SUMO development history

  Latest version: V1.62i from 22.07.2022

22.07.2022 Multi-class Kolmogorov-Smirnov test.
Non-parametric tests | Multi-class Kolmogorov-Smirnov

29.06.2022 Venn diagrams: 7 / 8 group Venn graphs.
Alternative Heatmap / Circlegraph result views.

22.11.2021 Co-expression / Relevance analysis with one /two matrices.
Main menu | Coexpression | Relevance neetworks

19.06.2021 CoLoM: Reactome pathways integrated.
CoLoM-DB builder added: Transorm Reatome-pathway file, NCBI Gene infom Specie => CoLoM-DB

22.04.2021 Mantel test: test similarity of (positive, distance) matrices.
Main menu | Utilities | Statistic tests | MAntel test

16.03.2021 List-Venn: Venn analysis for nearly unlimited number of groups.

04.02.2021 Agreement chart: Visualisation of crosstables.
Main menu | Utilities | Agreement chart

19.10.2020 Diversity indices: Analyze Condition wise (count) diversity in (library screening) matrices.
Main menu | Utilities | Statistic tests | Count indices

23.01.2020 Wrapper for UMAP, a dimensional reduction tool like tSNE / PCR
Main menu | Analyze | PCA/tSNE/Umap | umap

22.11.2019 Enrichement p-values for Venn diagrams.

08.11.2018 tSNE wrapper added.

16.03.2017 Kolmogorov-Smirnov test added.

Non-paramtric tests | 2-class Kolmogorov-Smirnov
A tool to explore the method: Utilities | Statistics test | Kolmorov-Smirnov

08.04.2016 Resampling tests added.
Bootstrap/Jackknife your groups and run t-/ANOVA/Man-Whitney-/Kruskal-Wallace tests.

22.04.2016 Methylaton tools: Generic changepoint detectors / Segmentation added.

25.03.2016 NMF added.

17.02.2016 Methylation tools:
- Window shift/ averager.
- Feature averages (i.g. average, eg. 200-bp Upstream sites,...

15.09.2015 Additional classification method Random Forest added (wrapping external tool).

05.07.2015 File table viewer added ( Utilities | Table/file viewer )

10.06.2015 Heatmap density plot viewer - transformation to cumulative density added

29.05.2015 Weighted Cox Regression for non-proportional hazards added.
(Survival | Cox regression)

29.05.2015 Basic editing function for data matrix in Heatmap viewer:
Insert/Delete/Copy/Paste rows or columns, Copy/Paste external data annotations.
Custom heatmap color schemes may be freely defined.
Manual scaling options

15.05.2015 Heatmap viewer - Customizable high resolution histogram / density plot viewer for genes /hybs added

07.03.2015 Methylation utilties adedd:
R-wrapper for extraction of quants from IDat files, BMIQ normalisation
Beta, M, CN, M=>Beta, Beta=>M computation
M/U missing value imputation

22.09.2015 More helper functions for generation / optimization of covariates for cox regression.
Forest plot for graphical display of Cox regresson results.

21.01.2014 Several helper functions for generation / optiomization of covariates for cox regression.

18.10.2013 Wrapper for R's cox regression implemented (Survival | Cox regressio)

15.05.2013 Outlier removal: Grubbs test (at p<0.05) may be used to exclude outliers in f/T-tests, Anova and replica averaging while importing RT-PCR data.

14.05.2013 Exclusion of non-numeric values in statistics calculation:
SUMO now excludes non numeric values from stattistic calculations (class tests).
Thus, non-regular data files (no-microarray data) may be more comfortably analyzed.

14.05.2013 Import ABI RT-PCR data:
Handling of Multiplex controls added.

04.05.2013 Generic outlier-tester and filter (Grubbs-test) added
(Utilities | grubbs outlier removal)

24.04.2013 Results from "Survival filter 4" analysis is included in an SUMO-analysis file, too.

22.04.2013 Bug fix: Fixed several prolems in heatmap display
Storing of multicolumn annotations colum width, display update after sorting,
Custom colors for group bars, ...

