Literature DB >> 20208531

Cell type-specific gene expression differences in complex tissues.

Shai S Shen-Orr1, Robert Tibshirani, Purvesh Khatri, Dale L Bodian, Frank Staedtler, Nicholas M Perry, Trevor Hastie, Minnie M Sarwal, Mark M Davis, Atul J Butte.   

Abstract

We describe cell type-specific significance analysis of microarrays (csSAM) for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. First, we validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejection, which revealed hundreds of differentially expressed genes that were otherwise undetectable.

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Year:  2010        PMID： 20208531      PMCID： PMC3699332          DOI： 10.1038/nmeth.1439

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  11 in total

1.  Significance analysis of microarrays applied to the ionizing radiation response.

Authors:  V G Tusher; R Tibshirani; G Chu
Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-17       Impact factor: 11.205

2.  Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations.

Authors:  Peng Lu; Aleksey Nakorchevskiy; Edward M Marcotte
Journal:  Proc Natl Acad Sci U S A       Date:  2003-08-21       Impact factor: 11.205

3.  Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types.

Authors:  S Debey; U Schoenbeck; M Hellmich; B S Gathof; R Pillai; T Zander; J L Schultze
Journal:  Pharmacogenomics J       Date:  2004       Impact factor: 3.550

4.  Whole blood and leukocyte RNA isolation for gene expression analyses.

Authors:  Robert J Feezor; Henry V Baker; Michael Mindrinos; Doug Hayden; Cynthia L Tannahill; Bernard H Brownstein; Adrian Fay; Sandra MacMillan; Jason Laramie; Wenzhong Xiao; Lyle L Moldawer; J Perren Cobb; Krzysztof Laudanski; Carol L Miller-Graziano; Ronald V Maier; David Schoenfeld; Ronald W Davis; Ronald G Tompkins
Journal:  Physiol Genomics       Date:  2004-11-17       Impact factor: 3.107

5.  Application of genome-wide expression analysis to human health and disease.

Authors:  J Perren Cobb; Michael N Mindrinos; Carol Miller-Graziano; Steve E Calvano; Henry V Baker; Wenzhong Xiao; Krzysztof Laudanski; Bernard H Brownstein; Constance M Elson; Douglas L Hayden; David N Herndon; Stephen F Lowry; Ronald V Maier; David A Schoenfeld; Lyle L Moldawer; Ronald W Davis; Ronald G Tompkins; Henry V Baker; Paul Bankey; Timothy Billiar; Bernard H Brownstein; Steve E Calvano; David Camp; Irshad Chaudry; J Perren Cobb; Ronald W Davis; Constance M Elson; Bradley Freeman; Richard Gamelli; Nicole Gibran; Brian Harbrecht; Douglas L Hayden; Wyrta Heagy; David Heimbach; David N Herndon; Jureta Horton; John Hunt; Krzysztof Laudanski; James Lederer; Stephen F Lowry; Ronald V Maier; John Mannick; Bruce McKinley; Carol Miller-Graziano; Michael N Mindrinos; Joseph Minei; Lyle L Moldawer; Ernest Moore; Frederick Moore; Robert Munford; Avery Nathens; Grant O'keefe; Gary Purdue; Laurence Rahme; Daniel Remick; Matthew Sailors; David A Schoenfeld; Michael Shapiro; Geoffrey Silver; Richard Smith; Gregory Stephanopoulos; Gary Stormo; Ronald G Tompkins; Mehmet Toner; Shaw Warren; Michael West; Steven Wolfe; Wenzhong Xiao; Vernon Young
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-21       Impact factor: 11.205

6.  Individuality and variation in gene expression patterns in human blood.

Authors:  Adeline R Whitney; Maximilian Diehn; Stephen J Popper; Ash A Alizadeh; Jennifer C Boldrick; David A Relman; Patrick O Brown
Journal:  Proc Natl Acad Sci U S A       Date:  2003-02-10       Impact factor: 11.205

7.  In silico dissection of cell-type-associated patterns of gene expression in prostate cancer.

Authors:  Robert O Stuart; William Wachsman; Charles C Berry; Jessica Wang-Rodriguez; Linda Wasserman; Igor Klacansky; Dan Masys; Karen Arden; Steven Goodison; Michael McClelland; Yipeng Wang; Anne Sawyers; Iveta Kalcheva; David Tarin; Dan Mercola
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-13       Impact factor: 11.205

8.  Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus.

