*  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
*  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 [1]. 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
*  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
*  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
*  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
*  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
*  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
*  Znf281 - Zinc finger protein 281 - Mus musculus (Mouse) - Znf281 gene & protein
Represses the transcription of a number of genes including GAST, ODC1 and VIM. Binds to the G-rich box in the enhancer region ... Transcription repressor that plays a role in regulation of embryonic stem cells (ESCs) differentiation. Required for ESCs ... negative regulation of gene expression Source: UniProtKB. *negative regulation of transcription, DNA-templated Source: ... Annotation score:5 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB ...
  http://www.uniprot.org/uniprot/Q99LI5
*  Comparative transcriptome analysis of aerial and subterranean pods development provides insights into seed abortion in peanut |...
Gene expression profiles were generated using a high-density peanut microarray with pooling three biological replicates ... Functional annotation showed their mainly involvement in biosynthesis, metabolism, transcription regulation, transporting, ... Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression ... The actin gene was amplified along with the target gene as reference to normalize expression between different samples. All ...
  https://link.springer.com/article/10.1007%2Fs11103-014-0193-x
*  Assessing the impact of human genome annotation choice on RNA-seq expression estimates | BMC Bioinformatics | Full Text
is the mean of expression estimates across replicates with the same biological condition, and n is the number of targeted genes ... The second dataset (accession number: SRP000727) studies alternative isoform regulation in human tissue transcriptomes [26]. It ... including AceView Genes, Ensembl Genes, H-InvDB Genes, RefSeq Genes, UCSC Known Genes, and Vega Genes. Since each annotation ... Ensembl Genes, H-InvDB Genes, RefSeq Genes, UCSC Known Genes, and Vega Genes. Characteristics of these annotations differ ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S8
*  IJMS | Free Full-Text | Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression | HTML
... while the expression of seven SR and SR-related genes is affected by alterations in key components of the ABA pathway. Finally ... despite pervasiveness of established ABA-responsive promoter elements in Arabidopsis SR and SR-like genes, their expression is ... Using real-time RT-qPCR, we analyzed total steady-state transcript levels of the 18 SR and two SR-like genes from Arabidopsis ... We also searched for ABA-responsive cis elements in the upstream regions of the 20 genes. We found that members of the plant- ...
  http://www.mdpi.com/1422-0067/15/10/17541/htm
*  Chrm4 - Muscarinic acetylcholine receptor M4 - Rattus norvegicus (Rat) - Chrm4 gene & protein
Covers cases where the annotation is inferred from the timing or location of expression of a gene.,/p> ,p>More information in ... regulation of locomotion Source: InterPro. *response to organic substance Source: RGD ,p>Inferred from Expression Pattern,/p> , ... help/gene_ontology' target='_top'>More...,/a>,/p>GO - Biological processi. *adenylate cyclase-inhibiting G-protein coupled ... Annotation score:5 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB ...
  http://www.uniprot.org/uniprot/P08485
*  PCBP1/HNRNP E1 Protects Chromosomal Integrity by Translational Regulation of CDC27 | Molecular Cancer Research
... we focused our attention on this group of genes. A heatmap of the Affymetrix array data showing relative expression of genes ... DAVID functional annotation analysis was performed. DAVID analysis (19, 20) allows for the categorization of genes within a ... HNRNP E1 regulates translation of mRNAs involved in several biological processes. We previously employed polyribosomal ... 4E) demonstrate that CDH1 expression is rescued in E1KD cells upon treatment with MG132, indicating that while the Fzr1 gene is ...
  http://mcr.aacrjournals.org/content/14/7/634
*  Nr5a2 - Nuclear receptor subfamily 5 group A member 2 - Rattus norvegicus (Rat) - Nr5a2 gene & protein
Plays a role in the regulation of gene expression in liver and pancreas. May play a role in embryonic development (By ... Binds to promoters containing the sequence element 5'-AACGACCGACCTTGAG-3'. Plays a role in the regulation of gene expression in ... Reviewed-Annotation score: Annotation score:5 out of 5. ,p>The annotation score provides a heuristic measure of the annotation ... help/gene_ontology' target='_top'>More...,/a>,/p>GO - Biological processi. *bile acid metabolic process Source: RGDInferred ...
  http://www.uniprot.org/uniprot/Q9QWM1
*  GIS1 - Transcriptional activator/repressor GIS1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) - GIS1...
