- WBPaper00056293:rpl-5(0)-rpl-33(0)_upregulated
Limma Package. When generating the contrast matrix in limma: wildtype data was counted as wild-type and rpl-33 & rpl-5 data were both counted as RP null data. For this reason there is only one fold change value per gene as calculated by the difference between RP null RNA and wild-type RNA.
Transcripts that showed significantly increased expression in rpl-5(cc5998) vs wild type (PD1074) and rpl-33(cc2558) vs wild type (PD1074) animals.
- WBPaper00056293:rpl-5(0)-rpl-33(0)_downregulated
Limma Package. When generating the contrast matrix in limma: wildtype data was counted as wild-type and rpl-33 & rpl-5 data were both counted as RP null data. For this reason there is only one fold change value per gene as calculated by the difference between RP null RNA and wild-type RNA.
Transcripts that showed significantly decreased expression in rpl-5(cc5998) vs wild type (PD1074) and rpl-33(cc2558) vs wild type (PD1074) animals.
- WBPaper00042067:Cu2+_upregulated_kgb-1_top66
N.A.
Genes whose induction by Cu2+ in kgb-1 mutants was <50% of the induction seen in wild-type animals. Cu2+-mediated gene induction were compared in wild-type versus kgb-1 mutant animals.
- WBPaper00044760:germline_specific
Authors extracted all genes with more than 25 mapped reads and computed fold changes for all gene loci between wild type and mutants. The group of genes with 4-fold up-regulation in wild type was considered to be specifically expressed in the germline, while genes with 4-fold down-regulation in wild type where assumed to be specific to somatic cell lineages.
Genes specifically expressed in germline when comparing RNAseq data of N2 to glp-4(bn2ts).
- WBPaper00044760:somatic_specific
Authors extracted all genes with more than 25 mapped reads and computed fold changes for all gene loci between wild type and mutants. The group of genes with 4-fold up-regulation in wild type was considered to be specifically expressed in the germline, while genes with 4-fold down-regulation in wild type where assumed to be specific to somatic cell lineages.
Genes specifically expressed in somatic tissue when comparing RNAseq data of N2 to glp-4(bn2ts).
- WBPaper00028474:dys-1_downregulated
With selection criteria of fold change more than 50 %, p-value lower than 0.01, and wild-type gene expression mean bigger than 100.
Genes with decreased expression in the two dys-1 mutant alleles cx35 and cx18 as compared to the wild-type expression level.