China
Africa
Explore chapters and articles related to this topic
RNA-seq Analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
Import curated pathway gene sets with Entrez identifiers from the MSIGDB database3 and re-do the GSEA for all curated gene sets. [Difficulty: Advanced]
Epilogue
Published in Merlin G. Butler, F. John Meaney, Genetics of Developmental Disabilities, 2019
Merlin G. Butler, F. John Meaney
Inlow and Restifo (2) have produced the most comprehensive recent analysis of the genetics of MR. One purpose of this elegant study was to determine as best as possible how many genes for MR have been identified on a molecular basis and to examine the existing information about the molecular and biological functions of these gene products. In their analysis, Inlow and Restifo (2) used a broad definition of MR to include “progressive disorders with onset of cognitive impairment in childhood and occasionally, as late as adolescence” (p. 836). The OMIM database was used initially to search for human MR genes and disorders that include MR in the phenotypic description. OMIM was accessed online (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM) on February 21, 2002, to search all fields using the phrase “mental retardation.” This search resulted in 1010 entries for which detailed reviews were conducted. These investigators conducted additional OMIM searches of the phrases “cognitive impairment” and “learning disabilities” to encompass milder MR and as a result identified another 38 nonoverlapping entries for further evaluation. Their final source of information included periodic searches of the National Center for Biotechnology PubMed resources, in part to identify MR genes that were missed, for a variety of reasons, by the OMIM search.
Molecular biology
Published in Maxine Lintern, Laboratory Skills for Science and Medicine, 2018
There are many web-based resources to help you prepare for your experiments. In fact a lot can be achieved in silico before you even put on a lab coat. Since the completion of the human and other genomes there is an increasing need to be computer savvy and make use of web-based programs and databases. The National Center for Biotechnology Information (NCBI) website7 supports the GenBank DNA sequence database. Using the Entrez tool,8 you’ll be able to search and retrieve RNA, DNA and protein sequences from various organisms. In addition NCBI supports databases such as Online Mendelian Inheritance in Man (OMIM),9 Unique Human Gene Sequence Collection (UniGene),10 and The Cancer Genome Anatomy Project (CGAP).11 Useful programs available on the NCBI website include BLAST,12 which is a powerful sequence similarity searching tool for nucleotide and protein sequences, and Open Reading Frame Finder (ORF Finder).13 For those important literature searches there’s PubMed,14 which provides access to MEDLINE,15 and will allow you to peruse over 11 million citations.
Primary tumors from mucosal barrier organs drive unique eosinophil infiltration patterns and clinical associations
Published in OncoImmunology, 2021
Sharon Grisaru-Tal, Michal Itan, Daniel G Grass, Javier Torres-Roca, Steven A Eschrich, Yaara Gordon, Avishay Dolitzky, Inbal Hazut, Shmuel Avlas, Elizabeth A Jacobsen, Tomer Ziv-Baran, Ariel Munitz
Eosinophil abundance in the TCC patient cohort was evaluated using the ‘Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data’ (ESTIMATE) algorithm (Estimate R package v1.0.13).30 Normalized gene expression probeset identifiers were mapped to Entrez GeneIDs. As defined in the ESTIMATE package, the data were filtered to only the common genes. A single probeset was then selected per gene by choosing the probeset having the highest median expression across all tumors. This resulting dataset was used in the ESTIMATE function to produce stromal and immune scores for each cohort. Next, the Human RSTA array was reduced to the LM22 signature genes (Supplementary Table 1) as defined by CIBERSORT31 by choosing a representative probeset that detects the gene and has the highest median expression among matching probesets. LM22 is a validated leukocyte signature matrix generated from microarray data, which contains 547 genes that distinguish 22 human hematopoietic cell phenotypes.31 The CIBERSORT web tool (https://cibersort.stanford.edu/index.php) was accessed on 2017–05-19 to generate signature scores (using quantile normalization).
Prader-Willi syndrome and Angelman syndrome: Visualisation of the molecular pathways for two chromosomal disorders
Published in The World Journal of Biological Psychiatry, 2019
Friederike Ehrhart, Kelly J. M. Janssen, Susan L. Coort, Chris T. Evelo, Leopold M. G. Curfs
General information on PWS and AS, the involved genes and their molecular interactions was obtained through literature research using PubMed. The studies were selected if they contained information about molecular interactions of the selected gene, ideally in a human PWS- or AS-related study (e.g., cell models), but also animal cell models or other disease context were investigated. DisGeNET (Pinero et al. 2017) and OMIM (Hamosh 1985–2017) provided collections of human disorders and phenotypes with their associated genes and variants. Through these two databases, an overview of the genes most often associated with either of the syndromes was obtained. UniProt, a protein database (The UniProt Consortium 2017), provides functional information about proteins and information to determine differences between, e.g., prohormones and active hormones. Ensembl (Yates et al. 2016) is a genome browser for vertebrate genomes, which was used to annotate genes and gene products in the genetic pathway, and it provided detailed information about gene transcripts and homologues in other species. Entrez Gene (Maglott et al. 2007) was used to find information and annotations for gene clusters, e.g., the SNORD116 gene cluster. WikiPathways (Pico et al. 2008) and Reactome (Milacic et al. 2012; Fabregat et al. 2016), two pathway databases, were used to find existing downstream pathways.
Two immune-enhanced molecular subtypes differ in inflammation, checkpoint signaling and outcome of advanced head and neck squamous cell carcinoma
Published in OncoImmunology, 2018
Bangrong Cao, Qifeng Wang, Huan Zhang, Guiquan Zhu, Jinyi Lang
For TCGA cohort, the RNA-seq data was profiled by the next-generation sequencing platform of Illumina®. The fragments per kilobase of gene per million fragments mapped with upper quartile normalization (FPKM-uq) were downloaded from TCGA Data Portal. Gene annotation was performed with the Ensembl database. The gene expression value was log2-transformed for subsequent analysis. The gene expression profiles of LHNG cohort were analyzed by Illumina® HT12 v4 Expression BeadChips.15 The normalized expression data and corresponding clinical information were downloaded from Gene Expression Omnibus (GEO) (GSE65858). Probe annotations of BeadChips were obtained from the GEO database. Entrez Gene IDs were used for mapping gene expression data between the two cohorts.