Schistosoma mansoni genome prioritization including C. elegans tissue-specific gene expression data

Posted by Santiago Carmona on 2011-06-15 23:33:13

This ranked list of S. mansoni targets was constructed from the published list 336 (for PLOS-NTD paper, http://tdrtargets.org/published/browse/336 ) by including additional criteria based on C. elegans tissue specific gene expression data.
C. elegans Neuron and Muscle specifically expressed genes (predicted) data was taken from "Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans", Chikina et. al.
Both gene sets were mapped to Schistosoma mansoni genome. More information available in http://tdrtargets.org/published/browse/392
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Queries in this set

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  Sma EC numbers - uploaded list (693 records). Show parameters.

  Orthologs of D. melanogaster genes with mutant phenotype lethal (2207 records). Show parameters.

  Orthologs of D. melanogaster genes with mutant phenotype neurophysiological defect (382 records). Show parameters.

  Embryonic Lethal/Arrest in C. elegans (2269 records). Show parameters.

  Growth Defect in C. elegans (1195 records). Show parameters.

  Larval/Adult Lethal/Arrest in C. elegans (1476 records). Show parameters.

  Morphology Defect in C. elegans (787 records). Show parameters.

  Sterility in C. elegans (1550 records). Show parameters.

  any essentiality evidence (3209 records). Show parameters.

  structural model available (8831 records). Show parameters.

  druggable genes inferred by sequence simiarity (846 records). Show parameters.

  expressed in adult worm (ESTs) (6961 records). Show parameters.

  expressed in egg stage (ESTs) (4955 records). Show parameters.

  expressed in schistosomula stage (ESTs) (5249 records). Show parameters.

  expressed in any relevant stage (ESTs) (8618 records). Show parameters.

  Sma all proteins (13167 records). Show parameters.

  Sma in Cel (5951 records). Show parameters.

  Sma uploaded list of metabolic chokepoint enzymes (Berriman et al, 2009) (151 records). Show parameters.

  Sma uploaded list of targets identified by STARlite search (Berriman et al, 2009) (90 records). Show parameters.

  Sma uploaded list of targets similar to known human targets (Berriman et al, 2009) (28 records). Show parameters.

  S. mansoni orthologs of C. elegans genes differentially expressed in muscle (305 records). Show parameters.

  S. mansoni orthologs of C. elegans genes differentially expressed in neurons (442 records). Show parameters.

  Union of (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 26) (13376 records). Show parameters.

  top-100 of ranked list for PLOS-NTD; Posted List 336, No tissue-differential gene expression data (100 records). Show parameters.

  genes raised to the top-100 target ranking due to incorporation of tissue differential gene expression data from C. elegans (37 records). Show parameters.

  top-25 of ranked list for PLOS-NTD; Posted List 336, No tissue-differential gene expression data (25 records). Show parameters.

  Weighted list for comparison of PLOS-NTD vs. this prioritization (13376 records). Show parameters.