Can act as a transcriptional activator (e.g. of stress genes like SSA3, HSP12 and HSP26) as well as a repressor (e.g. of ... Transcription factor involved in the regulation of gene expression upon nutrient starvation. Recognizes and binds to the post- ... expression (up-regulation, down-regulation, constitutive expression).,p>,a href='/help/induction' target='_top'>More...,/a>,/p> ... Biological processi. *chronological cell aging Source: SGD ,p>Inferred from Mutant Phenotype,/p> ,p>Describes annotations that ...
  http://www.uniprot.org/uniprot/Q03833
*  A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets | Springer...
This can be used to predict gene expression of protein coding genes, as well as microRNAs.... ... We develop a statistical framework to study the relationship between chromatin features and gene expression. ... Modifications of these core histones are central to many biological processes, including transcriptional regulation [1], ... Datasets and gene annotation. Expression levels for all annotated worm transcripts at different stages of development, ...
  https://rd.springer.com/article/10.1186/gb-2011-12-2-r15
*  Altered Gene Expression Profiles Define Pathways in Colorectal Cancer Cell Lines Affected by Celecoxib | Cancer Epidemiology,...
3A). The heterogeneity of response to celecoxib, also evident in GO Biological Processes (GOBP) annotations (data not shown), ... However, the expression levels of these genes at 5 ╬╝mol/L celecoxib, although generally confirmed the trend for up-regulation ... Numbers under the gene names indicate the extent of up-regulation or down-regulation and under the pathways provide an estimate ... However, the qPCR analysis showed a more pronounced trend of up-regulation or down-regulation of genes after 72 hours of ...
  http://cebp.aacrjournals.org/content/17/11/3051
*  Lonp2 - Lon protease homolog 2, peroxisomal - Rattus norvegicus (Rat) - Lonp2 gene & protein
Covers cases where the annotation is inferred from the timing or location of expression of a gene.,/p> ,p>More information in ... help/gene_ontology' target='_top'>More...,/a>,/p>GO - Biological processi. *misfolded or incompletely synthesized protein ... regulation of fatty acid beta-oxidation Source: Ensembl. *response to organic cyclic compound Source: RGD ,p>Inferred from ... help/expression_section' target='_top'>More...,/a>,/p>Expressioni. Gene expression databases. Bgee dataBase for Gene Expression ...
  http://www.uniprot.org/uniprot/Q3MIB4
*  TBCK - TBC domain-containing protein kinase-like protein - Homo sapiens (Human) - TBCK gene & protein
Involved in the regulation of cell proliferation and growth (PubMed:23977024, PubMed:24576458). Involved in the control of ... Involved in the modulation of mTOR signaling and expression of mTOR complex components (PubMed:27040691, PubMed:23977024). ... View the complete GO annotation on QuickGO .... Protein-protein interaction databases. The Biological General Repository for ... help/expression_section' target='_top'>More...,/a>,/p>Expressioni. Gene expression databases. Bgee dataBase for Gene Expression ...
  http://www.uniprot.org/uniprot/Q8TEA7
*  Hcls1 - Hematopoietic lineage cell-specific protein - Mus musculus (Mouse) - Hcls1 gene & protein
May also be involved in the regulation of gene expression (By similarity). ... Complete GO annotation.... Protein-protein interaction databases. The Biological General Repository for Interaction Datasets ( ... Expressioni. ,p>This subsection of the 'Expression' section provides information on the expression of a gene at the mRNA or ... May also be involved in the regulation of gene expression (By similarity).By similarity ...
  http://www.uniprot.org/uniprot/P49710
*  FOXO4 - Forkhead box protein O4 - Homo sapiens (Human) - FOXO4 gene & protein
Down-regulates expression of HIF1A and suppresses hypoxia-induced transcriptional activation of HIF1A-modulated genes. Also ... involved in negative regulation of the cell cycle. Involved in increased proteasome activity in embryonic stem cells (ESCs) by ... activating expression of PSMD11 in ESCs, leading to enhanced assembly of the 26S proteasome, followed by higher proteasome ... Transcription factor involved in the regulation of the insulin signaling pathway. Binds to insulin-response elements (IREs) and ...
  http://www.uniprot.org/uniprot/P98177