Release notes for Expander - version 1.2.1:
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Improvements from version 1.2:

File updates:

1) Uptodate fingerprint (of TF binding sites) files for human and mouse.

2) Uptodate gene annotation files for human, yest and mouse.


New features:

1) Biclustering - a new and improved Samba version has been incorporated.

2) Clustering - a new and improved Click version has been incorporated.enable more control of color rendering for the user.

3) Enabled saving a textual report of the results of promoter analysis (path is determined via promoter analysis settings).

4) Promoter Analysis can now be performed on biclusters as well as clusters.

5) An option has been added for existing users to access download page via help menu.

6) An option to export functional analysis and promoter analysis results to a text file via the display frame File menu has been added. 

7) An option to export images to jpg format has been added.


Bugs fixed:



1) Resolved problem of the functional promoter analysis processes getting stuck.

2) Problem with using spaces in path names has been solved.

3) The bug in click and biclustering which caused crashing problems when input file name did not end with .orig is fixed.

4) Cases in which std of a gene pattern is 0 have been handled by putting epsilon (0.0001) in the denominator of correlation calc instead of 0.

5) Bug of similarity tool menu item remaining disabled when loading a data set small enough after working on a dataset that is too big (moved handling the data set size issue into the tool initiation/operation using a message dialog) is resolved.

6) Histogram columns dislogs:
    - The bug  of inaccurate % has been resolved.
    - Table now contain three separate columns: Gene Id, Gene Symbol, Probe Ids

7) Small problem in input dialog combo-boxes of moving the last selected file to the top of the combo-list has been fixed.


Other changes:

1) Similarity calculation has been changed to correlation coefficient in all cases.

2) Default thresh p-value has been set to 0.0005.