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Genic insights from integrated human proteomics in GeneCards

Simon Fishilevich, Shahar Zimmerman, Asher Kohn, Tsippi Iny Stein, Tsviya Olender, Eugene Kolker, Marilyn Safran, Doron Lancet
2016 Database: The Journal of Biological Databases and Curation  
GeneCards is a one-stop shop for searchable human gene annotations  ...  GeneCards, the human gene compendium, is a genecentric database integrating data for 152 704 human genes from 125 sources (11) .  ...  With the aim of enhancing the derivation of gene-related biological insight from proteomic data, we focused on 216 proteome samples stemming from normal human anatomical entities (tissues, in vivo cells  ... 
doi:10.1093/database/baw030 pmid:27048349 pmcid:PMC4820835 fatcat:o2qmsm6l2ve7bpyvhbj2pnu6re

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

Erdahl T Teber, Edward Crawford, Kent B Bolton, Derek Van Dyk, Peter R Schofield, Vimal Kapoor, W Bret Church
2006 BMC Bioinformatics  
within inter-genic regions, genes, transcripts, and proteins.  ...  There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes.  ...  Thus, unneeded complexities related to gene annotations need to be hidden from view, and software tools need to be less complicated in an effort to help in integrating, storing and visualising annotations  ... 
doi:10.1186/1471-2105-7-33 pmid:16426464 pmcid:PMC1397871 fatcat:ovx32gwdwnguhebacb4jnxhb7a

Design of FRET Probes for SNP RS1006737, Related to Mood Disorder

Germano Orrù, Mauro Giovanni Carta, Alessia Bramanti
2018 Clinical Practice and Epidemiology in Mental Health  
Method: In this study we used the DINAMelt Web Server to predict the Tms of FRET oligo in the presence of the A and/or G allele in rs1006737.  ...  The PCR primers were designed by using oligo 4 and oligo 6 primer analysis software, Results: The molecular probe described in this study detected a Tm difference of 5-6°C between alleles A and G in rs1006737  ...  Giuseppe Serafi for valuable discussions and insights on molecular procedures.  ... 
doi:10.2174/1745017901814010053 pmid:29541152 pmcid:PMC5838627 fatcat:o6fwxc4aa5d3zldbpe6f7qw6km

Bioinformatics and statistical genomics

2008 Genomic Medicine  
In this study, attempts have been made to predict intein proteins, domains, and their sites. Intein data obtained from InBase Intein database.  ...  Protein Post-translational Modification (PTM) is a common phenomenon in biology which regulates the function of proteins.  ...  Studying further for essentiality, homology with known structures in PDB and lack of homology with human proteome led us to 41 proteins.  ... 
doi:10.1007/s11568-009-9081-x pmid:19488836 pmcid:PMC2694866 fatcat:kmyq6l3qefdhpaz5zsi6eyc37m

Cancer Genomics: Technology, Discovery, and Translation

Ben Tran, Janet E. Dancey, Suzanne Kamel-Reid, John D. McPherson, Philippe L. Bedard, Andrew M.K. Brown, Tong Zhang, Patricia Shaw, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, Benjamin G. Neel (+1 others)
2012 Journal of Clinical Oncology  
The discovery of genetic aberrations in human cancers has identified potential therapeutic targets and provided key insights into the mech- anisms underlying tumorigenesis,**' as described in an excellent  ...  Integrating data. NGS and the resulting rapid increase in genome-scale data production have created great challenges in data integration.  ... 
doi:10.1200/jco.2011.39.2316 pmid:22271477 fatcat:efui3h6tkvfxjikwa22ulao2ja

The gene expression profiling of hepatocellular carcinoma by a network analysis approach shows a dominance of intrinsically disordered proteins (IDPs) between hub nodes

Sakshi Singh, Giovanni Colonna, Giovanni Di Bernardo, Francesca Bergantino, Marcella Cammarota, Giuseppe Castello, Susan Costantini
2015 Molecular Biosystems  
The results evidence a strong presence of intrinsically disordered proteins in key roles as hubs in HCC sub-networks.  ...  Acknowledgements We thank Marilina Russo for her help in the figure preparation.  ...  compendium of human genes in the GeneCards Platform 50 .  ... 
doi:10.1039/c5mb00434a pmid:26267014 fatcat:nbyzt5mj6nasxpmcmoz4rcnpo4

Bayesian model comparison for rare variant association studies of multiple phenotypes [article]

Christopher DeBoever, Matthew Aguirre, Yosuke Tanigawa, Chris C. A. Spencer, Timothy Poterba, Carlos D Bustamante, Mark J. Daly, Matti Pirinen, Manuel A Rivas
2018 bioRxiv   pre-print
We also find evidence for novel protective associations between rare variants in ANGPTL7 and glaucoma (log10 Bayes Factor = 13.1).  ...  We are able to recover known associations such as the protective association between rs146597587 in IL33 and asthma (log10 Bayes Factor = 29.4).  ...  Genic insights from integrated human proteomics in GeneCards. Database : the journal of biological databases and curation. 2016;2016. 32.  ... 
doi:10.1101/257162 fatcat:3dga4r4xgfh3rj7el3yewhipuq

Regulation of the 20S proteasome by a novel family of inhibitory proteins [article]

