Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat ...
Functional assignments using GO annotations showed that genes involved in transport, oxidation-reduction, and stress response ... The levels of expression of these genes were highly influenced by the initial rate and the duration of the gene's response to ... Using gene-specific ANOVA we identified 12,901 genes (at p < 0.001) that change in expression with respect to both genotype and ... Global expression of genes in the crowns of 3-leaf stage plants cold-acclimated at 6°C for 0, 2, 14, 21, 38, 42, 56 and 70 days ...https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-299
Semantic annotation of biological concepts interplaying microbial cellular responses | BMC Bioinformatics | Full Text
... regulation and metabolism. Namely, it includes annotations for genetic information carriers (genes and DNA, RNA molecules), ... Our corpus is a unique resource in that it annotates biomedical concepts that play a functional role in expression, ... Availability is granted for the full-text corpora of 130 freely accessible documents, the annotation scheme and the annotation ... To the best of our knowledge, a corpus that details such a wide range of biological concepts has never been presented to the ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-460
ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization
Annotation also create the possibility of integrating expression profile data to predict gene expression regulation. ChIPseeker ... We can use it as an index to estimate how well biological replications are. Even more important is applying to infer ... these two proteins may form a complex or have interaction in regulation chromosome remodelling or gene expression. ChIPseeker1 ... assigning genomic annotation... 2018-01-21 11:42:34 PM ## ,, adding gene annotation... 2018-01-21 11:42:52 PM ## ,, assigning ...http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
Genome assembly and genome annotation, Analysis of gene expression & regulation, Gene science and engineering, Computational ... Gene Ontology and taxonomy study, Biological data integration, mining and visualization, Genetic and biochemical networks and ... regulation, High performance bio-computing, Modeling software in Bioinformatics, Makeup language in systems biology, ... evolutionary biology, Measuring biodiversity, Molecular docking, Comparative genomics, Modeling biological systems, High- ...http://www.serialspublications.com/journals/journal-detail.php?jid=284
ZC3H7B - Zinc finger CCCH domain-containing protein 7B - Homo sapiens (Human) - ZC3H7B gene & protein
... help/gene_ontology' target='_top'>More...,/a>,/p>GO - Biological processi. *posttranscriptional regulation of gene expression ... Annotation score:5 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB ... help/expression_section' target='_top'>More...,/a>,/p>Expressioni. Gene expression databases. Bgee dataBase for Gene Expression ... p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of ...http://www.uniprot.org/uniprot/Q9UGR2
Computational Methods for Annotation Transfers from Sequence | SpringerLink
... which can survey gene expression regulation, genomic organization, and variation on a large scale . Similarly, parallel ... 5 De Novo Function Annotation Using Biological Features. The function annotation methods described so far make use of homology ... Rogozin IB, Managadze D, Shabalina SA, Koonin EV (2014) Gene family level comparative analysis of gene expression in mammals ... Evaluating functional annotations of enzymes using the gene ontology. In: Dessimoz C, Škunca N (eds) The gene ontology handbook ...https://link.springer.com/protocol/10.1007/978-1-4939-3743-1_5
Databases | Bioinformatics.ca Links Directory
... gene expression regulation, functional annotation, genomic variation and systems biology information. Integrated are the most ... biological models cluster analysis computational biology forecasting human genome humans metabolic networks and pathways ... gene expression regulation genetic databases genomics human genome humans mice nucleic acid databases sequence alignment tumor ... gene expression profiling genetic databases humans nucleic acid databases plant genome protein databases rna sequence analysis ...https://links.bioinformatics.ca/links_directory/category/rna/databases
DROSHA drosha ribonuclease III [Homo sapiens (human)] - Gene - NCBI
positive regulation of gene expression IEA Inferred from Electronic Annotation. more info ... Inferred from Biological aspect of Ancestor. more info. PubMed rRNA catabolic process IEA Inferred from Electronic Annotation. ... Gene Expression, organism-specific biosystem (from REACTOME) Gene Expression, organism-specific biosystemGene Expression covers ... Gene neighbors Overlapping genes and two nearest non-overlapping genes on either side ...https://www.ncbi.nlm.nih.gov/gene/29102