11.04.2013 Bug fix: workaround for display problems with Windows Themes/Styles

03.04.2013 Additional classification method added: NBC Naive Bayes Classifier

28.03.2013 Additional classification method added: SVM Support Vector machines

14.03.2013 Survival filter 4:
missing LRT added, more grouping options (perenctile ...), better integration, some bug-fixes

08.03.2013 Additional classification method added: ANN Artificial Neural netwwork

06.03.2013 Additional classification method added: Closest centroid

04.03.2013 Additional classification method added: KNN k-nearest neighbours

27.02.2013 Classification added: LDA linear discriminant analysis

12.01.2013 Several bug-fixes:
Network builder; Snapshots in Heatmap, Scatterplot, Histogram window

05.01.2013 Migration to new compiler: Delphi XE3

12.06.2012 Heatmap-viewer: New correlation distances: Pearson-JackKnife,Spearman, Kendall's-Tau

15.05.2012 Heatmap-viewer: New Minkowski distances: Manhattan,Chebyshev

20.04.2012 Adjust data - Data transformation: Exp2 (rt-PCR-cycles to ratio), Ratio to "intensity" added.

14.02.2012 Some bug fixes:
COLOM can now work with insufficient Reference/Selection lists, where selection may contain keys nof present in reference.
COLOM - KEGG pathway viewer can now handle very large pathway map images.
rt-PCR data import : Empty Sample/Probe entries are not used for computation of Mean Rn/CT.

15.03.2012 COLOM - GO-terms: can be evaluated seperately fort the three main classes(Molecular function, Biological process,
Cellular component), avoiding memory overflow problems with the internal database.

01.12.2011 PTM - Grouping and group names are passed to Heatmap ... and subsequent views.
Problems with saving analysis fixed.

09.11.2011 COLOM : A new p-value column is added to the result tables. This column combines the enrichement-p-value with a mean of the genes p-value, weighing the enrichemnt of a biological theme with the significance of it's assigned genes.
To use this feature supply a gene list:
- one line per gene
- tab delimited: Gene, Regulation, p-value

12.11.2011 COLOM now supports also Metabolites (not only genes symbols) with KEGG pathways.

05.11.2011 During import of exported ABI-SDS ampification data files SUMO non numerical values (e.g. "not determined") for ct-values are automatically replaced by "40.000". Genes or conditions where there are not in all cases ct-values found are searched. Such missing values might due to incosistent sample or probe-set names accross multiple measured plates.

25.10.2011 Bug fix: Import of CR delimited text files enabled. Normally, lines in standard text files are delimited by CR-LF (Carriage return + Line Feed) characters (in e.g. Microsoft based operation systems ) or with Line Feed only (UNIX based OS).
Some strange systems may also create CR only delimited files. These may be used with SUMOnow too.

05.10.2011 During import of exported ABI-SDS ampification data files SUMO computes means and standard deviation for RN and CT values from all samples of a particular gene. Those values are added as gene annotations to the data matrix.

05.09.2011 Import of multiple exported ABI-SDS ampification data files enabled.
!!! NB: Values from replicated gene/sample names in the multiple source files will automatically be averaged !!!
In case you want to use genes for inter-plate quality tracking you should name such genes like "ACT-Plate1" ...

31.08.2011 Loading of Comma-Separated-Value (CSV) data tables added
Main menu | Open data | Set file type to "Comma separated text (*.csv)"

24.08.2011 Colom: Download and set up of data bases for GO, KEGG, Chromomal localisation
Colom | Preferences Tab | Donwmloa and install ... Button

22.08.2011 Search genes in SUMO main program
Main menu | Analyse | Find genes

17.08.2011 Demo data sets added
Synthetic dataset, Real gene expression, Random data
Main menu | Utilities | Demo data | ...

13.08.2011 Result browser for splicing analyses added
Main menu | Utilities | Splicing viewer

05.08.2011 Splicing analyser for Exon microarray data added
Main menu | Utilities | Splicing index

05.08.2011 COLOM - KEGG: Automatic download and installation of KEGG pathways in COLOM added.
COLOM | Preferences tab | Download and install KEGG database

25.07.2011 Problem with KEGG pathway images fixed: COLOM now can load either GIF or PNG formatted pathway images.

22.05.2011 Replica averaging may be performed with different replica means:.
arithmetic-/ geometric-/ median / percentile mean (Main menu | Adjust data | Replica averaging | ...)

