Estimating large scale signaling networks through nested effects models from intervention effects in microarray data

Proceedings of the German Conference on Bioinformatics, GCB 2007

Volumn , Issue , 2007, Pages 45-54

  Fröhlich, Holger ^a   Fellmann, Mark ^a   Sltmann, Holger ^a   Poustka, Annemarie ^a   Beissbarth, Tim ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL DATA; DATA DISCRETIZATION; DIFFERENTIAL GENE EXPRESSIONS; EXTENSIVE SIMULATIONS; HYPERPARAMETERS; LARGE-SCALE NETWORK; MCF-7 BREAST CANCER CELLS; MICROARRAY DATA; MIXTURE DISTRIBUTIONS; MODULE NETWORKS; NESTED EFFECT; NETWORK STRUCTURES; P-VALUES; PRIOR DISTRIBUTION; REVERSE ENGINEERS; SCALE-UP; SCORING SCHEMES; SIGNALING CASCADES; SIGNALING NETWORKS; STATISTICAL FRAMEWORK;

BIOINFORMATICS; GENES; SIGNALING;

COMPUTER SIMULATION;

EID: 39149129302     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (7)

1. [AAU72] M. Garey A. Aho and J. Ullman. The Transitive Reduction of a Directed Graph. SIAM Journal on Computing, 1(2):131-137, 1972.
2. [BAP02] M. Boutros, H. Agaisse, and N. Perrimon. Sequential activation of signaling pathways during innate immune responses in Drosophila. Developmental Cell, 3(5):711-722, 2002.
3. [DLR77] A. Dempster, N. Laird, and D. Rubin. Maximum likelihood from incomplete data via the EM algorithm. J. Royal Statistical Soc., Series B, 39(1):1-38, 1977.
4. [MBS05] F. Markowetz, J. Bloch, and R. Spang. Non-transcriptional pathway features reconstructed from secondary effects of RNA interference. Bioinformatics, 21(21):4026-4032, 2005.
5. [MKTS07] F. Markowetz, D. Kostka, O. Troyanskaya, and R. Spang. Nested Effects Models for High-dimensional Phenotyping Screens. In Proc. Int. Conf. on Int. Syst. for Mol. Biol. (ISMB), 2007. in press.
6. [PM03] S. Pounds and S. Morris. Estimating the occurence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics, 19(10):1236-1242, 2003.
7. [Rou87] P.J. Rousseeuw. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comp. and Applied Mathematics, 20:53-65, 1987.