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Dynamic covariation between gene expression and proteome characteristics

Mansour Taghavi Azar Sharabiani, Markku Siermala, Tommi O Lehtinen, Mauno Vihinen
2005 BMC Bioinformatics  
Since the majority of genes encode proteins, we investigated possible correlations between protein parameters and gene expression patterns to identify proteome-wide characteristics indicative of trends  ...  Thus, our results suggest that a dynamic relationship exists between proteome properties and gene expression in many biological systems, and therefore this relationship is fundamental to understanding  ...  Acknowledgements Teemu Kivioja, Petteri Sintonen and Timo Tiirikka are thanked for spirited discussions and helpful comments.  ... 
doi:10.1186/1471-2105-6-215 pmid:16131395 pmcid:PMC1236912 fatcat:esr3bgoshjeendv7rfu3wucawq

Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population

Evan G. Williams, Yibo Wu, Witold Wolski, Jun Yong Kim, Jiayi Lan, Moaraj Hasan, Christian Halter, Pooja Jha, Dongryeol Ryu, Johan Auwerx, Ruedi Aebersold
2018 Molecular & Cellular Proteomics  
Across tissues, expression covariation between genes' proteins and transcripts-measured in the same individuals-broadly aligned.  ...  Lastly, we compared the quantitative proteomic measurements between the total cell and mitochondrial fractions for the five tissues.  ...  We next examined links between genes' transcript and protein expression for all 3574 genes with matching multiomics measurements.  ... 
doi:10.1074/mcp.ra118.000554 pmid:29945935 fatcat:jntkrhqygrfyxek4ec2faca2pq

Expression genetics and the phenotype revolution

Robert W. Williams
2006 Mammalian Genome  
Genetic analysis of variation demands large numbers of individuals and even larger numbers of genotypes.  ...  Covariance between two messages depends on a cascade of protein intermediaries.  ...  sequence tags, and genes.  ... 
doi:10.1007/s00335-006-0006-x pmid:16783631 fatcat:pen6fvdzpvc2zh6lfqf5mz5wpa

Integrated Analysis of Transcriptomic and Proteomic Data

Saad Haider, Ranadip Pal
2013 Current Genomics  
Based on the central dogma, it was generally assumed that there exist a direct correspondence between mRNA transcripts and generated protein expressions.  ...  However, recent studies have shown that the correlation between mRNA and Protein expressions can be low due to various factors such as different half lives and post transcription machinery.  ...  For this reason, the idea of multiple regres-sion analysis is used to relate characteristics of different covariates of each individual gene with the mRNA-protein correlation.  ... 
doi:10.2174/1389202911314020003 pmid:24082820 pmcid:PMC3637682 fatcat:l3ubyjnahjg55nk2bhyyqalhou

Genome-wide postnatal changes in immunity following fetal inflammatory response

Daniel Costa, Núria Bonet, Amanda Solé, José Manuel González de Aledo-Castillo, Eduard Sabidó, Ferran Casals, Carlota Rovira, Alfons Nadal, Jose Luis Marin, Teresa Cobo, Robert Castelo
2020 The FEBS Journal  
Comparing FIR-affected and unaffected ELGANs, we identified 782 gene and 27 protein expression changes of 50% magnitude or more, and an experiment-wide significance level below 5% false discovery rate.  ...  Using RNA sequencing and mass spectrometry proteomics, we profiled the transcriptome and proteome of archived neonatal dried blood spot (DBS) specimens from 21 ELGANs.  ...  The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS Omics Tech) and is a member of Proteored, PRB3, which is supported by grant PT17/0019 of the PE I + D+i 2013  ... 
doi:10.1111/febs.15578 pmid:33006196 fatcat:q2ygxgaoh5ctflfzhfrio2icry

Clinical trans-omics: an integration of clinical phenomes with molecular multiomics

Xiangdong Wang
2018 Cell Biology and Toxicology  
For example, the expression of genomic and proteomic profiles can be presented as the density or rationales a digital values, while most of the clinical phenotypes are recorded as worddescriptive or image-based  ...  The most critical and challenging factor in the application of clinical transomics is to have automatic learning systems, which can dynamically generate, collect, integrate, and analyze large-scale data  ...  It was coined as a personalized dysfunctional gene network by simultaneously integrating genes with different features, e.g., the differential gene expression, expression variance, and differential expression  ... 
doi:10.1007/s10565-018-9431-3 pmid:29691682 fatcat:arvm5j62zjbfvnm6gq7ezesvnm

