Selection of Reprogramming Factors of Induced Pluripotent Stem Cells Based on the Protein Interaction Network and Functional Profiles

被引：4
作者：
Huang, Tao [3 ,4 ]
Cai, Yu-Dong [1 ,2 ,9 ]
Chen, Lei [8 ]
Hu, Le-Le [1 ]
Kong, Xiang-Yin [5 ,6 ,7 ]
Li, Yi-Xue [3 ,4 ]
Chou, Kuo-Chen [9 ]
机构：
[1] Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
[2] Fudan Univ, Ctr Computat Syst Biol, Shanghai 200433, Peoples R China
[3] Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Syst Biol, Shanghai 200031, Peoples R China
[4] Shanghai Ctr Bioinformat Technol, Shanghai 200235, Peoples R China
[5] Chinese Acad Sci, Key Lab Stem Cell Biol, Inst Hlth Sci, Shanghai Inst Biol Sci, Shanghai 200025, Peoples R China
[6] Shanghai Jiao Tong Univ, Sch Med, Shanghai 200025, Peoples R China
[7] Shanghai Jiao Tong Univ, State Key Lab Med Genom, Ruijin Hosp, Shanghai 200025, Peoples R China
[8] E China Normal Univ, Shanghai Key Lab Trustworthy Comp, Shanghai 200062, Peoples R China
[9] Gordon Life Sci Inst, San Diego, CA 92130 USA
来源：
PROTEIN AND PEPTIDE LETTERS | 2012年 / 19卷 / 01期
基金：
中国国家自然科学基金;
关键词：
Stem cells; reprogramming factors; protein interaction network; gene functional profiles; disease investigation; SHORTEST-PATH ANALYSIS; BETA-CATENIN; STAT3; ASSOCIATIONS; FIBROBLASTS; GENERATION; INDUCTION;
D O I：
10.2174/092986612798472884
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Induced pluripotent stem cells have displayed great potential in disease investigation and drug development applications. However, selection of reprogramming factors in each cell type or disease state is both expensive and time consuming. To deal with this kind of situation, a fast computational framework was developed by optimize the reprogramming factors via the protein interaction network and gene functional profiles. It can be used to select reprogramming factors from millions of possibilities. It is anticipated that the novel approach will become a very useful tool for both basic research and drug development.
引用
收藏
页码：113 / 119
页数：7
相关论文
共 47 条
  • [1] Prospective identification of tumorigenic breast cancer cells
    Al-Hajj, M
    Wicha, MS
    Benito-Hernandez, A
    Morrison, SJ
    Clarke, MF
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (07) : 3983 - 3988
  • [2] [Anonymous], 1992, APPL ALGORITHMIC GRA
  • [3] Stat3 as an oncogene
    Bromberg, JF
    Wrzeszczynska, MH
    Devgan, G
    Zhao, YX
    Pestell, RG
    Albanese, C
    Darnell, JE
    [J]. CELL, 1999, 98 (03) : 295 - 303
  • [4] Protective Effects of Human iPS-Derived Retinal Pigment Epithelium Cell Transplantation in the Retinal Dystrophic Rat
    Carr, Amanda-Jayne
    Vugler, Anthony A.
    Hikita, Sherry T.
    Lawrence, Jean M.
    Gias, Carlos
    Chen, Li Li
    Buchholz, David E.
    Ahmado, Ahmad
    Semo, Ma'ayan
    Smart, Matthew J. K.
    Hasan, Shazeen
    da Cruz, Lyndon
    Johnson, Lincoln V.
    Clegg, Dennis O.
    Coffey, Pete J.
    [J]. PLOS ONE, 2009, 4 (12):
  • [5] Mammalian Grb2 regulates multiple steps in embryonic development and malignant transformation
    Cheng, AM
    Saxton, TM
    Sakai, R
    Kulkarni, S
    Mbamalu, G
    Vogel, W
    Tortorice, CG
    Cardiff, RD
    Cross, JC
    Muller, WJ
    Pawson, T
    [J]. CELL, 1998, 95 (06) : 793 - 803
  • [6] Cormen T., 2001, Introduction to Algorithms
  • [7] Primer: induced pluripotency
    de Souza, Natalie
    [J]. NATURE METHODS, 2010, 7 (01) : 20 - 21
  • [8] Dijkstra E. W., 1959, Numerische Mathematik, V1, P269, DOI [10.1007/BF01386390, DOI 10.1007/BF01386390]
  • [9] Esteban M.A., 2009, Cell Stem Cell
  • [10] Shortest path analysis using partial correlations for classifying gene functions from gene expression data
    Fitch, A. Marie
    Jones, M. Beatrix
    [J]. BIOINFORMATICS, 2009, 25 (01) : 42 - 47
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