esr1 - Estrogen receptor - Danio rerio (Zebrafish) - esr1 gene & protein
The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular ... Biological process. Transcription, Transcription regulationUniRule annotation. ,p>Information which has been generated by the ... help/expression_section' target='_top'>More...,/a>,/p>Expressioni. Gene expression databases. Bgee dataBase for Gene Expression ... Unreviewed-Annotation score: Annotation score:3 out of 5. ,p>The annotation score provides a heuristic measure of the ...https://www.uniprot.org/uniprot/A5PMH3
Lonp1 - Lon protease homolog, mitochondrial precursor - Mus musculus (Mouse) - Lonp1 gene & protein
Participates in the regulation of mitochondrial gene expression and in the maintenance of the integrity of the mitochondrial ... May regulate mitochondrial DNA replication and/or gene expression using site-specific, single-stranded DNA binding to target ... View the complete GO annotation on QuickGO .... Protein-protein interaction databases. The Biological General Repository for ... Expressioni. ,p>This subsection of the 'Expression' section provides information on the expression of a gene at the mRNA or ...http://www.uniprot.org/uniprot/Q8CGK3
DNA annotation - Wikipedia
biochemical function biological function involved regulation and interactions expression These steps may involve both ... Educational materials on some aspects of biological annotation from the 2006 Gene Ontology annotation camp and similar events ... DNA annotation or genome annotation is the process of identifying the locations of genes and all of the coding regions in a ... The simpliest way to perform gene annotation relies on homology based search tools, like BLAST, to search for homologous genes ...https://en.wikipedia.org/wiki/DNA_annotation
Sequence mining and transcript profiling to explore differentially expressed genes associated with lipid biosynthesis during...
Here, we evaluated changes in gene expression over the course of seed development using Illumina (formerly Solexa) RNA- ... We selected 12 differentially expressed genes and analyzed their expressions using qRT-PCR. The results were consistent with ... However, it is still uncertain how many genes and which genes are involved in lipid biosynthesis. ... All of the genes identified in our research have significance for breeding soybeans with increased oil contents. ...https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-122
Hdac5 - Histone deacetylase - Mus musculus (Mouse) - Hdac5 gene & protein
Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell ... GO - Biological processi. *regulation of gene expression, epigenetic Source: InterPro. View the complete GO annotation on ... help/expression_section' target='_top'>More...,/a>,/p>Expressioni. Gene expression databases. Bgee dataBase for Gene Expression ... Annotation score: Annotation score:5 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content ...https://www.uniprot.org/uniprot/A2AWS5
SPRR2A - Wikipedia
2006). "Expression and Regulation of Cornified Envelope Proteins in Human Corneal Epithelium". Invest. Ophthalmol. Vis. Sci. 47 ... 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... 2004). "Estrogen regulates the expression of the small proline-rich 2 gene family in the mouse uterus". Mol. Cells. 17 (3): 477 ... "Interdependent transcription control elements regulate the expression of the SPRR2A gene during keratinocyte terminal ...https://en.wikipedia.org/wiki/SPRR2A
Regulatory RNAs - Basics, Methods and Applications | Bibekanand Mallick | Springer
... will provide a major information resource on current research in the fast-moving fields of RNA and gene expression regulation. ... It addresses both the biogenesis and mechanism of action of regulatory RNAs with a primary focus on their annotation, ... applications of these revolutionary regulatory molecules in understanding biological systems and diseases, including ... These RNAs most often act as riboregulators, and actively participate in the regulation of important cellular functions at the ...http://www.springer.com/us/book/9783642225161
Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic...
In this report, we examine the role of histone acetylation in gene expression regulation in mouse embryonic stem cells ... undergo morphological and gene expression changes indicative of differentiation. Gene profiling utilizing Affymetrix ... The establishment of H3K27 trimethylation is required for stable gene suppression whereas in its absence, genes can be ... and differentiation-associated genes in an opposite manner. This analysis provides information about genes that are important ...https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-4-r65
Tumor suppressor miR-1 restrains epithelial-mesenchymal transition and metastasis of colorectal carcinoma via the MAPK and PI3K...
