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Dynamic covariation between gene expression and proteome characteristics
2005
BMC Bioinformatics
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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
2018
Molecular & Cellular Proteomics
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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
2006
Mammalian Genome
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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
2013
Current Genomics
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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
2020
The FEBS Journal
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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
2018
Cell Biology and Toxicology
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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
2013
Advanced Drug Delivery Reviews
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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
2015
Journal of Cellular Physiology
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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
2018
Translational Psychiatry
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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]
2022
bioRxiv
pre-print
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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
2017
Journal of Proteomics
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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
2014
Cancer Science
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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
2018
Genome Medicine
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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
2010
Proceedings of the National Academy of Sciences of the United States of America
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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
2011
Journal of Proteomics
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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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