Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Third party annotation gene data set of eutherian lysozyme genes.

ABSTRACT: The eutherian comparative genomic analysis protocol annotated most comprehensive eutherian lysozyme gene data set. Among 209 potential coding sequences, the third party annotation gene data set of eutherian lysozyme genes included 116 complete coding sequences that first described seven major gene clusters. As one new framework of future experiments, the present integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new classification and nomenclature of eutherian lysozyme genes.

SUBMITTER: Premzl M

PROVIDER: S-EPMC4535835 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Third party annotation gene data set of eutherian lysozyme genes.

Premzl Marko M

Genomics data 20140820

The eutherian comparative genomic analysis protocol annotated most comprehensive eutherian lysozyme gene data set. Among 209 potential coding sequences, the third party annotation gene data set of eutherian lysozyme genes included 116 complete coding sequences that first described seven major gene clusters. As one new framework of future experiments, the present integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new classification and nomenclatur ...[more]

PMID: 26484105

Similar Datasets

Third party data gene data set of eutherian growth hormone genes.

Project description:Among 146 potential coding sequences, the most comprehensive eutherian growth hormone gene data set annotated 100 complete coding sequences. The eutherian comparative genomic analysis protocol first described 5 major gene clusters of eutherian growth hormone genes. The present updated gene classification and nomenclature of eutherian growth hormone genes integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis into new framework of future experiments. The curated third party data gene data set of eutherian growth hormone genes was deposited in European Nucleotide Archive under accession numbers LM644135-LM644234.

| S-EPMC4664738 | biostudies-literature

Curated eutherian third party data gene data sets.

Project description:The free available eutherian genomic sequence data sets advanced scientific field of genomics. Of note, future revisions of gene data sets were expected, due to incompleteness of public eutherian genomic sequence assemblies and potential genomic sequence errors. The eutherian comparative genomic analysis protocol was proposed as guidance in protection against potential genomic sequence errors in public eutherian genomic sequences. The protocol was applicable in updates of 7 major eutherian gene data sets, including 812 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets.

| S-EPMC4707174 | biostudies-literature

Annotation- and Batch Effect Correction in TCGA IsomiR Expression Data [Third-party re-analysis]

Project description:The Cancer Genome Atlas (TCGA) Isoform Expression Quantification Data is the largest ressource of isomiR level sequenced cancer data publicly available. Since the datasets were built up over years and through different contributing institutions, it is not free of batch effects. We evaluated different batch correction approaches to remove batch effects in the data, details of the best performing algorithm and batch variables are included in the supplementary file. Additionally, annotation of the chromosomal end position of each isomiR feature was corrected by the offset of 1 to account for exclusive annotation.

2021-02-17 | GSE164767 | GEO

Prevalence of Third-Party Data Tracking by US Hospital Websites.

Project description: Not available

| S-EPMC8459186 | biostudies-literature

Molecular Classification of AIDS-Related Lymphomas [including third-party data]

Project description:Gene expression profiling (GEP) of ARL patient samples was done to determine whether gene expression signatures derived from HIV- lymphomas retained their ability to molecularly classify HIV+ lymphomas. The GEP-based predictors robustly classified ARL tumors, distinguishing molecular Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), as well as activated B-cell-like (ABC) and germinal center B-cell-like (GCB) molecular subtypes of DLBCL. Gene expression profiles were used to identify coordinately regulated gene sets and pathways that differ between HIV+ and HIV- lymphomas of corresponding molecular subtype. Frozen tumor biopsies were obtained from 20 HIV-positive patients with an AIDS-defining lymphoma. Cases were ascertained at the University of Nebraska Medical Center and through the NCI AIDS and Cancer Specimen Resource tumor bank. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on 17 ARL cases. Details of all 20 HIV-positive patients can be found in the supplementary file below. Third party array data from HIV- lymphomas of corresponding molecular subtype were used for the comparison and molecular classification of the HIV+ cases in this study. The third party HIV- lymphoma samples include the following. [1] HIV- lymphoma, BL cases: 84 samples profiled on the Affymetrix HG U133 Plus 2 array. The data are publicly available on the website companion to Dave et al. NEJM 2006; Volume 354:13-24 (http://llmpp.nih.gov/BL/) and were used 'as is' (ie, not reanalyzed). [2] HIV- lymphoma, DLBCL cases: 200 of the 414 cases in Series GSE10846 (listed in the supplementary file below). These included all R-CHOP treated cases of either ABC or GCB subtype. These data were also used as is. These data were published in Lenz et al. NEJM 2008; Volume 359: 2313-2323.

