kegggraphs: kegggraphs

In ddepn: Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.

Description

Contains a list of selected KEGG pathways, downloaded in October 2010.

Format

List of 78, each Element holding the KEGG pathway id and an adjacency matrix.

Details

The KEGG Hierarchy was downloaded and transformed into graphNEL objects by using the KEGGgraph R-package. Each graphNEL was converted to simple adjacency matrices. A selection of pathways was performed to restrict to the signalling and disease pathways:

The following pathways are included:

KEGG pathway ID	Name
04010	MAPK signaling pathway
04012	ErbB signaling pathway
04020	Calcium signaling pathway
04060	Cytokine-cytokine receptor interaction
04080	Neuroactive ligand-receptor interaction
04110	Cell cycle
04115	p53 signaling pathway
04120	Ubiquitin mediated proteolysis
04130	SNARE interactions in vesicular transport
04140	Regulation of autophagy
04150	mTOR signaling pathway
04210	Apoptosis
04310	Wnt signaling pathway
04320	Dorso-ventral axis formation
04330	Notch signaling pathway
04340	Hedgehog signaling pathway
04350	TGF-beta signaling pathway
04360	Axon guidance
04370	VEGF signaling pathway
04510	Focal adhesion
04512	ECM-receptor interaction
04514	Cell adhesion molecules (CAMs)
04520	Adherens junction
04530	Tight junction
04540	Gap junction
04610	Complement and coagulation cascades
04612	Antigen processing and presentation
04614	Renin-angiotensin system
04620	Toll-like receptor signaling pathway
04630	Jak-STAT signaling pathway
04640	Hematopoietic cell lineage
04650	Natural killer cell mediated cytotoxicity
04660	T cell receptor signaling pathway
04662	B cell receptor signaling pathway
04664	Fc epsilon RI signaling pathway
04670	Leukocyte transendothelial migration
04710	Circadian rhythm
04720	Long-term potentiation
04730	Long-term depression
04740	Olfactory transduction
04742	Taste transduction
04810	Regulation of actin cytoskeleton
04910	Insulin signaling pathway
04912	GnRH signaling pathway
04914	Progesterone-mediated oocyte maturation
04916	Melanogenesis
04920	Adipocytokine signaling pathway
04930	Type II diabetes mellitus
04940	Type I diabetes mellitus
04950	Maturity onset diabetes of the young
05010	Alzheimer's disease
05012	Parkinson's disease
05014	Amyotrophic lateral sclerosis (ALS)
05110	Vibrio cholerae infection
05120	Epithelial cell signaling in Helicobacter pylori infection
05130	Pathogenic Escherichia coli infection - EHEC
05131	Pathogenic Escherichia coli infection - EPEC
05200	Pathways in cancer
05210	Colorectal cancer
05211	Renal cell carcinoma
05212	Pancreatic cancer
05213	Endometrial cancer
05214	Glioma
05215	Prostate cancer
05216	Thyroid cancer
05217	Basal cell carcinoma
05218	Melanoma
05219	Bladder cancer
05220	Chronic myeloid leukemia
05221	Acute myeloid leukemia
05222	Small cell lung cancer
05223	Non-small cell lung cancer
05310	Asthma
05320	Autoimmune thyroid disease
05322	Systemic lupus erythematosus
05330	Allograft rejection
05332	Graft-versus-host disease
05340	Primary immunodeficiency

Source

http://www.genome.jp/kegg/

References

Kanehisa: Kyoto Encyclopaedia of Genes and Genomes

Examples

## Not run: 
library(ddepn)
data(kegggraphs)
names(kegggraphs)

## End(Not run)

ddepn documentation built on May 2, 2019, 4:42 p.m.