Bi-correlation clustering algorithm for determining a set of co- regulated genes BIOINFORMATICS vol. 25 no.21 2009 Anindya Bhattacharya and Rajat K. De.
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Bi-correlation clustering algorithm for determining a set of co- regulated genes BIOINFORMATICS vol. 25 no.21 2009 Anindya Bhattacharya and Rajat K. De
Introduction Biclustering Performs simultaneous grouping on genes and conditions of a dataset to determine subgroups of genes that exhibit similar behavior over a subset of experimental condition. A new correlation-based biclustering algorithm called bi-correlation clustering algorithm (BCCA) Produce a diverse set of biclusters of co-regulated genes All the genes in a bicluster have a similar change of expression pattern over the subset of samples.
Introduction Cluster analysis Most cluster analysis try to find group of genes that remains co-expressed through all experimental conditions. In reality, genes tends to be co-regulated and thus co-expressed under only a few experimental conditions.
Bi-correlation clustering algorithm Notation A set of n genes Each gene has m expression values For each gene g i there is an m-dimensional vector, there is the j-th expression value of g i. A set of m microarry experiments (measurements) n genes will have to be grouped into K overlapping biclusters
Bi-correlation clustering algorithm Bicluster: A bicluster can be defined as a subset of genes possesing a similar behavior over a subset of experiments Represented as A bicluster contains a subset of genes and a subset of experiments where each gene in is correlated with a correlation valued greater than or equal to specified threshold, with all other genes in over the measurements in.
Bi-correlation clustering algorithm BCCA Use person correlation coefficient for measuring similarity between expression patterns of two genes and.
Bi-correlation clustering algorithm Step 1: The set of bicluster S is initialized to NULL and number of bicluster Bicount is initialized to 0 Step 2A BCCA generate a bicluster (C) for each pair of genes in a dataset under a set of conditions For each pair of genes.BCCA creates a bicluster, where and.
Bi-correlation clustering algorithm In step 2C: For a pair of genes in C, if then a sample is detected from C, deletion of which caused maximum increase in correlation value between and. If being a threshold, the sample is deleted from. otherwise, C is discarded. Deletion of a measurement for which genes differ in expression value the most will result in the highest increase in correlation value. BCCA deletes one measurement at a time from.
Bi-correlation clustering algorithm In step 2D(a): Other genes from, which satisfy the definition of a bicluster are included in C for its augmentation. In step 2D(b): Whether present bicluster C has been found. If it is so then we do not to include C, otherwise, C is considered as a new bicluster.
Results Datasets We demonstrate the affectiveness of BCCA in determining a set of co-regulated genes (i.e. the genes having common transcription factors) and functionally enriched clusters (and atributes) on five dataset
Results Variation with respect to threshold Plot of YCCD dataset : Average number of functionally enriched attributes (computed using P-values) versus correlation threshold value
Results Follow a guideline on this value from a previous study by Allocco et al. (2004) which has concluded that if two genes have a correlation between their expression profiles >0.84 then therre is >50% chance of being bounded by a common transcription factor.
Results By locating common transcription factors At first, we only consider those biclusters that have less than or equal to 50 genes. Use a software TOUCAN 2 (Aerts et al., 2005) for performance comparison by extracting information on the number of transcription factors present in proximal promoters of all the genes in a single bicluster. Presence of common transcription factors in the promoter regions of a set of genes is a good evidence toward co-regulation.
Sequences of all the five genes found in a bicluster generated by BCCA from SPTD dataset. Any transcription factor may be found present in more than one location in upstream region.
Results Functional enrichment : P-value The functional enrichment of each GO category in each of the bicluster employed the software Funcassociate (Berriz et al., 2003). P-value represents the probability of observing the number of genes from a specific GO functional category within each cluster. A low P-value indicates that the genes belonging to the enriched functional categories are biologically significant in the corresponding clusters.
Results P-value of a functional category Suppose we have total population of N genes, in which M has a particular annotation. If we observe x genes with that annotation, in a sample of n genes, then we can calculate the probability of that observation. The probability of seeing x or more genes with an annotation, out of n, given that M in the population of N have that annotation
Results Only functional categories with are reported. Analysis of the 10 biclusters obtained for the YCCD, the highly enriched category in bicluster Bicluster 1 is the ‘ribosome’ with P-value of
Conclusion BCCA is able to find a group of genes that show similar pattern of variation in their expression profiles over a subset of measurements. Better than other biclustering algorithm: Find higher number of common transcription factors of a set of gene in a bicluster More functionally enriched