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Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
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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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Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. |
N.A. |
WBPaper00026929:sir-2.1_overexpression_regulated
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Germline-intrinsic transcripts. |
Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization. |
[cgc6390]:intrinsic
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_9
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Germline-enriched and sex-biased expression profile cluster E. |
hierarchical clustering |
[cgc6390]:Cluster_E
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Transcripts that showed significantly decreased expression in adr-1(tm668) comparing to in N2. |
DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. |
WBPaper00055226:adr-1(tm668)_downregulated
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Transcripts that showed significantly decreased expression in animals overexpression human amylin (driven by hsp-16.2). |
Differential gene expression analysiswas conducted using the DESeq R package (available from Bio-conductor). The DESeq analysis resulted in the determination of potential differentially expressed genes when compared between the DMH46 and N2 (wildtype) samples. The read counts for each sample were normalized for sequencing depth and distortion caused by highly differentially expressed genes.Then the negative bi nomial (NB) model was used to test the significance of differential expression between two genotypes.The differentially expressed genes were deemed significant if the FDR (False Discovery Rate) was less than 0.05, and the gene expression was above the 10th percentile, and showed greater than 2-fold change difference(overexpressed or underexpressed) between the conditions. |
WBPaper00056731:human-amylin_downregulated
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Genes downregulated in dpl-1(n3316) and efl-1(n3639) mutants. |
For each set of mutant data, the repeats were averaged, and a Z test [Z=(observedexpected)\/SE] was performed in Excel. A moderate correction for multiple testing (~17,600 genes) was performed by multiplying the calculated P-value by 10,000. After this correction, all genes with up- or downregulation greater than twofold, P<0.05 in any given mutant were selected. The hypergeometric probability test was used to calculate the significance of overlap of gene groups. Authors determined whether transcripts of Group I-IV genes are bound by GLD-1, based on a minimum criteria of >1.5 enrichment in GLD-1 immunoprecipitated samples compared to control immunoprecipitations (P < 0.01). |
WBPaper00027758:Group_I
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