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Coexpression clique No. 203, sre-33-ZK1025.1_8337, on the genome-wide coexpression clique map for the nematode GPL200 platform. |
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. |
WBPaper00061527:sre-33-ZK1025.1_8337
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Heat shock: 35C for 1 hour. |
Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite N2 animals were exposed to 35C for 1 hour. |
The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. |
WBPaper00065749:Heat-Shock_upregulated_N2
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Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
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Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
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Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. |
Sleuth |
WBPaper00051558:aging_regulated
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Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. |
DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. |
WBPaper00048971:daf-16(mgDf50)_downregulated_L1
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Transcripts that showed significantly increased expression in oocyte germline cells comparing to in mitosis germline cells. |
Log2 Fold change > 2 or <-1, p-value < 0.05. |
WBPaper00053599:oocyte_vs_mitosis_upregulated
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Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2. |
Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. |
WBPaper00053810:daf-2(e1370)_upregulated
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Transcripts that showed significantly increased expression in nuo-6(qm200) comparing to in N2. |
Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. |
WBPaper00053810:nuo-6(qm200)_upregulated
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Transcripts that showed significantly decreased expression in rbr-2(tm3141) comparing to in N2 animals. |
Mapped reads were analyzed for transcript assembly and differential expression using Cufflinks 2.1.1 with a filter of twofold difference and FDR correction (P < 0.05). |
WBPaper00050080:rbr-2(tm3141)_downregulated
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Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066594:ilc-17.1(syb5296)_upregulated
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Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00067044:hda-1(RNAi)_upregulated
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Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. |
All three experiments have CPM >= 1. |
WBPaper00067147:germline_expressed
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Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis. |
To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. |
WBPaper00045521:Gender_Neutral
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Genes that showed decreased expression in wdr-5(ok1417) comparing with in N2. |
Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated. |
WBPaper00045861:wdr-5(ok1417)_downregulated
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Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-3-adult_vs_L4_upregulated_glp-1(e2141)
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Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2. |
DESeq2, fold change > 2, p-value < 0.01. |
WBPaper00061203:spr-1(ok2144)_upregulated
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Transcripts that showed significantly lower expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). |
DESeq2, fold change >= 2, FDR <= 0.01. |
WBPaper00056826:hmc_biased
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Genes identified as down-regulated at a 5% false discovery rate through RNAseq experiments with three tatn-1(qd182) and three N2 RNA samples. |
ANOVA with FDR <= 0.05. |
WBPaper00044656:tatn-1(qd182)_downregulated
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Genes down regulated in the absence of TDP-1, when the threshold was set at a fold change (FC) of 1.2. |
The management and statistical analysis of the microarray data were performed using the Partek Genomic Suite (Partek, Missouri) and Spotfire DecisionSite software (TIBCO, California). |
WBPaper00040603:tdp-1(lf)_down_vs_N2_FC_1.2
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Transcripts that showed significantly decreased expression in ins-11(tm1053) young adult animals comparing to in N2. |
For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18. 75th percentile were defined as down-regulated. |
WBPaper00053664:ins-11(tm1053)_downregulated
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Transcripts that showed significantly increased expression in daf-1(m40) comparing to in N2 at 1-day post L4 adult hermaphrodite animals. |
CuffDiff fold change >= 2, q < 0.05. |
WBPaper00059421:daf-1(m40)_upregulated
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Genes that exhibit a differential enrichment (p-value < 0.05 and a fold enrichment (log2fold)> 0.5) between the ADR-2 IPs from N2 and adr-2(ok735)worms. |
DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. |
WBPaper00055226:ADR-2_target_N2
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Transcripts depleted at neuron synapses (enriched at the somatic fragments) by comparing presynaptic and somatic cell fragments labeled with different protein markers and sorted by FACS. |
DESeq2, FDR < 0.05 |
WBPaper00059027:neuron-synapses_depleted
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Transcripts that showed significantly increased expression in the germline of iff-1(RNAi) animals comparing to the germine of N2 animals applied with control vector at 15C. |
Statistical comparisons were made by two-tailed t-test, n=3 (each replicate contains 150 extruded germ lines from N2 wild-type worms), P < 0.01 was considered significant. |
WBPaper00057288:iff-1(RNAi)_upregulated_transcript
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Transcripts significantly enriched in AVK neurons comparing to all cell types at L1 larva stage. |
edgeR, FDR < 0.001, fold change > 2. |
WBPaper00055565:AVK_enriched
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Transcripts that showed significantly increased expression in elli-1(sam-3) comparing to in N2 animals, accordingto tiling array analysis. |
Fold change > 1.2, q-value < 0.05. |
WBPaper00050743:elli-1(sam-3)_downregulated
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Transcripts of noncoding genes that showed significantly increased expression in muscle. |
DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. |
WBPaper00062325:muscle_enriched_noncoding-RNA
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Transcripts that showed significantly decreased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. |
DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. |
WBPaper00050859:downregulated_P-granule(-)GFP(+)_vs_control_day2-adult
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Transcripts that showed increased expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, and their mRNAs co-purify with SMG-2. |
edgeR |
WBPaper00053308:SMG-2_associated_NMD(-)_upregulated_ClassI
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