Maya A Olshina, Fanindra Kumar-Deshmukh, Galina Arkind, Irit Fainer, Mark Taranavsky, Daniel Hayat, Shifra Ben-Dor, Gili Ben-Nissqan, Michal Sharon
2019 bioRxiv   pre-print
They coordinate the function of the 20S proteasome and are involved in the oxidative stress response via Nrf2.  ...  The protein degradation machinery plays a critical role in the maintenance of cellular homeostasis, preventing the accumulation of damaged or misfolded proteins and controlling the levels of regulatory  ...  Annu Rev Biochem 78: 477-513 Fishilevich S, Zimmerman S, Kohn A, Iny Stein T, Olender T, Kolker E, Safran M, Lancet D (2016) Genic insights from integrated human proteomics in GeneCards.  ... 
doi:10.1101/617415 fatcat:f6qotaxwt5epvagfb3yfxz6psu

HGM 2010 Programme / Abstract

2010 The HUGO Journal  
We are currently RT-PCR-amplifying RNA from the lymphocytes of patients to identify aberrant transcripts.  ...  Conclusion: Heterozygous patients in the two families studied may carry an intronic EYS mutation causing exon skipping.  ...  researchers in their quest to glean insights from ever finer data on human genetic variation.  ... 
doi:10.1007/s11568-010-9143-0 fatcat:oykxd6u7snfi5o7m6tst7wi6yq

Uncovering the mechanism of Ge-Gen-Qin-Lian decoction for treating ulcerative colitis based on network pharmacology and molecular docking verification

Lin Xu, Jiaqi Zhang, Yifan Wang, Zedan Zhang, Fengyun Wang, Xudong Tang
2021 Bioscience Reports  
Furthermore, the present study provided new insight into the mechanisms of GGQLD against UC.  ...  Method: In this research, a GGQLD-compound-target-UC network was constructed based on public databases to clarify the relationship between active compounds in GGQLD and potential targets.  ...  Trends Genet 13:163, 29.Fishilevich S., Zimmerman S., Kohn A., Iny Stein T., Olender T., Kolker E., et al. (2016) Genic 556 insights from integrated human proteomics in GeneCards.  ... 
doi:10.1042/bsr20203565 pmid:33409535 pmcid:PMC7876598 fatcat:73w5cveuwzdmxj3si77vpulpla

RNA sequencing for the study of splicing

Mar Gonzàlez-Porta, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository
those obtained from proteomics experiments.  ...  Finally, in the last chapter, I explore the validation of changes in alternative transcript abundance at the protein level, through the integration of results derived from RNA sequencing datasets with  ...  All the information on gene function was retrieved from Genecards [Safran et al., 2010] unless otherwise indicated in the text.  ... 
doi:10.17863/cam.15986 fatcat:k2fweoddofhiphmkoxitwvpgwa

Global analysis of human genetic variations in protein-coding regions

Eman Alhuzimi, Michael Sternberg, King Abdulaziz City For Science
of 17,975 human protein-coding genes.  ...  Our analysis presented consistent results obtained from several well-established tools which showed that genes enriched in rare variants have far greater similarities in the biological and network properties  ...  Genomic and Proteomic Data Human protein-coding gene attributes were downloaded from the Ensembl database using the Biomart data-mining tool .  ... 
doi:10.25560/68381 fatcat:icyzdjdvhjfshkveueqq4czloi

Exome sequencing for understanding phenotypic variability in subjects with 16p11.2 CNV

Jila Dastan
I hypothesized that while some unique features reported in individuals with dup16p11.2 may be explained by the over-expression of its integral genes, co-occurrence of other genetic alterations in the genome  ...  This hypothesis was explored in two unrelated subjects with NDD who each inherited the dup16p11.2 from an apparently healthy carrier parent.  ...  Table 3.2: RNA expression intensity of genes located within 16p11.2 region in normal human tissue (GeneCards-Microarray-BioGPS).  ... 
doi:10.14288/1.0300131 fatcat:ci4wkrwc4ffybhokeggvqzvluq

A novel bioinformatic approach for comprehensive genome scale analysis identifies key regulators of macrophage activation

Samuel Katz, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Clare Bryant, Iain Fraser
Applying TRIAGE analysis to three genome-scale studies of LPS treatment in macrophages of mouse and human cell lines, I identified an enrichment for regulators relating to alternative splicing and protein  ...  Advancements in genome-wide screening technologies have made it possible to interrogate the regulatory landscape of signaling pathways such as those activated by TLR4.  ...  SQANTI categorizes transcripts as full splice match (FSM), incomplete splice match (ISM), novel in catalog (NIC), novel not in catalog (NNC), genic intron, and genic genomic (Figure 7 .9).  ... 
doi:10.17863/cam.52100 fatcat:zdsk3n6fv5f7xbu7debbdlaaje

Genetic and genomic investigations of Amyotrophic lateral sclerosis

Emily Pamela McCann
This work expands our understanding of the genetic causes of ALS, and in turn provides much needed insight for the development of diagnostic and carrier-screening regimes, as well as relevant models of  ...  Novel ALS gene discovery in four small families identified 19, 11, 16 and 64 candidate causal mutations in each.  ...  , and only rarely in sporadic cases.  ... 
doi:10.25949/19436378 fatcat:6quzr6tmnrbrjmu6geaz25dvvi
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