- WBPaper00055311:ppa-daf-19_upregulated
Differentially expressed genes were identified by the program cuffdiff (version 2.2.1) from the comparison of both Ppa-daf-19 alleles with two wildtype control samples. The sets of up- and down-regulated genes (FDR corrected p-value <0.05).
Transcripts that showed significantly increased expression in ppa-daf-19(tu1035) and ppa-daf-19(tu1124) comparing to RS2333 wild type control samples.
- WBPaper00055311:ppa-daf-19_downregulated
Differentially expressed genes were identified by the program cuffdiff (version 2.2.1) from the comparison of both Ppa-daf-19 alleles with two wildtype control samples. The sets of up- and down-regulated genes (FDR corrected p-value <0.05).
Transcripts that showed significantly decreased expression in ppa-daf-19(tu1035) and ppa-daf-19(tu1124) comparing to RS2333 wild type control samples.
- WBPaper00065623:19
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 19 expressed in: sh3_sh4 (gonadal sheath proximal).
- WBPaper00049635:dop-1(vs100)_upregulated
EdgeR with a Benjamini and Hochberg correction. Transcriptions that showed more than 1.5-fold of change in expression, as well as FDR-adjusted q-value < 0.01 were considered differentially expressed.
Transcripts that showed significantly increased expression in dop-1(vs100); [Pcol-19-UbG76V-GFP] comparing to in control animal odIs77[Pcol-19-UbG76V-GFP]
- WBPaper00049635:dop-1(vs100)_downregulated
EdgeR with a Benjamini and Hochberg correction. Transcriptions that showed more than 1.5-fold of change in expression, as well as FDR-adjusted q-value < 0.01 were considered differentially expressed.
Transcripts that showed significantly decreased expression in dop-1(vs100); [Pcol-19-UbG76V-GFP] comparing to in control animal odIs77[Pcol-19-UbG76V-GFP]
- WBPaper00033131:dapk-1_upregulated
N.A.
Genes upregulated in L4 larva of dapk-1(ju4) worms. The dapk-1 mutant transcriptional profile overlapped strikingly with that of animals infected with Drechmeria (19/303 genes in common with the top 419 Drechmeria-up-regulated.
- WBPaper00060764:swsn-9(ok1354)_upregulated
DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.)
Transcripts that showed significantly increased expression in RA629 swsn-9(ok1354);rdIs49[Cb-unc-119] comparing to in RA577 swsn-9(ok1354); rdIs52 [Pric-19::swsn-9::gfp; Cb-unc-119] (swsn-9 neuronal rescue) animals at young adult worms.
- WBPaper00060764:swsn-9(ok1354)_downregulated
DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.)
Transcripts that showed significantly decreased expression in RA629 swsn-9(ok1354);rdIs49[Cb-unc-119] comparing to in RA577 swsn-9(ok1354); rdIs52 [Pric-19::swsn-9::gfp; Cb-unc-119] (swsn-9 neuronal rescue) animals at young adult worms.
- WBPaper00061527:Y116A8C.19-F38C2.7
All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.
Coexpression clique No. 28, Y116A8C.19-F38C2.7, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00053550:daf-19(m86)_downregulated_3-fold-embryo
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).
Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 3-fold embryo stage.