AT_Stress_Space_RNASeq: Arabidopsis thaliana Stress Space Based on RNA-seq SRA Data

In JRC-COMBINE/PlantPhysioSpace: Plant Stress Response Analysis by Mapping into Physiological Spaces

Description

AT_Stress_Space_RNASeq spans a 7-dimension physiological space constructed from 8 different Arabidopsis thaliana stress-response gene expression datasets from "Sequence Read Archive" (SRA).

Usage

data(AT_Stress_Space_RNASeq)

Format

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.

Details

Here's the list of datasets used for making this Space: PRJEB13938 (E.MTAB.4683), PRJNA232536 (GSE53641), PRJNA263595 (GSE62256), PRJNA272425 (GSE64870), PRJNA315516, PRJNA319318 (GSE80565), PRJNA348676 (GSE88798), PRJNA412447

The difference between AT_Stress_Space_RNASeq and AT_Stress_Space_RNASeq_detailed is that in AT_Stress_Space_RNASeq 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_RNASeq_detailed stress responses from different datasets have their own dedicated dimension.

Source

https://www.ncbi.nlm.nih.gov/bioproject/[PRJXXXX] (Replace PRJXXXX 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.