AT_Stress_Space_Detailed: Detailed arabidopsis thaliana Stress Space Based on ATH1 Chip...

Description Usage Format Details Source


AT_Stress_Space_Detailed spans a 569-dimension physiological space constructed from 50 different Arabidopsis thaliana stress-response gene expression datasets from "Gene Expression Omnibus" (GEO). All datasets are measured by Affymetrix Arabidopsis ATH1 Genome Array.




A matrix with genes as rows and different physiological dimensions in columns. Gene Entrez IDs are stored in rownames and space-dimension names in colnames.


Here's the list of datasets used for making this Space: GSE10643, GSE10670, GSE11558, GSE12029, GSE12619, GSE13739, GSE14496, GSE14502, GSE15577, GSE16474, GSE16765, GSE17464, GSE17479, GSE18217, GSE18666, GSE19264, GSE19271, GSE19273, GSE19520, GSE19700, GSE22107, GSE22671, GSE24177, GSE2473, GSE26679, GSE26983, GSE27861, GSE27985, GSE28297, GSE30095, GSE30702, GSE34130, GSE35258, GSE35580, GSE38030, GSE39236, GSE39268, GSE39384, GSE40061, GSE40354, GSE40998, GSE43724, GSE41626, GSE42007, GSE44053, GSE44655, GSE44922, GSE46107, GSE46205, GSE49596, GSE50526, GSE52117, GSE5520, GSE5539, GSE55431, GSE55835, GSE55906, GSE55907, GSE5615, GSE5616, GSE5617, GSE5620, GSE5621, GSE5622, GSE5623, GSE5624, GSE5625, GSE5626, GSE5627, GSE5628, GSE5686, GSE5727, GSE58370, GSE58616, GSE58620, GSE60960, GSE61484, GSE61684, GSE6177, GSE6583, GSE7631, GSE7641, GSE7642, GSE8787, GSE9719

The difference between AT_Stress_Space and AT_Stress_Space_detailed is that in AT_Stress_Space all stressed dimensions with the same stress type are summarized to make a universal axis for each stress type, while in the space of AT_Stress_Space_detailed stress responses from different datasets have their own dedicated dimension.

Source[GSEXXXX] (Replace GSEXXXX by one of the actual dataset series names listed in 'Details' section.)

JRC-COMBINE/PlantPhysioSpace documentation built on Nov. 25, 2020, 8:01 a.m.