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Gene ontology

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Gene ontology analysis of expanded porcine blastocysts from gilts fed organic or inorganic selenium combined with pyridoxine

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Description of data: Complete list of Gene Ontology terms (GORILLA and REVIGO) related with MSeB 6 10 vs CONT, OSeB 6 10 vs CONT, and OSeB 6 10 vs MSeB 6 10 comparisons.

InfAcrOnt: Calculating cross-ontology term similarities using information flow by a random walk

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Hu Y, Zhou W, Ren J, Dong L, Wang Y, Jin S, Cheng L: Annotating the function of the human genome with gene ontology and disease ontology.. Kumar A, Smith B, Borgelt C: Dependence relationships between Gene Ontology terms based on TIGR gene product annotations. Coordinators NR: Database Resources of the National Center for Biotechnology Information

Predicting metabolic pathway membership with deep neural networks by integrating sequential and ontology information

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Topoicsim: a new semantic similarity measure based on gene ontology. A relation based measure of semantic similarity for gene ontology annotations

GraphTeams: A method for discovering spatial gene clusters in Hi-C sequencing data

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To this end, we make use of Gene Ontology (GO) [21] anno- tations and relate between gene functions by means of the gene ontology hierarchy that corresponds to the domain “Biological Process”. denotes the set of GO terms, i.e., vertices of the GO hierarchy G, with which gene g is associated.

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

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Putative transcriptional target genes tend to include similar function of genes. enrichments of transcriptional target genes in the other annotation databases except for microRNAs and Protein domains were significantly higher than gene expression information alone, independent of transcriptional target genes, as well as Gene Ontology annotations (Table 1)..

Gene expression of Hanwoo satellite cell differentiation in longissimus dorsi and semimembranosus

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Table 3 Gene Ontology of the differentially expressed genes in LD and SM muscles for days 1, 7 and 14 in relation to day 0. Forced expression of HOXA11 reduces the abun- dance of MYOD in the limb of embryo chickens and a similar repression of MYOD was observed in C2C12 cells transfected with HOXA11 [24]. 3) observed in LD in relation to SM due to the higher expression of HOXA11 in SM.

Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)

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Differential gene expression of control and EE2-treated males or females at different developmental stages. Top 25 gene ontology terms enriching the genes of EE2-treated males at embryo stage. Top 25 gene ontology terms enriching the genes of EE2-treated males at hatching. Top 25 gene ontology terms enriching the genes of EE2-treated females at hatching. Top 25 gene ontology terms enriching the genes of EE2-treated females at first feeding.

Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies

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In conclusion, we used a deep transcriptome sequen- cing method for comparing three anti-CD3 antibodies regarding Gene Ontology enrichment and immuno- logical marker expression. PBMCs were cultured in RPMI media (Invitro- gen, Carlsbad, CA, USA) supplemented with 4 mM L- glutamine and 10% FBS in the presence or absence of soluble anti-CD3 antibodies. 1.2) gene set enrichment analyses were performed using functional categories of the database Gene Ontology (GO).

Comparative transcriptomic analysis and endocuticular protein gene expression of alate adults, workers and soldiers of the termite Reticulitermes aculabialis

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As a result, a total of 10,210 differentially expressed genes were divided into 51 functional categories, which were annotated in the Gene Ontology database.

Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations – a next generation sequencing approach in the gopher tortoise

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First, these genes were enriched relative to the rest of the genome for gene ontology functions relating to the modification of macromolecules and proteins, which usually fold and mature in the lumen of the endoplasmic reticulum [56].

Core promoter mutation contributes to abnormal gene expression in bladder cancer

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By Gene Ontology analysis, we observed that the core promoter-mutated genes were enriched in the func- tional pathways highly relevant to oncogenesis (Fig. We compared the core promoter-mutated genes with altered gene expression to the cancer driver gene list and observed that the somatic-mutated TERT and PRRX1, and germline-mutated GAB2 were on the list (Table S7)..

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

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Both the ABC transporter and HMA gene families were highly conserved among subfamilies of flax and with those of Arabidopsis . Gene ontology analyses suggested that most flax ABC transporter and HMA genes had a role in ATP binding, transport, catalytic activity, ATPase activity, and metal ion binding.

3’Pool-seq: An optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling

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A Gene Ontology analysis of the pathways ranked by p -value represented by the DEGs detected by 3 ’ Pool-seq in the Wild-Type vs. A Gene Ontology analysis of the pathways ranked by p-value represented by the DEGs detected by TruSeq in the Wild-Type vs. GS conceptualized 3 ’ Pool-seq and carried out 3 ′ -end sequencing. The entire study, including the design of the study and collection, analysis, and interpretation of data was funded by Pfizer, Inc.

Comparative transcriptome analysis reveals ectopic delta-5 and delta-6 desaturases enhance protective gene expression upon Vibrio vulnificus challenge in Tilapia (Oreochromis niloticus)

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The GO analysis showed that genes associated with in- flammation, chemokine synthesis, iron homeostasis and immune response are altered by D56 expression in Table 6 Gene ontology analysis of wild-type and transgenic tilapia fish expressing delta-6 desaturase plus delta-5 desaturase (D56) infected with V.

Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density

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Additional file 4: Gene Ontology enrichment of skin gene modules: Full GO enrichment results of gill gene co-expression modules. (PDF 80 kb) Additional file 5: Summary of skin gene ontology enrichment:. Additional file 6: Summary of gill gene ontology enrichment: Summary of gene ontology (GO) term enrichment of gill genes differentially expressed between control (uninfected) and Saprolegnia-infected Oreochromis niloticus density treatment groups (LD.

Exposure to maternal obesity alters gene expression in the preimplantation ovine conceptus

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An official GO term is not available for placental development and function, so this DEG ca- tegory was developed in-house by identifying DEGs that have been studied in the placenta, trophectoderm and/or trophoblast of humans, rodents and/or domestic animals.. hormones, metabolites) may be promoting changes in conceptus gene expression, al- though we have not identified any indication of this type of regulation in the gene ontology screening.

Resilience, plasticity and robustness in gene expression during aging in the brain of outbred deer mice

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Specifically, we assessed the correlation in the expression in each gene in the transcriptome with every other gene, and then we tested how this correlation changes during aging. Gene Ontology (GO) studies were also performed to unveil biological processes related to the genes that exhibited inversion of transcriptome coord- ination in the aging group..

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

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The GO annotation of zebrafish coding-gene was down- loaded from Gene Ontology Consortium (only biological process annotations were considered). While, GO anno- tation of zebrafish lncRNA was predicted using the goatools (version which determines the GO annotation of one gene in our network according to the GO annotations of its immediate neighbor genes (P-value <.

Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

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To further discriminate the BnLPP genes’ functions, we implemented gene ontology (GO) annotation and en- richment analysis based on three classes, i.e., biological process (BP), molecular function (MF), and cellular com- ponent (CC). These GO terms boost our understanding of the precise gene functions. Nearly all GO-CC terms are consistent with the subcellular localization of the BnLPP proteins.

Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation)

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While some chlorophyte sequences were present, the PR-3. 3 Distribution of biological process and molecular function Gene Ontology (GO) terms in the assembled transcriptomes. Despite being initially identified from a dicot, putative PR-19 sequences, as expected, were only identified in the lycophyte S.