If you see a problem (ie bugs, inconsistancies, etc ) or have a suggestion (ie a commonly used search query ) please let us know. Please be very specific where possible. Complex queries may be more easily done offline, again just send us the request.

Updates:

• "MC3 Mapper" is available here for sequence analysis. (2014)
  

• "Event Utility" is available here to convert bed files to an event list. (April-2013)
  

• "MC Mapper" is available from 'Further Analysis' or Stand alone. (July-2012)
  This is Melissa Cline's R-script motif mapper. It currently only uses edmjay and edhjay events. Updated (Sep-2012) to include distal intron sequences. The sequence extraction was redone and there are slight differences from the original sequences.

• "Word-Gap-Word" Counting is available from 'Further Analysis' or Stand alone. (Nov-2011)

• UTR Word Counting is available from 'Further Analysis' or Stand alone. (Nov-2011)

• GO analysis updated. It is based on GO Term finder. Originally implemented here.(Mar-2011)

• GREAT analysis is available and recomended over GOminer. (Jun-2010)

• Secondary cutoff can be chosen individually for each analysis. Primary cutoff is the q-value and will be used for all experiments. A secondary cutoff can be set for each experiment. If the secondary cutoff is set to zero, it is not used. For gene expression the secondary cutoff is fold change. For SAM event analyses (ie isoform_ratio) , the secondary cutoff is d-value. For sepscore type analyses , the secondary cutoff is the seperation score. (Nov-2009)

• Default behaviour only aligns strictly overlapping events (Nov-2009)

• Background 'depth' option for 'Tim', the post analysis word significance calculator (Oct-2009)

• GO track for mm9 (July-30-2009)

• mm9 viewer (Spring 2009)

• Local sequence logo maker (Sep-25-2008)

• Experiments can be documented by users, ask me how! (Aug-15-2008)

• Select 'Only view public data' to view published data as a guest(June-10-2008)

• Blue/yellow color scheme is available (June-5-2008)

• Uberevent transition in progress, please let me know of persistant inconsistancies (June-5-2008).

• mjay documentation is available (May-20-2008)

• mjay sepscore now displays analysis details such as intensity per path and gene intensity (April-1-2008)

• mjay_multi_sepscore_... and mjay_multi_isoform_ratio_... use N-path event definitions.

• mjay_multi_sepscore_expr_... uses expression as the comparison value.

• alt notes (ie 'altCassette') have been cleaned so that if an event was in both a complex region and an altCassette, it is labelled only 'altCassette'.

• Tablesummary and Vennviewer are deprecated, equivalent functionality is on the results page under 'Classification Summary'. For equivalent Tablesummary, make sure to select tracks of interest (Feb-28-2008)

• Affy MOE430 array data available, (access restriced depending on data) (Feb-21-2008)

• Default behaviour changed (Feb-15-2008)

  "Classify" and "Grouping" are turned off by default !!

  "Classify" refers to classifying events by color groups (ie red,red,green aka up,up,down).

  "Grouping refers to grouping related events together.

• mm5 splice site strength, based on Exalin score (Feb-5-2008)

• known motif counts (natively done in mm8) (Feb-4-2008)

• web 3.0 style usertrack input directly from OmniViewer (Jan-24-2008) (select "User Defined Track" on the left and watch the magic)

• submission to GO analysis directly from OmniViewer (Jan-18-2008)

• miRNA on mm5 (Nov-14-2007)

• miRNA TargetScan Binding Sites (Nov-12-2007)

• mjay trial data is available on mm8 (Oct-31-2007)

• N-filter removed, HTML is displayed in segments of 100 to help speed up rendering of large tables. (Oct-31-2007)

• Short circuit event and gene search field added (Sep-22-2007)

• Roland C2C12 data updated with QC'ed arrays (Sep-12-2007)

• Transcription Factor Binding Site track added (Aug-24-2007, mm5 only)

• Iverson E-G tracks added Aug-21-2007 (Access restricted)

• Isoform_ratio intensity option added Aug-9-2007

• GO search term added Aug-9-2007

• 3-frame stop track added Aug-8-2007

• MH MEF tracks added Aug-7-2007 (Access restricted)

• Validation data track available June-2007 (Access restricted)

Links:

• Ares Lab

• Local GOMiner

• UCSC Genome Browser

• Sequence extracter

• Historical Uber Links

Questions, Comments or Problems ?

email donohue at biology.ucsc.edu

Other Alt Splicing databases

• FAST-DB
• MAASE
• SpliceMiner