17.04.2011 Data (in form of a tab-delimited expression matrix) may be pasted from clipboard
(Main menu | File | Paste Matrix from clipboard>

10.03.2011> Venn diagrams added. For details go here

15.02.2011 Paired samples t-tests added.

02.02.2011 Direct call of Network Builder from heatmap viewer implemented

15.01.2011 KEGG pathway map viewer added to COLOM.

15.06.2010 Gene network builder implemented. For details go here.

15.05.2010 New normalisation in conditons: hybridisation centering, Control normalisation and centering (Main menu | Adjust Data Coditions | ... )

15.04.2010 Mosaic Scatter plots implemented ( View | Scatterplots | ... )

15.03.2010 Search for control genes according to Van de Sompele's method ( Main menu | Utilities | Control genes | Van de Sompele

15.02.2010 Import of ABIs RQ-Manager Amplification-Data Export files ( Main menu | Import | ABI rtPCR amplification data )

15.01.2010 Dot chart/plot data viewer added to Heatmap viewer ( Heat map Main menu | Vew | Dot chart )

15.01.2009 Import of EXCEL data sheets added

05.12.2008 Principal Component Analysis (PCA) added

21.11.2008 K-Means clustering added.

08.11.2008 Survivalfilter: Fixed some internal problems, visualisation "Population map" added, filtering now via Median survival, accelerated.
For details go here

25.10.2008 COLOM: fixed problem with chromosomal co-localization using Mus Musculus ideograms (slightly different format compared to Homo Sapiens).

15.10.2008 Gene lists -  auto generated from analyses, or manually created from scatter plots - and Boolean operations between gene lists implemented (AND, NAND, OR, NOR, XOR)

20.09.2008 COLOM: Term enrichment tests implemented. For single Biological themes, or scan over all themes.

10.09.2008 COLOM: Select to view only sub-branches or direct children in data table (context menu Tree | => table)

12.06.2008 COLOM's data filtering reorganised. Tree and table are filtered independent.
All columns may be filtered (like MS-Excel's Auto-filter). Context menu column header | Filter | ...

03.06.2008 Search for genes supports aliases.
Term search returns matches and their tree-paths

28.05.2008 CoLOcalization Mapper supports additional Gene Alias columns in gene index

16.05.2008 Data Back-up/Restore added (Main menu | Adjust data | Backup)

10.05.2008 Principal support for KEGG pathways in Co-localisation mapper added.

28.05.2008 2-class prediction (with t-test / U-Mann-Whitney test) implemented

20.04.2008 Merging of new hybridisations with already loaded data matrix based on unique gene-id implemented.

10.04.2008 Several new data adjustment function (z-transformation, mean/median intensity filter, group pool-normalisation, geometric means for all mean based operations, Replicate gene averaging, Change sign ...)

29.03.2008 Graphical Chromosomal-band co-localization viewer implemented

24.03.2008 Selection in  Scatter plots may be converted into SUMO gene lists and can be logically combined.

19.03.2008 Scatter plots improved: additional regulation indicators, rhombic selection, view selection in all open viewers, ...

07.03.2008 Co-localisation mapper with Chromosomal bands implemented

25.02.2008 Co-localisation mapper with GO-terms implemented

18.02.2008 Save Analysis now saves Mann-Whitney and Kruskal-Wallis tests too.

12.02.2008 Program version check and auto-update (only registered version) implemented.

02.02.2008 Prediction cross-validation with 2-class tests (t-test / U-Mann-Whitney) implemented.

20.12.2007 Adjust data: new function Shift all positive: shift whole data matrix so, that no negative values are remaining.

19.12.2007 Column patterns for data and gene annotations can be defined for loading of interlaced or irregular expression data files.

18.12.2007 Add additional condition; annotations via common "key" (Main menu | Adjust data | Annotation | Add condition annotation )

14.12.2007 Filtering of genes where mean / median from selected conditions is below user defined threshold ( Main menu | Adjust data | Filter| Genes | Mena / Median intensities)

11.12.2007 2-factor ANOVA implemented. For details go here<.