Authors:  Alexander R Abbas; Kristen Wolslegel; Dhaya Seshasayee; Zora Modrusan; Hilary F Clark
Journal:  PLoS One       Date:  2009-07-01       Impact factor: 3.240

9.  In silico microdissection of microarray data from heterogeneous cell populations.

Authors:  Harri Lähdesmäki; Llya Shmulevich; Valerie Dunmire; Olli Yli-Harja; Wei Zhang
Journal:  BMC Bioinformatics       Date:  2005-03-14       Impact factor: 3.169

10.  Cell-type specific gene expression profiles of leukocytes in human peripheral blood.

Authors:  Chana Palmer; Maximilian Diehn; Ash A Alizadeh; Patrick O Brown
Journal:  BMC Genomics       Date:  2006-05-16       Impact factor: 3.969
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  232 in total

1.  Transplantomics and biomarkers in organ transplantation: a report from the first international conference.

Authors:  Minnie M Sarwal; Jacqueline Benjamin; Atul J Butte; Mark M Davis; Kathryn Wood; Jeremy Chapman
Journal:  Transplantation       Date:  2011-02-27       Impact factor: 4.939

2.  Gene expression deconvolution in linear space.

Authors:  Yi Zhong; Zhandong Liu
Journal:  Nat Methods       Date:  2011-12-28       Impact factor: 28.547

3.  Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain.

Authors:  Alexandre Kuhn; Doris Thu; Henry J Waldvogel; Richard L M Faull; Ruth Luthi-Carter
Journal:  Nat Methods       Date:  2011-10-09       Impact factor: 28.547

Review 4.  Molecular diagnostics in transplantation.

Authors:  Maarten Naesens; Minnie M Sarwal
Journal:  Nat Rev Nephrol       Date:  2010-08-24       Impact factor: 28.314

5.  Standing out from the crowd.

Authors:  Mary Muers
Journal:  Nat Rev Genet       Date:  2010-05       Impact factor: 53.242

Review 6.  New tools for classification and monitoring of autoimmune diseases.

Authors:  Holden T Maecker; Tamsin M Lindstrom; William H Robinson; Paul J Utz; Matthew Hale; Scott D Boyd; Shai S Shen-Orr; C Garrison Fathman
Journal:  Nat Rev Rheumatol       Date:  2012-05-31       Impact factor: 20.543

Review 7.  Systems immunology of human malaria.

Authors:  Tuan M Tran; Babru Samal; Ewen Kirkness; Peter D Crompton
Journal:  Trends Parasitol       Date:  2012-05-15

Review 8.  Systems immunology: just getting started.

Authors:  Mark M Davis; Cristina M Tato; David Furman
Journal:  Nat Immunol       Date:  2017-06-20       Impact factor: 25.606

9.  MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples.

Authors:  David A Liebner; Kun Huang; Jeffrey D Parvin
Journal:  Bioinformatics       Date:  2013-10-01       Impact factor: 6.937

10.  A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.

Authors:  Maayan Baron; Adrian Veres; Samuel L Wolock; Aubrey L Faust; Renaud Gaujoux; Amedeo Vetere; Jennifer Hyoje Ryu; Bridget K Wagner; Shai S Shen-Orr; Allon M Klein; Douglas A Melton; Itai Yanai
Journal:  Cell Syst       Date:  2016-09-22       Impact factor: 10.304
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