CLCL

ABSTRACT

  • The non-coding RNA (ncRNA) elements in the 3' untranslated regions (3'-UTRs) are known to participate in the genes' post-transcriptional regulation, such as their stability, translation efficiency, and subcellular localization. Inferring co-expression patterns of the genes by clustering their 3'-UTR ncRNA elements will provide invaluable knowledge for further studies of their functionalities and interactions under specific physiological processes. In this work, we propose an improved RNA structural clustering pipeline that takes into account the length-dependent distribution of the structural similarity measure. Benchmark of the proposed pipeline on Rfam data clearly demonstrates over 10% performance gain, when compared to a traditional hierarchical clustering pipeline. By applying the proposed clustering pipeline to Drosophila melanogaster 's 3'-UTRs, we have successfully identified 184 ncRNA clusters, of which 91.3% appear to be true RNA structural elements, based on RNAz's prediction. Among the clusters, we have rediscovered the well-known histone ncRNA family as well as a number of other families whose potential functionalities may be inferred from existing studies. One of such families contains genes that are preferentially expressed in male Drosophila. In situ hybridization further reveals their characteristic 'cup' or 'comet' localization patterns in Drosophila testis. The complete clustering results are available from supplementary materials.

    • Full Article

    README

    Usage:

     

    Finding cliques in an undirected, unit-weighted graph:

    CLCL -i graph -n num_of_nodes [-c clique_size_cutoff] [-e connectivity_cutoff]

     

    '-i' specify the graph to be processed by the algorithm. The graph is represented

    by a n-by-n binary matrix, where a '1' in the matrix indicates that the corresponding

    vertices are connected, and a '0' otherwise. DO NOT INCLUDE HEADER IN THE MATRIX!

     

    '-n' specify the number of nodes in the graph, which is expected to be a positive

    integer.

     

    '-c' specify the minimum number of nodes in the output clique. If a clique has less

    nodes that this cutoff, it will not be output. The default value is 3.

     

    '-e' specify the connectivity cutoff for merging (please see the article for detail).

    The default value is 0.4.

     

    Example:             CLCL -i Test_Graph -n 100

    The outputs are a number of rows of tab-delimited numbers. Each row represents a clique,

    and the tab-delimited numbers represents nodes in the clique. The number is the row/column

    index of the node in the input graph. MAKE SURE A CORRESPONDENCE LIST IS MAINTAINED

    CORRECTLY TO MAP BACK THE CLIQUES!

    DOWNLOADS

    CLCL_ver1.0.tar.gz

    Supplementary information

    Performance of clustering on all families in the Rfam data set
    Additional_File_1

    Clustering results of RNA elements in Drosophila 3'-UTR
    Additional_File_2

    Differential expression of each cluster
    Additional_File_3

    Other companion information

    The entire Rfam data set and raw clustering file
    Companion_RfamRawClustering.pdf

    Original FlyAtlas T-test results used to generate Additional file 3
    FlyAtlas_Ttest