20.11.2007 Kruskal-Wallis (non-parametric multi-class) test implemented. For details go here.

08.11.2007 Results of statistical tests are passed as additional "gene-annotations" to heat map viewer. There, they may be used for filtering.

19.10.2007 U-/Mann-Whitney test implemented (non parametric 2-class test). For details go here.

23.09.2007 Imputation of missing values (e.g. "nan"). For details go here.

22.09.2007 Filtering for genes containing too many NAN values added (Main menu | Adjust data | Filter | Genes | NAN values).
For details go here.

21.09.2007 SUMO recognizes and handles non-numerical data cells (e.g. "nan" or "13.May").
For data processing they are automatically converted => 0.00

20.09.2007 Bug fix: Wrong number of rows (=genes) when interrupting loading of data matrix.

19.07.2007 Mai menu | Adjust data | Genes | Hybridisation | pool normalisation implemented. For details go here.

28.06.2007 Correlation maps implemented (Main menu | View | Correlation maps )

14.06.2007 Histogram viewer implemented (Main menu | View |Histogram )

10.05.2007 Scatter plot viewer implemented ( Main menu | View | Scatterplots). For details go here.

02.05.2007 Quantile normalisation implemented (Main menu | Adjust data | Condition | Quantile normalisation). For details go here.

26.04.2007 Drag and drop data files for expression matrices and SUMO analysis files implemented.
Last header rows/columns when loading expression matrices are automatically recalled.

15.04.2007 Parallel processing implemented.
Select Main menu | Preferences | Multithreaded to select number of multiprocessing / -threading.
Number of processes / threads should not exceed number of CPUs / Cores.
Presently only normal T-tests, ANOVA, PTM are supported.

10.04.2007 Bug fix: Centroid profiles now show real centroids

06.04.2007 Scripting: Scripting may be used to automate multiple analysis.
Supported are t-tests, ANOVA, PTM, multi-class SAM
For details go here

05.04.2007 Kaplan Meier survival curves implemented.
For details go here.

04.04.2007 Statistics auto-run generator implemented.
- all single class t-test/SAM may (both unique single groups / all unique combinations of groups)
 - 2-class t-tests/SAM with pair-wise single groups
other will come later.
For details go here.

01.03.2007 Documentation functions implemented.
Save working parameters and snapshots of graphs into Word / PDF documents.
For details go here.

15.02.2007 Save and later on load complete analyses.
Works for t-test, ANOVA and PTM.
SAMs will come later.

09.11.2006 Box plot of data distribution
Select Main menu | View | Box plot to view box plots from all conditions, illustrating signal distribution within the conditions (hybridizations).

08.11.2006 Data adjustment functions added
This functions allow to normalise centre and transform all data in the loaded expression matrix
for details go here

28.08.2006 Group selection dialog:
View of detailed condition annotation for selected conditions (Context menu Condition list | View all details)
Manage selections (Context menu Button Find | Copy / Paste / Save / Load selection)

25.08.2006 Group selection Dialog:
Find condition: Find NEW, AND, AND NOT, OR, OR NOT added
Find special modifiers:
  • "|empty|" = search conditions without any annotation
  • "|full|" = search only perfect matches
    (e.g. find "|full| RT" will not highlight e.g. "IMRT")
Copy (internal buffer) / Paste selection, Save / Load selection
Bug fix: Disappearing numbers in Group List
Bug fix: Find history
Detailed view of a single condition's annotations
Progress bar for all data views, Display may be cancelled with Cancel button.
More info in Parameter node of Analysis tree
Bug Fix: Memory leak with data tables / huge data sets

16.08.2006 Display of selected / all conditions in data views

10.08.2006 Multi-class T-test implemented

15.05.2006 PTM / Regression response implemented

01.05.2006 Profile editor for regression SAM / PTM implemented
Web based documentation interfaced

27.04.2006 Regression SAM implemented

22.04.2006 Multi-class SAM implemented

17.04.2006 Two class SAM implemented

12.04.2006 Single class SAM implemented.

05.04.2006 Basic WEB-based documentation

01.04.2006 First versionreleased.