CBS ENCODE Predictions

CBS Prediction Data Predictions for All Sequences - Collected CBS Predictions This table has links to all CBS annotations. Note that only the sequences with more than one isoform have annotation pages. CBS Predictions This is the summary of what has been done on the set (ENCODE CDS data set of 1097 transcripts from 434 loci) using tools from CBS. Of these, variable transcripts occur in 258 loci, accounting for 921 of the proteins, according to our analysis. Many of CBS's protein annotation servers have been run on all the peptides including SignalP, TargetP, TMHMM, NetNGlyc, NetOGlyc, ProP, NetAcet, NetNES, NetPhos. A short summary of the analysis can be found at the CBS along with a file with all annotation results and figures for easy viewing of the annotations for each transcript, which shows variation in CBS predictions within transcripts from the same locus. Looking specifically at signal peptides and propeptides, a total of 112 of all the 434 genes have predicted signal peptides. 31 of the 258 variably transcribed genes have transcripts both with, and without a signal peptide. This appears to be an example of transcriptional variation with fundamental difference in the gene products. The same is true for the 47 loci that display variation in propeptide prediction. Transcripts that have variation in both signal peptides and propeptides are found on 6 occasions.<7p> It should be noted though that these are raw predictions on the protein sequence and are served without any validation of the CDS. We plan to do more work on the trends in the PTM changes. This work was carried out by Pall Olason of Soren Brunak's group at the CBS. All Data from the CBS Annotations for All Sequences. - Annotations from the Data Below All Predictions for All Sequences. These may take a while to load. - Acetylation Prediction - Membrane Prediction - NC Secretion Prediction - NES Signal Prediction - N-glycosylation Peptide Prediction - O-glycosylation Prediction - Phosphorylation Prediction Part 1 - Phosphorylation Prediction Part 2 - Phosphorylation Prediction Part 3 - Phosphorylation Prediction Part 4 - Pro-peptide Prediction - Signal Peptide Prediction - Target P Prediction