Project description:Based on fuzzy logic selection and classification algorithms, our selection method measures the contribution of each gene for each of two pre-defined classes in order to find the best discrimination. This algorithm extracts and ranks the most pertinent markers, since it is based on feature weighting according to optimal error rate, sensitivity and specificity. We applied the fuzzy logic selection on four breast cancer microarray databases to obtain new gene signatures based on histological grade. To validate these gene signatures, we designed probes for the selected genes on Nimblegen custom microarrays and tested them on a series of 151 consecutive invasive breast carcinomas displaying clinicopathological features similar to those observed in routine practice. 151 frozen breast cancer tumors from the tumor bank of the Claudius Regaud Institute (ICR Toulouse, France) were selected. This cohort consisted of consecutive invasive breast carcinoma patients treated at Claudius Regaud Institute between 2009 and 2011. All patients included in this cohort signed an informed consent. Clinico-pathological characteristics of the series were similar to those observed in routine clinical practice (i.e. majority of pre-menopausal patients presenting with T1c, node negative, ER+ invasive ductal carcinoma of intermediate grade).

2014-01-12 | E-GEOD-53958 | biostudies-arrayexpress

Biogas reactor metagenomic communities

Project description:Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community

| PRJNA723176 | ENA

biogas fermenter metagenome

Project description:anaerobic conversion of CO to H2 Raw sequence reads

| PRJNA294844 | ENA

Steady-state samples of Methanococcus maripaludis MM901 grown on formate under hydrogen limited conditions

Project description:Hydrogenotrophic methanogenic Archaea are defined by a H2 requirement for growth. Despite this requirement, many hydrogenotrophs are also capable of growth with formate as an electron donor for methanogenesis. Hydrogenotrophs respond to H2 starvation both phenotypically and at the level of gene expression; however, the responses during growth on formate have not been characterized. Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H2 excess or formate excess, suggesting that energy spilling occurs. Using microarray analysis, we show that the expression of genes encoding F420-dependent steps of methanogenesis, including one of two formate dehydrogenases, increased with H2 starvation, but with formate occurred at high levels regardless of limitation or excess. One gene, encoding H2-dependent methylene-tetrahydromethanopterin dehydrogenase, decreased in expression with either H2 limitation or formate limitation. Expression of genes for the second formate dehydrogenase, molybdenum-dependent formylmethanofuran dehydrogenase, and molybdenum transport increased specifically with formate limitation. Of the two formate dehydrogenases, only the first could support growth on formate in batch culture where formate was in excess.

2013-05-03 | GSE42111 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data