Sentences with phrase «ogsv2 gene set»

The method identifies gene sets that show evidence for positive selection in comparison with matched controls, and thus highlights genes for further functional studies.

I also note that you must be democrat because you want to redistribute oxygen from beleivers to those your party finds to have a superior gene set.

All the babies start with the same gene set: They're either all boys or all girls, and they'll look alike.

A new meta - analysis suggests that low expression levels of 10 related gene sets responsible for mitochondrial machinery play an important role in this disorder — all previously unlinked to Parkinson's.

The study, published online today in Science Translational Medicine, further points to a master switch for these gene sets as a potential target of future therapies.

But it's associated with liver problems in rare individuals carrying another specific gene set.

However, the MIT team adapted it to randomly turn on or off distinct gene sets across large populations of cells, allowing the researchers to identify genes that protect cells from a protein associated with Parkinson's disease.

«The state of the art right now is targeting two or three genes simultaneously and then looking at the effects, but we think that perhaps the gene sets that need to be modulated to address some of these diseases are actually broader than that,» says Lu, who is the senior author of the study.

The scientists were thus for the first time able to identify gene sets responsible for steering specific memory processes.

The genes set off production of a protein, neurogenin - 3 (Ngn3); thus, generating new, healthy insulin - producing beta cells.

When ants are born with two of the same sex determination gene sets, they become sterile diploid males, even if they should develop as females.

«Three gene sets could predict response to rheumatoid arthritis therapies.»

From these efforts, we identified a high - quality orthologous gene set across avian species, consisting of exons from 8251 syntenic protein - coding genes (~ 40 % of the proteome), introns from 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~ 1000 bp of flanking sequences.

«BinoX works so well thanks to the high density of the FunCoup networks, which makes it possible to find many functional network links between gene sets, even if they have no shared genes.

«Ten years ago, people would have laughed at the idea of bacteria with such a small gene set.»

To make BinoX directly usable for other researchers, a public web server http://PathwaX.sbc.su.se (Ogris et al., 2016b) was set up for on - line pathway analysis of single gene sets, which applies the BinoX algorithm to all KEGG pathways and FunCoup networks.

The paper demonstrates how BinoX can be used to find many biologically meaningful pathway annotations for gene sets from cancer and other diseases, which are not found by other methods.

The second tool, SuperExactTest, establishes the very first theoretical framework for assessing the statistical significance of multi-set intersections and enables users to compare very large sets of data, such as gene sets produced from genome - wide association studies (GWAS) and differential expression analysis.

Surprisingly, these conserved gene sets were also associated with several other biological traits, which evolved multiple times in ants, such as number of queens in a colony, whether an ant species is invasive or not, and the degree of worker sterility.

All these cells were isogenic, which means they all had the same gene set.

One gene set that stood out involved components of the spliceosome, the molecular complex that helps prepare messenger RNA (mRNA) transcripts for protein production by removing noncoding segments called introns.

Still, he notes that the predictive power of the gene set is low, and «because of the experimental design we can't really say that other exposures might [not] be an issue.»

«And this approach could be used in conjunction with high - throughput screening techniques to identify gene sets associated with problems such as multidrug resistance or benefits, like those related to probiotics.»

Because of the usefulness of this information, we set ourselves the goals of constructing a zebrafish gene set based on RNA - Seq alone and then identifying the highest quality models.

SAP domain - dependent Mkl1 signaling stimulates proliferation and cell migration by induction of a distinct gene set indicative of poor prognosis in breast cancer patients.

Through both automated and manual approaches, the team curated a refined collection of MSigDB gene sets that reduce redundancy and produce more robust analyses.

A team led by Pablo Tamayo and Jill Mesirov of the Broad Institute and University of California, San Diego, and Broad bioinformatician Arthur Liberzon, has generated «hallmark» gene sets from the Molecular Signatures Database (MSigDB), one of the most comprehensive and widely used databases for gene set enrichment analysis.

This running sum increased when a gene defined as belonging to a particular gene set was encountered; otherwise, the sum decreased.

The ES was computed for every gene set using actual data and the maximum ES (MES) over all of the gene sets was recorded.

