- WBPaper00028802:intestine_unique
To select a set of genes that are candidates to be expressed strongly and exclusively in the intestine, authors consider only genes for which the I/S tag ratio >= 3 and for which the tag number in the intestine library is >= 50. One hundred genes meet these two criteria. Twenty of these 100 genes encode ribosomal proteins or are involved in ribosome assembly, suggesting that the intestine persists as the major site of ribosome synthesis in the adult worm. However, because most ribosomal protein genes are unique in the genome and therefore must be widely expressed at other developmental stages, these genes were removed from the list to leave the set of 80 highly-expressed intestine-specific or intestine-enriched (non-ribosomal) genes.
Genes with unique expression in intestine, according to SAGE analysis on dissected intestine.
- WBPaper00061527:C36C5.12-F57G8.7
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. 134, C36C5.12-F57G8.7, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00062056:dpl-1(n2994)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in dpl-1(n2994) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-15B(we23)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in lin-15B(we23) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:met-2(n4256)_upregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly increased expression in met-2(n4256) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:efl-1(se1)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in efl-1(se1) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-15B(n744)_upregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly increased expression in lin-15B(n744) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-35(n745)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in lin-35(n745) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-36(we31)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in lin-36(we31) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-35(n745)_upregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly increased expression in lin-35(n745) comparing to in N2 animals at starved L1 larva stage.