ROBNCA

Robust network component analysis for recovering transcription factor activities

Amina Noor, Aitzaz Ahmad, Erchin Serpedin, Mohamed Nounou, Hazem Nounou

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Network component analysis (NCA) is an efficient method of reconstructing the transcription factor activity (TFA), which makes use of the gene expression data and prior information available about transcription factor (TF)-gene regulations. We propose ROBust Network Component Analysis (ROBNCA), a novel iterative algorithm that explicitly models the possible outliers in the microarray data. ROBNCA algorithm provides a closed form solution for estimating the connectivity matrix, which was not available in prior contributions. The ROBNCA algorithm is compared to FastNCA and the Non-iterative NCA (NI-NCA) and is shown to estimate the TF activity profiles as well as the TF-gene control strength matrix with a much higher degree of accuracy than FastNCA and NI-NCA, irrespective of varying noise, and/or amount of outliers in case of synthetic data. The run time of the ROBNCA algorithm is comparable to that of FastNCA, and is hundreds of times faster than NI-NCA.

Original languageEnglish
Title of host publication2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Proceedings
Pages19-22
Number of pages4
DOIs
Publication statusPublished - 2013
Event2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Houston, TX, United States
Duration: 17 Nov 201319 Nov 2013

Other

Other2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013
CountryUnited States
CityHouston, TX
Period17/11/1319/11/13

Fingerprint

Network components
Transcription factors
Transcription Factors
Gene expression
Genes
Noise
Microarrays
Gene Expression

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computational Theory and Mathematics
  • Signal Processing
  • Biomedical Engineering

Cite this

Noor, A., Ahmad, A., Serpedin, E., Nounou, M., & Nounou, H. (2013). ROBNCA: Robust network component analysis for recovering transcription factor activities. In 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Proceedings (pp. 19-22). [6735919] https://doi.org/10.1109/GENSIPS.2013.6735919

ROBNCA : Robust network component analysis for recovering transcription factor activities. / Noor, Amina; Ahmad, Aitzaz; Serpedin, Erchin; Nounou, Mohamed; Nounou, Hazem.

2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Proceedings. 2013. p. 19-22 6735919.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Noor, A, Ahmad, A, Serpedin, E, Nounou, M & Nounou, H 2013, ROBNCA: Robust network component analysis for recovering transcription factor activities. in 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Proceedings., 6735919, pp. 19-22, 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013, Houston, TX, United States, 17/11/13. https://doi.org/10.1109/GENSIPS.2013.6735919
Noor A, Ahmad A, Serpedin E, Nounou M, Nounou H. ROBNCA: Robust network component analysis for recovering transcription factor activities. In 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Proceedings. 2013. p. 19-22. 6735919 https://doi.org/10.1109/GENSIPS.2013.6735919
Noor, Amina ; Ahmad, Aitzaz ; Serpedin, Erchin ; Nounou, Mohamed ; Nounou, Hazem. / ROBNCA : Robust network component analysis for recovering transcription factor activities. 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Proceedings. 2013. pp. 19-22
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