Molecular function annotation indicated that miR-1 may participate in cell signal transduction, regulation of gene expression ... D) The histogram indicated main biological processes involved in miR-1 using Gene Ontology. (E) Both enlarged DIGE images and ... Because the effect of miR-1 on cell migration and gene expression regulation, we detected the change of EMT markers in SW480 ... Because we have observed miR-1-mediated reduction of migration ability and gene expression regulation, we asked whether miR-1 ...https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-014-0244-8
WBP2 - WW domain-binding protein 2 - Homo sapiens (Human) - WBP2 gene & protein
GO - Biological processi. *cellular response to estrogen stimulus Source: InterPro. *positive regulation of gene expression, ... Annotation score: Annotation score:5 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content ... help/expression_section' target='_top'>More...,/a>,/p>Expressioni. Gene expression databases. Bgee dataBase for Gene Expression ... Annotation score: Annotation score:1 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content ...https://www.uniprot.org/uniprot/K7ESN4
Novel molecules lncRNAs, tRFs and circRNAs deciphered from next-generation sequencing/RNA sequencing: computational databases...
... sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation. ... long noncoding and circRNA genes is done and followed by Gene Ontology enrichment analyses for particular biological processes ... Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev ... host gene expression from counting junction and nonjunction reads to test for host gene-independence of circRNA expression ...https://www.deepdyve.com/lp/ou_press/novel-molecules-lncrnas-trfs-and-circrnas-deciphered-from-next-xW1cvLGRQc
BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles | BMC Genomics | Full Text
Gene ontology biological process (GO-BP) annotations were downloaded from the Gene Ontology Website on April 15th 2012. The ... "regulation of expression" suggesting that miRNAs have substantial influence in gene regulation through their control of other ... relevant biological model and uses a large collection gene expression data to decipher the impact of miRNAs on gene expression ... Example of combinatorial regulation masking inverse correlation. Shown in green is the expression level of a target gene and in ...https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-592
MPK17 - Mitogen-activated protein kinase 17 - Oryza sativa subsp. japonica (Rice) - MPK17 gene & protein
... help/gene_ontology' target='_top'>More...,/a>,/p>GO - Biological processi. *regulation of gene expression Source: GO_Central ... Annotation score:3 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB ... expression (up-regulation, down-regulation, constitutive expression).,p>,a href='/help/induction' target='_top'>More...,/a>,/p> ... Gene expression databases. Genevisible search portal to normalized and curated expression data from Genevestigator ...http://www.uniprot.org/uniprot/Q6L5F7
JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
JoVE publishes peer-reviewed scientific video protocols to accelerate biological, medical, chemical and physical research. ... whether genetic variability in the SNCA gene modulates the risk to develop sporadic PD via regulation of SNCA expression ... which lead to a detailed understanding of the role of single genes in well-defined biological problems. However, ... Flexible model organisms such as Drosophila are ideal for adapting these new technologies because of their strong annotation ...https://www.jove.com/visualize/abstract/19834617/genetic-regulation-alpha-synuclein-mrna-expression-various-human
Effects of insufficient sleep on circadian rhythmicity and expression amplitude of the human blood transcriptome | PNAS
... and the regulation of gene expression (e.g., TCEA3, ELP2, ELAV1, SNRPF, HNRNPU). Functional annotation analyses of the rhythmic ... Biological processes affected included chromatin modification, gene-expression regulation, macromolecular metabolism, and ... of all genes, 61.1% of circadian genes) in-phase and 281 genes (1.3% of all genes, 19.0% of circadian genes) in antiphase with ... The affected genes are involved in chromatin remodeling, regulation of gene expression, and immune and stress responses. The ...http://www.pnas.org/content/110/12/E1132
Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological...
The data include time course gene expression profiles, genome-wide location analysis data, binding sequence data, and gene ... Comparison with previously reported results in the literatures to confirm the inferred regulations. The major contribution of ... The proposed computational framework was tested using gene expression data associated with cell cycle progression in yeast. ... The identified relationships between TFs and gene clusters were evaluated using the following biological validation and ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-203
Whole Blood Transcriptome Sequencing Reveals Gene Expression Differences between Dapulian and Landrace Piglets
... biological processes, and cellular components (Figure 2). The GO annotation indicated that the DEGs were involved in many ... "Regulation of neutrophil and eosinophil secondary granule gene expression by transcription factors C/EBPε and PU.1," Blood, vol ... To verify the gene expression data by RNA-seq, qRT-PCR was performed for six genes according to their biological function, ... 2.4.2. Gene Annotation and DEGs Analysis. The FPKM value ratio was used to estimate gene expression level between those samples ...https://www.hindawi.com/journals/bmri/2016/7907980/