Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of yeast predicted transcription factor deletion mutant with a wild type congenic strain

ABSTRACT: Stress experiments repeating Gasch et al.,2000 conditions. For each set of conditions I compared a deletion mutant for a predicted transcription regulator with a congenic wt strain.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-1822 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.

Segal Eran E Shapira Michael M Regev Aviv A Pe'er Dana D Botstein David D Koller Daphne D Friedman Nir N

Nature genetics 20030601 2

Much of a cell's activity is organized as a network of interacting modules: sets of genes coregulated to respond to different conditions. We present a probabilistic method for identifying regulatory modules from gene expression data. Our procedure identifies modules of coregulated genes, their regulators and the conditions under which regulation occurs, generating testable hypotheses in the form 'regulator X regulates module Y under conditions W'. We applied the method to a Saccharomyces cerevis ...[more]

PMID: 12740579

Similar Datasets

Project description:The study sought to investigate differences in onset and progression of renal disease in the Dahl salt-sensitive (S), S.SHR(2) congenic, and spontaneously hypertensive rat (SHR) using a time-course. The data clearly demonstrates that the locus on chromosome 2 has a major and sustained ability to attenuate renal damage. As early as week 4, significant interstitial changes were observed between the S and the congenic which preceded any significant difference in proteinuria. Gene expression profiling was performed at week 4, 12, and 20 using kidney from the S and S.SHR(2) congenic to: (1) identify expression differences of positional candidates within the QTL region; (2) correlate temporal gene expression changes between the S and congenic with degree of renal damage; and (3) identify biochemical pathways potentially involved in the attenuated renal damaged observed in the congenic. Gene pathway analysis (IngenuityÂ® Systems) performed at week 4, 12, and 20 revealed that pathways involved in cellular assembly and organization, cellular movement, and immune response were controlled differently between the S and congenic. Considering all the data, the chromosome 2 congenic appears to attenuate renal damage primarily through an altered fibrotic response. Experiment Overall Design: DNA microarray analysis was performed using Affymetrix GenechipÂ® Rat Genome 230 2.0 array at three timepoints. The chip contains 31,000 probe sets from more than 30,000 transcripts on one array. Three male S and three male S.SHR(2) congenic were selected at random from each group test for proteinruia at week 4, 12 and 20. Kidney was cut into ~ 0.5cM size cubes, suspended in RNAlater (Ambion, Austin, TX) and stored overnight at 4ÂºC. RNA was extracted using TrizolÂ® reagent (Invitrogen, Carlsbad, CA) and purified using Mini RNeasy kit (Qiagen,Valencia, CA ) according to manufacturerâs protocols. RNA quality was assessed by an OD260/280 ratio > 2.0 and visually by ethidium bromide staining on an agarose gel. Experiment Overall Design: Biotinylated cRNA was synthesized from 10 ug of total RNA using the One-Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA) as directed by the user manual. cRNA quality for each sample was assessed by hybridization of 5ug adjusted kidney cRNA to Affymetrix GenechipÂ® Test3 array. Subsequently, 15ug adjusted kidney cRNA was hybridized to the GenechipÂ® Rat 230 2.0 array. Hybridized chips were automatically washed, stained and scanned at the Medical University of Ohio Bioinformatics & Proteomics/Genomics Program gene array facility using Affymetrix equipment.

Dataset Information

Transcription profiling of yeast predicted transcription factor deletion mutant with a wild type congenic strain

Publications

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure