SPELL - Nematode

Citation	Singh KD, Roschitzki B, Snoek LB, Grossmann J, Zheng X, Elvin M, Kamkina P, Schrimpf SP, Poulin GB, Kammenga JE, Hengartner MO. Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways. PLoS One, 2016.
PubMed ID	26985669
Short Description	Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways. GEO Record: GSE77905 Platform: GPL10094 Download gene-centric, log2 transformed data: WBPaper00049380.ce.mr.csv
# of Conditions	78
Full Description	Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch, and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains N2 (Bristol) and CB4856 (Hawaii) to enable quantitative trait locus (QTL) mapping. About half of the cases from the 44 genes tested showed a statistically significant change in protein abundance between various strains, most of these were however very weak (below 1.3-fold change). We detected a distant QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels. Experimental Details: WBPaper00049380:WN190_Array01_Cy3 WBPaper00049380:WN124_Array02_Cy3 WBPaper00049380:WN116_Array03_Cy3 WBPaper00049380:WN110_Array04_Cy3 WBPaper00049380:control_Array05_Cy3 WBPaper00049380:control_Array06_Cy3 WBPaper00049380:WN021_Array07_Cy3 WBPaper00049380:control_Array08_Cy3 WBPaper00049380:WN174_Array09_Cy3 WBPaper00049380:WN153_Array10_Cy3 WBPaper00049380:WN072_Array11_Cy3 WBPaper00049380:N2_Array12_Cy3 WBPaper00049380:WN128_Array13_Cy3 WBPaper00049380:WN162_Array14_Cy3 WBPaper00049380:WN034_Array15_Cy3 WBPaper00049380:control_Array16_Cy3 WBPaper00049380:control_Array17_Cy3 WBPaper00049380:WN158_Array18_Cy3 WBPaper00049380:control_Array19_Cy3 WBPaper00049380:WN176_Array20_Cy3 WBPaper00049380:WN177_Array21_Cy3 WBPaper00049380:WN152_Array22_Cy3 WBPaper00049380:control_Array23_Cy3 WBPaper00049380:control_Array24_Cy3 WBPaper00049380:WN140_Array25_Cy3 WBPaper00049380:control_Array26_Cy3 WBPaper00049380:WN186_Array27_Cy3 WBPaper00049380:control_Array28_Cy3 WBPaper00049380:control_Array29_Cy3 WBPaper00049380:control_Array30_Cy3 WBPaper00049380:control_Array31_Cy3 WBPaper00049380:CB4856_Array32_Cy3 WBPaper00049380:control_Array33_Cy3 WBPaper00049380:WN076_Array34_Cy3 WBPaper00049380:WN106_Array35_Cy3 WBPaper00049380:WN109_Array36_Cy3 WBPaper00049380:WN142_Array37_Cy3 WBPaper00049380:WN135_Array38_Cy3 WBPaper00049380:control_Array39_Cy3 WBPaper00049380:control_Array01_Cy5 WBPaper00049380:WN098_Array02_Cy5 WBPaper00049380:control_Array03_Cy5 WBPaper00049380:control_Array04_Cy5 WBPaper00049380:WN020_Array05_Cy5 WBPaper00049380:WN038_Array06_Cy5 WBPaper00049380:CB4856_Array07_Cy5 WBPaper00049380:WN071_Array08_Cy5 WBPaper00049380:control_Array09_Cy5 WBPaper00049380:WN048_Array10_Cy5 WBPaper00049380:WN161_Array11_Cy5 WBPaper00049380:control_Array12_Cy5 WBPaper00049380:control_Array13_Cy5 WBPaper00049380:WN146_Array14_Cy5 WBPaper00049380:control_Array15_Cy5 WBPaper00049380:WN058_Array16_Cy5 WBPaper00049380:WN185_Array17_Cy5 WBPaper00049380:control_Array18_Cy5 WBPaper00049380:WN129_Array19_Cy5 WBPaper00049380:N2_Array20_Cy5 WBPaper00049380:WN113_Array21_Cy5 WBPaper00049380:control_Array22_Cy5 WBPaper00049380:WN159_Array23_Cy5 WBPaper00049380:WN057_Array24_Cy5 WBPaper00049380:control_Array25_Cy5 WBPaper00049380:WN134_Array26_Cy5 WBPaper00049380:control_Array27_Cy5 WBPaper00049380:WN041_Array28_Cy5 WBPaper00049380:WN098_Array29_Cy5 WBPaper00049380:WN046_Array30_Cy5 WBPaper00049380:N2_Array31_Cy5 WBPaper00049380:control_Array32_Cy5 WBPaper00049380:CB4856_Array33_Cy5 WBPaper00049380:control_Array34_Cy5 WBPaper00049380:control_Array35_Cy5 WBPaper00049380:control_Array36_Cy5 WBPaper00049380:control_Array37_Cy5 WBPaper00049380:control_Array38_Cy5 WBPaper00049380:WN075_Array39_Cy5.
Tags	Method: microarray, Species: Caenorhabditis elegans, Topic: natural variant