Delivering systems pharmacogenomics towards precision medicine through mathematics

Yaqun Wang, Ningtao Wang, Jianxin Wang, Zhong Wang, Rongling Wu
2013 Advanced Drug Delivery Reviews  
Here we describe a statistical framework for mapping dynamic genes that affect drug response by incorporating its pharmacokinetic and pharmacodynamic pathways.  ...  interact with genes in a complex web to determine drug efficacy and toxicity at the  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.  ... 
doi:10.1016/j.addr.2013.03.002 pmid:23523629 pmcid:PMC3988791 fatcat:ngee2wpz6nag7ndu5qnkhvs6sm

Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis

Robert E. Scott, Prachi N. Ghule, Janet L. Stein, Gary S. Stein
2015 Journal of Cellular Physiology  
In addition, WebGestalt, a gene ontology tool, facilitated the identification of expression networks of genes that co-vary with key cell cycle targets, especially Cdc20 and Plk1 (www.bioinfo.vanderbilt.edu  ...  Cell cycle expression networks of such covariate mRNAs exist in multiple proliferative tissues including liver, lung, pituitary, adipose and lymphoid tissues among others but not in brain or retina that  ...  Of these Rb1, Cenpe and Nek2 showed no network characteristics. In contrast, the other eight probes identified networks consisting of between 70 to 95 cell cycle mRNAs.  ... 
doi:10.1002/jcp.24990 pmid:25808367 pmcid:PMC4481160 fatcat:iyzq2jbumzemtlzj53z5wvsavq

Temporal proteomic profiling of postnatal human cortical development

Michael S Breen, Sureyya Ozcan, Jordan M Ramsey, Zichen Wang, Avi Ma'ayan, Nitin Rustogi, Michael G Gottschalk, Maree J Webster, Cynthia Shannon Weickert, Joseph D Buxbaum, Sabine Bahn
2018 Translational Psychiatry  
Moreover, the correspondence between RNA and protein expression significantly decreases as a function of cortical aging, especially for genes involved in myelination and cytoskeleton organization.  ...  However, the dynamics of how proteins are expressed, function and interact across postnatal human cortical development remain poorly understood.  ...  Correspondence between transcriptome and proteome module organization A total of 556 common HGNC symbols were detected between our high confidence, reproducible proteins and transcriptome-wide gene expression  ... 
doi:10.1038/s41398-018-0306-4 pmid:30518843 pmcid:PMC6281671 fatcat:avvnyqxxrjactf37vffbus5z3e

Pan-cancer proteomic map of 949 human cell lines reveals principles of cancer vulnerabilities [article]

Emanuel Goncalves, Rebecca C Poulos, Zhaoxiang Cai, Syd Barthorpe, Srikanth Manda, Natasha Lucas, Alexandra Beck, Daniel Bucio-Noble, Michael Dausmann, Caitlin Hall, Michael Hecker, Jennifer Koh (+18 others)
2022 bioRxiv   pre-print
The proteome provides unique insights into biology and disease beyond the genome and transcriptome. Lack of large proteomic datasets has restricted identification of new cancer biomarkers.  ...  Integrating multi-omics, drug response and CRISPR-Cas9 gene essentiality screens with a deep learning-based pipeline revealed thousands of protein-specific biomarkers of cancer vulnerabilities.  ...  Acknowledgments We thank Ricard Argelaguet for helpful comments and discussions on the implementations of the MOFA analysis, and Keith Ashman for discussions on optimizing the bank of mass  ... 
doi:10.1101/2022.02.26.482008 fatcat:nuibkaf7araqvgfdrjpdkfiz6q

Complementarity of SOMAscan to LC-MS/MS and RNA-seq for quantitative profiling of human embryonic and mesenchymal stem cells

