We present a novel method for simultaneous inference and nonparametric clustering of transcriptional dynamics from gene expression data. The proposed method uses gene expression data to infer time-varying TF profiles and cluster these temporal profiles according to the dynamics they exhibit. We use the latent structure of factorial hidden Markov model to model the transcription factor profiles as Markov chains and cluster these profiles using nonparametric mixture modeling. An efficient Gibbs sampling scheme is proposed for inference of latent variables and grouping of transcriptional dynamics into a priori unknown number of clusters. We test our model on simulated data and analyse its performance on two expression datasets; S. cerevisiae cell cycle data and E. coli oxygen starvation response data. Our results show the applicability of the method for genome wide analysis of expression data.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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