CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics.
The Central Carbon Metabolic Flux Database (CeCaFDB, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. It encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information gathered from hundreds of journal articles. In addition to its comprehensive literature-derived data, the CeCaFDB supports a common text search function among the data and interactive visualization of the curated flux distributions with compartmentation information based on the Cytoscape Web API, which facilitates data interpretation. The CeCaFDB offers four modules to calculate a similarity score or to perform an alignment between the flux distributions. One of the modules was built using an inter programming algorithm for flux distribution alignment that was specifically designed for this study. Based on these modules, the CeCaFDB also supports an extensive flux distribution comparison function among the curated data. The CeCaFDB is strenuously designed to address the broad demands of biochemists, metabolic engineers, systems biologists and members of the -omics community.
College of Computer Science and Technology, Guizhou University, Guiyang, Guizhou 550025, P.R. China.
Zhengdong
Z
Zhang
Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Tie
T
Shen
School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China.
Bin
B
Rui
Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Wenwei
W
Zhou
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Xiangfei
X
Zhou
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Chuanyu
C
Shang
School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China.
Chenwei
C
Xin
Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Xiaoguang
X
Liu
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Gang
G
Li
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Jiansi
J
Jiang
Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Chao
C
Li
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Ruiyuan
R
Li
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Mengshu
M
Han
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Shanping
S
You
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Guojun
G
Yu
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China.
Yin
Y
Yi
School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China swhx12@ahau.edu.cn.
Han
H
Wen
Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China liuzj@gznu.edu.cn.
Zhijie
Z
Liu
Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China xyx@gznu.edu.cn.
Xiaoyao
X
Xie
D000818:Animals; D002244:Carbon / Q000378:metabolism*; D002247:Carbon Isotopes; D003196:Computer Graphics; D062126:Databases, Chemical; D004926:Escherichia coli / Q000378:metabolism; D020407:Internet; D020601:Methylobacterium extorquens / Q000378:metabolism
D002247:Carbon Isotopes; D002244:Carbon