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FastNCA specifications

Information


Unique identifier OMICS_20016
Name FastNCA
Alternative name Fast Network Component Analysis
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Chunqi Chang

Publication for Fast Network Component Analysis

FastNCA citations

 (5)
library_books

An Overview of NCA Based Algorithms for Transcriptional Regulatory Network Inference

2015
Microarrays
PMCID: 4996402
PMID: 27600242
DOI: 10.3390/microarrays4040596

[…] FastNCA [] provides a closed form solution to NCA, and it overcomes in the same time the speed limitations of the original NCA. FastNCA employs a series of matrix partitionings and orthogonal projecti […]

library_books

Iterative sub network component analysis enables reconstruction of large scale genetic networks

2015
BMC Bioinformatics
PMCID: 4634733
PMID: 26537518
DOI: 10.1186/s12859-015-0768-9

[…] ultiple local solutions. Tikhonov regularization method (termed as GNCA-r) overcomes these two issues but is computationally expensive for solving larger networks []. Fast network component analysis (FastNCA) is a stable and fast approach, up to several hundred times faster than GNCA-r but limited to smaller networks []. Recently, the robust network component analysis (ROBNCA) was developed that o […]

library_books

mAPC GibbsOS: an integrated approach for robust identification of gene regulatory networks

2013
BMC Syst Biol
PMCID: 4028818
PMID: 24564939
DOI: 10.1186/1752-0509-7-S5-S4

[…] he method will be hard to analyze data with large candidate TF pool, which limits its application to real biological studies. Network component analysis (NCA) [] and several NCA-based methods such as FastNCA [] are among several successful integrative methods, which are specifically developed to interpret gene regulatory network as a bipartite network. With some reasonable assumptions referred to […]

library_books

Reconstructing genome wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

2011
BMC Bioinformatics
PMCID: 3224099
PMID: 21668997
DOI: 10.1186/1471-2105-12-233

[…] m of calculating TFAs as optimization of a linear least square matrix decomposition. Liao et al. solve the problem using an expectation maximization (EM) approach []. Fast Network Component Analysis (FastNCA) uses singular value decomposition (SVD) and a matrix projection technique to approximate the linear least square matrix decomposition problem defined in NCA[]. Similarly, Alter and Golub use […]

library_books

Motif guided sparse decomposition of gene expression data for regulatory module identification

2011
BMC Bioinformatics
PMCID: 3072956
PMID: 21426557
DOI: 10.1186/1471-2105-12-82

[…] posed integrative approach, we applied mSD to synthetic and real yeast cell cycle data for regulatory module identification, and then compared its performance with those of other approaches including FastNCA [] and sparse decomposition []. For the synthetic data set, we used a network generator, SynTReN [], to produce a benchmark gene expression data set based on a synthetic S. cerevisiae transcri […]

Citations

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FastNCA institution(s)
Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong; Department of Electrical and Computer Engineering, University of California, Davis, CA, USA; Department of Medicine, The University of Hong Kong, Hong Kong
FastNCA funding source(s)
Supported in part by the University of Hong Kong CRCG under Small Project Funding.

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