accession numbers have been combined the variable NCBIref will contain multiple accession numbers separated by commas. We note that different accession numbers may exist for transcript variants of the same gene.

Karolchik, D., Hinrichs, A. S., Furey, T. S., Roskin, K. M., Sugnet, C. W., Haussler, D., and Ken, W. J. (2004). The UCSC Table Browser data retrieval tool. Nucleic Acids Res. Accessed on 20 February 2018.

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., and Haussler, D. (2002). The human genome browser at UCSC. Genome Res, 12(6):996-1006.

Poon, H., Quirk, C., DeZiel, C., and Heckerman, D. (2014). Literome: Pubmed-scale genomic knowledge base in the cloud. Bioinformatics, 30:2840-2842. Accessed on 20 February 2018.

SimRVSequences documentation built on July 1, 2020, 6:03 p.m.