- PhylomeDB
PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes).
- Expression data of worms under different caloric restriction mimetic treatments
We used microarray analysis to further our understanding of the mode of action of the well know caloric restriction mimetic rapamycin and the compound Allantoin first studied in the context of aging in this study. His work helps build on our understanding of potential caloric restriction mimetics predicted from our bioinformatic aproach of quering the Connectivity Map, a database of drug-induced gene expression profiles, using the transcriptional profile of CR to identify drugs that induce a similar or opposite gene expression profile.
- Aging time course
Transcriptional Profile of Aging in C. elegans Whole-genome analysis of gene expression during chronological aging of the worm provides a rich database of age-specific changes in gene expression and represents one way to distinguish among these models. Using a rigorous statistical model with multiple replicates, we find that a relatively small number of genes (only 164) show statistically significant changes in transcript levels as aging occurs (<1% of the genome). Expression of heat shock proteins decreases, while expression of certain transposases increases in older worms, and these findings are consistent with a higher mortality risk due to a failure in homeostenosis and destabilization of the genome in older animals. Finally, a specific subset of genes is coordinately altered both during chronological aging and in the transition from the reproductive form to the dauer, demonstrating a mechanistic overlap in aging between these two processes. Groups of assays that are related as part of a time series. Age: Age of organism Keywords: time_series_design
- Rfam
The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).
- eggNOG
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).
- RACE_Vidal_elegans
The general scheme for our RACE experiments is shown in the figure. For our 5' RACE experiments we made use of the trans-spliced SL1 and SL2 leader sequences, instead of ligating a universal sequence to 5' of the transcripts. Approximately 70% of all C. elegans mRNAs have a trans-spliced leader sequence. The great majority of these correspond to a 22 base-long sequence known as "SL1," with "SL2" being the next most frequent, making up 15% of the worm's trans-spliced leaders. The use of SL1/SL2, as opposed to the ligation of an arbitrary sequence to the transcripts' 5' ends has the following advantages: i) no additional manipulation of RNA is needed, ii) the presence of SL1 on a mRNA ensures that the mRNA has an intact 5' end and is full length.nnTo generate the RACE fragments, we reverse transcribed total C. elegans RNA (isolated from mix-stage, asynchronously growing N2 worm population) using either dT16 (for 5' RACE) or used our tailed dT primer (for 3' RACE). Nested PCRs were performed to increase sensitivity and specificity. The generated PCR products were then cloned recombinationally and sequenced from the 5' end, generating "RACE Sequence Tags" (or "RSTs").nnThe RSTs included in this searchable database are vector and quality trimmed (SL and poly(A) sequences were not removed from RSTs). In quality trimming, the first sliding window of 20 nt long with an average quality score higher than 15 marks the start of good quality sequences. Likewise, the first sliding window of 20 nt with average quality score lower than 15 marks the end of good quality sequences.