Anja M. Billing, Hisham Ben Hamidane, Aditya M. Bhagwat, Richard J. Cotton, Shaima S. Dib, Pankaj Kumar, Shahina Hayat, Neha Goswami, Karsten Suhre, Arash Rafii, Johannes Graumann
2017 Journal of Proteomics  
Expression between cell types (ESC and MSC) was compared across techniques and uncovered the expected large differences.  ...  Dynamic range limitations are challenging to proteomics, particularly in clinical samples. Affinity proteomics partially overcomes this, yet suffers from dependence on reagent quality.  ...  Acknowledgements J.G. and the Proteomics Core at WCMC-Q are supported by "Biomedical Research Program" funds at Weill Cornell Medical College in Qatar, a program funded by Qatar Foundation.  ... 
doi:10.1016/j.jprot.2016.08.023 pmid:27613379 fatcat:3ea5qgz6djgrte64yohnhl5k3e

Prognostic significance of promyelocytic leukemia expression in gastrointestinal stromal tumor; integrated proteomic and transcriptomic analysis

Hiroshi Ichikawa, Akihiko Yoshida, Tatsuo Kanda, Shin-ichi Kosugi, Takashi Ishikawa, Takaaki Hanyu, Takahiro Taguchi, Marimu Sakumoto, Hitoshi Katai, Akira Kawai, Toshifumi Wakai, Tadashi Kondo
2014 Cancer Science  
For proteins showing differential expressions, global mRNA expression was compared between 9 I-GIST and 23 S-GIST.  ...  We conducted integrated proteomic and transcriptomic analysis to identify genes showing differential expressions according to the tumor site.  ...  with I-GIST and a shorter RFS period. Prognostication using PML expression may help to optimize the treatment strategy for GIST patients.  ... 
doi:10.1111/cas.12565 pmid:25457157 pmcid:PMC4317774 fatcat:yte4hof2cjdnhcshs4s2bfqoam

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Wei Tang, Ming Zhou, Tiffany H. Dorsey, DaRue A. Prieto, Xin W. Wang, Eytan Ruppin, Timothy D. Veenstra, Stefan Ambs
2018 Genome Medicine  
We then applied an integrated analysis of the proteomic and transcriptomic data to examine relationships between them, disease characteristics, and patient survival.  ...  Additional gene expression data from Affymetrix Gene Chip Human Gene ST Arrays were available for 59 tumors and 38 non-cancerous tissues in our study.  ...  We also downloaded the publicly available CPTAC breast cancer proteomics dataset from the Cancer Genomics Data Server, consisting of high-quality proteome and corresponding gene expression data for 77  ... 
doi:10.1186/s13073-018-0602-x fatcat:k4cno2wy7vdzvnfxr43ev7xw34

Dynamic antibody responses to the Mycobacterium tuberculosis proteome

S. Kunnath-Velayudhan, H. Salamon, H.-Y. Wang, A. L. Davidow, D. M. Molina, V. T. Huynh, D. M. Cirillo, G. Michel, E. A. Talbot, M. D. Perkins, P. L. Felgner, X. Liang (+1 others)
2010 Proceedings of the National Academy of Sciences of the United States of America  
Rational biomarker discovery requires understanding host-pathogen interactions leading to biomarker expression.  ...  tuberculosis proteome.  ...  Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession number GSE19433). ACKNOWLEDGMENTS.  ... 
doi:10.1073/pnas.1009080107 pmid:20668240 pmcid:PMC2930474 fatcat:wlgcqia35rfcdd5apob776d3je

Green systems biology — From single genomes, proteomes and metabolomes to ecosystems research and biotechnology

Wolfram Weckwerth
2011 Journal of Proteomics  
next-generation genome sequencing, gene reconstruction and annotation, (ii) genome-scale molecular analysis using OMICS technologies and (iii) computer-assisted analysis, modeling and interpretation of  ...  This process relies on the development of new technologies for the analysis of molecular data, especially genomics, metabolomics and proteomics data.  ...  Acknowledgements I thank Stefanie Wienkoop and Wolfgang Hoehenwarter for many years of fruitful collaborations. I thank Anke Bellaire for many helpful discussions and useful comments.  ... 
doi:10.1016/j.jprot.2011.07.010 pmid:21802534 fatcat:dzfnovn2o5derdtd3wgtncf23q
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