2012-07-17 | E-GEOD-17372 | biostudies-arrayexpress

Molecular Classification of AIDS-Related Lymphomas [including third-party data]

2012-07-18 | GSE17372 | GEO

No third-party punishment in chimpanzees.

Project description:Punishment can help maintain cooperation by deterring free-riding and cheating. Of particular importance in large-scale human societies is third-party punishment in which individuals punish a transgressor or norm violator even when they themselves are not affected. Nonhuman primates and other animals aggress against conspecifics with some regularity, but it is unclear whether this is ever aimed at punishing others for noncooperation, and whether third-party punishment occurs at all. Here we report an experimental study in which one of humans' closest living relatives, chimpanzees (Pan troglodytes), could punish an individual who stole food. Dominants retaliated when their own food was stolen, but they did not punish when the food of third-parties was stolen, even when the victim was related to them. Third-party punishment as a means of enforcing cooperation, as humans do, might therefore be a derived trait in the human lineage.

| S-EPMC3443148 | biostudies-literature

'To quarterback behind the scenes, third-party efforts': the tobacco industry and the Tea Party.

Project description:BackgroundThe Tea Party, which gained prominence in the USA in 2009, advocates limited government and low taxes. Tea Party organisations, particularly Americans for Prosperity and FreedomWorks, oppose smoke-free laws and tobacco taxes.MethodsWe used the Legacy Tobacco Documents Library, the Wayback Machine, Google, LexisNexis, the Center for Media and Democracy and the Center for Responsive Politics (opensecrets.org) to examine the tobacco companies' connections to the Tea Party.ResultsStarting in the 1980s, tobacco companies worked to create the appearance of broad opposition to tobacco control policies by attempting to create a grassroots smokers' rights movement. Simultaneously, they funded and worked through third-party groups, such as Citizens for a Sound Economy, the predecessor of AFP and FreedomWorks, to accomplish their economic and political agenda. There has been continuity of some key players, strategies and messages from these groups to Tea Party organisations. As of 2012, the Tea Party was beginning to spread internationally.ConclusionsRather than being a purely grassroots movement that spontaneously developed in 2009, the Tea Party has developed over time, in part through decades of work by the tobacco industry and other corporate interests. It is important for tobacco control advocates in the USA and internationally, to anticipate and counter Tea Party opposition to tobacco control policies and ensure that policymakers, the media and the public understand the longstanding connection between the tobacco industry, the Tea Party and its associated organisations.

| S-EPMC3740007 | biostudies-literature

GARNET--gene set analysis with exploration of annotation relations.

Project description:BACKGROUND: Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information. RESULTS: GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations. CONCLUSIONS: GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/).

| S-EPMC3044280 | biostudies-literature

Changing minds: Children's inferences about third party belief revision.

Project description:By the age of 5, children explicitly represent that agents can have both true and false beliefs based on epistemic access to information (e.g., Wellman, Cross, & Watson, 2001). Children also begin to understand that agents can view identical evidence and draw different inferences from it (e.g., Carpendale & Chandler, 1996). However, much less is known about when, and under what conditions, children expect other agents to change their minds. Here, inspired by formal ideal observer models of learning, we investigate children's expectations of the dynamics that underlie third parties' belief revision. We introduce an agent who has prior beliefs about the location of a population of toys and then observes evidence that, from an ideal observer perspective, either does, or does not justify revising those beliefs. We show that children's inferences on behalf of third parties are consistent with the ideal observer perspective, but not with a number of alternative possibilities, including that children expect other agents to be influenced only by their prior beliefs, only by the sampling process, or only by the observed data. Rather, children integrate all three factors in determining how and when agents will update their beliefs from evidence.

| S-EPMC5888193 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data