WormBase Tree Display for Expression_cluster: WBPaper00025141:unc-4::GFP_Expressed_Genes

WBPaper00025141:unc-4::GFP_Expressed_Genes Description: Genes expressed in embryonic motor neurons (identified by unc-4::GFP expressing cells).
  Species: Caenorhabditis elegans
  Algorithm: Genes called Present by MAS 5.0 in 2 out of 3 unc-4::GFP hybridizations.
  Reference: WBPaper00025141
  Microarray_results (6217)
  Gene (6183)
  Attribute_of: Microarray_experiment: WBPaper00025040:DM39_unc-4::GFP_1
      WBPaper00025040:DM51_unc-4::GFP_2
      WBPaper00025040:DM59_unc-4::GFP_3
  Associated_with: Life_stage: WBls:0000003
    Anatomy_term: WBbt:0004740 Expressed
        FACS
      WBbt:0005278 Expressed
        FACS
      WBbt:0005396 Expressed
        FACS
      WBbt:0005656 Expressed
        FACS
  Remark: unc-4::GFP is expressed in 13 embryonic motor neurons. (1) I5 (pharynx), (3) SAB (retrovesicular ganglion), and (9) DA (ventral nerve cord).
    Expressed transcripts were initially identified on the basis of a Present call in 2 out of 3 unc-4::GFP experiments as determined by Affymetrix MAS 5.0. Intensity values were then normalized using RMA (Robust Multi-Array Analysis) and statistically analyzed using Significance Analysis of Microarrays software (SAM, Stanford). A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.7-fold from the wildtype reference at a False Discovery Rate (FDR) of <= 1%. These genes were considered significantly enriched. This analysis also identified ~1600 transcripts that are depleted (1.7x, <= 1% FDR) in unc-4::GFP cells vs the wildtype reference. Although 729 of these transcripts are also scored as present in the unc-4::GFP motor neuron dataset, we attribute their detection to high expression in the small fraction (~10%) of non-GFP cells contaminating this preparation. Therefore, all 729 of these wildtype-enriched transcripts were excluded from the list of present calls. Finally, to compute the overall sum of Expressed Genes (EGs) in the unc-4::GFP data set we restored 118 unc-4::GFP-enriched genes that were initially excluded from the present list due to high mismatch signals. These considerations produce a final list of 6,217 genes that are detected in unc-4::GFP motor neurons.