RNASeq asymmetry signal data

These are regions marked up on the genome to allow curators to identify the likely start and end of a gene in combination with other features such a ATG and polyA features. These regions occur where there is more than 5 times the number of reads from the reverse sense of the RNA than the forward sense. These asymmetric read regions are characteristic of the start or end of a transcript. The value stored in the corresponding feature is the sum of the number of reads observed in this region from all aligned RNASeq libraries. This data is available in the gff3 with this source/method combination [RNASeq_(F/R)_asymmetry transcript_region].

PHA-4 organogenesis

The pha-4 locus encodes a forkhead box A (FoxA/HNF3) transcription factor homolog that specifies organ identity for Caenorhabditis elegans pharyngeal cells. We used microarrays to identify pharyngeal genes and analyzed those genes to determine which were direct PHA-4 targets. Our data suggest that PHA-4 directly activates most or all pharyngeal genes. Furthermore, the relative affinity of PHA-4 for different TRTTKRY (R = A/G, K = T/G, Y = T/C) elements modulates the onset of gene expression, providing a mechanism to activate pharyngeal genes at different developmental stages. We suggest that direct transcriptional regulation of entire gene networks may be a common feature of organ identity genes. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design

PQM-1 controls hypoxic survival via regulation of lipid metabolism.

Worms were exposed to 5 mM CoCl2 at the early day 1 of adulthood stage for 6 hr and 20 hr. Untreated worms were used as controls. Worms were collected, RNA isolated and hybridized on 4x44K C. elegans arrays (Agilent) at 60C overnight, as previously described 1). Three biological replicates were used. Significant differentially-expressed gene sets were identified using one or two-class SAM 2). 1) Shaw, W. M., Luo, S., Landis, J., Ashraf, J. & Murphy, C. T. The C. elegans TGF-beta Dauer pathway regulates longevity via insulin signaling. Curr Biol 17, 1635-1645, doi:10.1016/j.cub.2007.08.058 (2007). 2) Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98, 5116-5121, doi:10.1073/pnas.091062498 (2001).