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Frontiers of Medicine

ISSN 2095-0217

ISSN 2095-0225(Online)

CN 11-5983/R

Postal Subscription Code 80-967

2018 Impact Factor: 1.847

Front. Med.    2014, Vol. 8 Issue (4) : 433-444     DOI: 10.1007/s11684-014-0336-0
REVIEW |
Transcriptomics and proteomics in stem cell research
Hai Wang,Qian Zhang,Xiangdong Fang()
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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Abstract  

Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.

Keywords embryonic stem cells      transcriptomics      proteomics     
Corresponding Authors: Xiangdong Fang   
Online First Date: 26 June 2014    Issue Date: 18 December 2014
URL:  
http://academic.hep.com.cn/fmd/EN/10.1007/s11684-014-0336-0     OR     http://academic.hep.com.cn/fmd/EN/Y2014/V8/I4/433
Fig.1  Unsupervised clustering of genome-wide gene expression is provided for ESCs form different sequencing studies. These ESCs constitute of ESC.1 (H1 cell line), ESC.2 (H1 cell line), ESC.3 (H7 cell line), ESC.4 (human embryonic stem cell line), HESC (human hematopoietic stem cells), 48hrESC (ESC.2 differentiated for 48 h), MSC (mesenchymal stem cells), CSC cells (cancer stem cells). Gene expression tracks use red and green to represent over- and under-expression, respectively.
Repository Data type Species URL Reference
ESCAPE Transcriptomics, proteomics, ??phosphoproteomics Human, mouse http://www.maayanlab.net/ESCAPE/ [51]
Stem Cell Omics Repository Transcriptomics, proteomics, ??phosphoproteomics Human http://scor.chem.wisc.edu/ [49,5257]
Stem Base Transcriptomics Human, mouse, rat http://www.stembase.ca/?path=/ [58]
SCDE Transcriptomics Human, mouse, rat http://discovery.hsci.harvard.edu/ [59,60]
ESCD Transcriptomics Human, mouse http://biit.cs.ut.ee/escd/ [61]
Stem Cell Commons Transcriptomics Human, mouse, rat, zebrafish http://stemcellcommons.org/node/13552 [62]
Tab.1  Database for stem cell omics research
Fig.2  Systemic analysis brings insights into physiological and pathological molecular mechanisms of stem cells and promotes stem cell clinical utilities.
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