Data linking genes and pathways.

Description

Table knownGene from track UCSC Genes was downloaded from the UCSC table browser for the human genome assembly (hg18, May 2006) and filtered for a selection of pathways associated with human metabolism was obtained from KEGG PATHWAY database. Bioconductor package KEGG.db was used to provide mappings between gene and pathway identifiers.

Usage

1

Format

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'data.frame':	2768 obs. of  14 variables:
 $ value     : int  9 9 9 9 9 9 9 9 10 10 ...
 $ name      : Factor w/ 59950 levels "uc001aab.2","uc001aac.2",..: 43054 43058 43053 43055 43056 43057 58586 58587 58588 43059 ...
 $ chrom     : Factor w/ 24 levels "chr1","chr2",..: 8 8 8 8 8 8 8 8 8 8 ...
 $ strand    : Factor w/ 2 levels "-","+": 2 2 2 2 2 2 2 2 2 2 ...
 $ txStart   : int  18111894 18113073 18111894 18111894 18113073 18113073 18113073 18123836 18301793 18293034 ...
 $ txEnd     : int  18125100 18125100 18125100 18125100 18125100 18125100 18125100 18124709 18302666 18303003 ...
 $ cdsStart  : int  18123836 18123836 18123836 18118682 18118682 18123836 18123836 18123836 18301793 18301793 ...
 $ cdsEnd    : int  18124709 18124709 18124709 18124709 18124709 18124709 18124709 18124709 18302666 18302666 ...
 $ exonCount : int  4 4 3 4 4 4 3 1 1 2 ...
 $ exonStarts: Factor w/ 64524 levels "0,1137,5766,12786,",..: 19845 19848 19847 19846 19849 19848 19850 19868 20093 20084 ...
 $ exonEnds  : Factor w/ 64568 levels "100000370,100002888,100004625,100007887,100009499,100010117,",..: 19917 19920 19919 19918 19922 19921 19923 19944 20170 20161 ...
 $ proteinID : Factor w/ 36856 levels "","A0A183","A0A4V9",..: 13218 13218 13218 23139 23139 13218 13218 13218 694 694 ...
 $ alignID   : Factor w/ 66803 levels "uc001aaa.2","uc001aab.2",..: 48418 48422 48417 48419 48420 48421 65330 65331 65332 48423 ...
 $ path      : chr  "hsa00232" "hsa00232" "hsa00232" "hsa00232" ...

References

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2010 Oct 18. http://genome.ucsc.edu/index.html?org=Human&db=hg19&hgsid=289810087

Marc Carlson, Seth Falcon, Herve Pages and Nianhua Li (). KEGG.db: A set of annotation maps for KEGG. R package version 2.6.1.

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., and Tanabe, M.; KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res. 40, D109-D114 (2012)

Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

Examples

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library(ggplot2)
library(RColorBrewer)
genes$chrom <- factor(genes$chrom, levels=c(paste("chr", 1:22, sep=""),
  "chrX", "chrY"))
ggparallel(
  list("path", "chrom"),
  text.offset = c(0.03, 0,-0.03),
  data = genes,
  width = 0.1,
  order = c(1, 0),
  angle = 0,
  color = "white",
  factorlevels =  c(sapply(unique(genes$chrom), as.character),unique(genes$path))
) +
 scale_fill_manual(
   values = c(brewer.pal("YlOrRd", n = 9), rep("grey80", 24)),
   guide = "none"
 ) +
 scale_colour_manual(
   values = c(brewer.pal("YlOrRd", n = 9), rep("grey80", 24)),
   guide = "none"
 ) +
 coord_flip()