SAM analysis was used to identify statistically significant changes in microarray data, and the bioinformatics programs GoMiner, Gene Set Enrichment Analysis (GSEA), and HiMAP were used to identify significant ontological categories and analyze the N - methyl - D - aspartate (NMDA) receptor interactome.

These genes will be incorporated in new gene sets, which will be tested and validated.

Gene Set Enrichment Analysis (GSEA) is a microarray data - mining technique used to determine whether there is coordinated differential expression or «enrichment» in a set of functionally related genes when comparing control and experimental samples [35].

Genes involved in redox activity («oxidoreductase activity» GO: 0016491; P = 7.46 e − 04), those associated with responses to various stimuli, e.g., phytohormones («response to hormone» GO: 0009725; P = 2.96 e − 06), and «meristem determinacy» (GO: 0010022; P = 7.74 e − 05) were also overrepresented in the DE gene set (Table 2; Supplemental Figure 8 and Supplemental Data Set 5).

Genes encoding proteins of unknown function constitute 28 % of the essential protein - coding genes set.

We applied gene set enrichment analysis (GSEA)(23) to expression array data using KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways.

Downregulated gene sets include pathways involved in oxidative phosphorylation and amino acid, carbohydrate, and lipid metabolism; and upregulated gene sets include pathways involved in inflammation and glycan metabolism.

The GSEA yielded 14 significant gene sets with downregulated expression and 17 gene sets with upregulated expression in adipose tissue from diabetic versus nondiabetic co-twins (q < 0.05; Table 2).

Heterogeneity between males and females was identified in gene sets associated with T2DM in humans (189), 5 pathways were identified in the male group and 13 in the female group, with only 3 pathways overlapping.

Significant gene sets with differential expression in adipose tissue of diabetic compared with nondiabetic co-twins (GSEA analysis with q < 0.05)

A broad range of biological processes, molecular functions, cell cycle pathways (Supplementary Table S5) and gene sets from the MSigDB (Supplementary Table S6) was enriched across these different modules.

Genes contributing to the enrichment for significant gene sets are presented in Supplementary Tables 1 and 2.

As revealed by gene set enrichment analysis, the MAPK pathway was inactivated in the combination treatment group compared with the untreated group.

With the substantial increase in predicted gene number and gene quality obtained with the OGSv2 gene set, it is clear that an updated annotation of infection responsive genes would be valuable.

Overall, based on homology and structural evidence alone, we find evidence for 34 AMPs in the OGSv2 gene set.

Here, we report the infection - induced transcriptome of the non-eusocial parasitic wasp Nasonia vitripennis, combined with a new homology - based characterization of immune - related genes in the Official Gene Set V2.0 (OGSv2: http://arthropods.eugenes.org/EvidentialGene/nasonia/).

Annotation release 1.0 was derived by comparing and merging gene sets generated independently by VectorBase and TIGR.

Automated and manual annotation to produce the GENCODE reference gene set (v7) of protein - coding genes, pseudogenes, and non-coding RNAs.

Here, we extracted protein sequences (either whole proteins or single domains) from the manually curated Dipteran immune gene sets available on ImmunoDB (http://cegg.unige.ch/Insecta/immunodb), aligned them with FSA [75]-RRB-(options: — fast), and generated profile HMMs with HMMER 3.0 (http://hmmer.janelia.org/).

We thank D.L. Court (National Cancer Institute) for plasmid pSIM18 for the generation of BAC - transgenic mice; J.G. Cyster (UC San Francisco) for Hy10 mice; E. Hobeika and M. Reth (Max Planck Institute of Immunobiology and Epigenetics) for Mb1 - Cre mice; M. Nussenzweig (The Rockefeller University) for B1 - 8hi mice, anti-DEC205 — OVA and anti-DEC205 — CS; G.D. Victora (Whitehead Institute for Biomedical Research) for gene sets for the gene - set - enrichment analysis; O. Ohara, T. Watanabe and Y. Mochizuki for transcriptome analysis; W. Ise for discussions; M. Tochigi, C. Kawai, A. Arakawa and H. Masuda for technical assistance; P. Burrows for critical reading; and R. Brink for communicating unpublished results.

Fisher's exact test as implemented in R66 was run to test for enrichment or depletion of numbers of gene families for each molecular function category in the novel versus ancestral gene sets.