The following steps lead to an Euler diagram:
VennMaster can import three different file formats.
This is a very simple tab delimited file format with an element/group pair in each line which can easily be generated by e.g. Microsoft Excel or OpenOffice.
Toy example:
cat mammal
dog mammal
rose plant
rose spiny
dog animal
lobster animal
lobster spiny
:
:
This example can be downloaded: example1.list.
VennMaster can import the pair of GoMiner summary export and gene-category export files. A brief summary of using GoMiner to generate these files is given in the Appendix below. An example file pair can be downloaded: go1.se go1.gce.
VennMaster can import the single .gce-file which can be exported by the new high-throughput GoMiner.
VennMaster can perform a simplistic statistical analysis given appropriate input files. It may analyse whether a given intersection contains more than the expected number of elements. E.g. consider a list of differentially expressed genes from 3 different experiments. Given e.g. the fold change for each gene in each experiment, VennMaster can display the overlap of genes with at least 10 fold differential expression, and how this overlaps cadinality compares to its expected cardinality.
The input format for this type of data contains of a tab seperated file for each experiment. The File should contain an identifyer column and an arbitrary number of numerical values. The columns all should have a heading row. Numerical field should be named equaly between files of different experiments. One file might look like this:
GENE | absolute_expr | diff_expr | p-value |
gene1 | 15 | 1.4 | 0.212 |
gene2 | 80 | 0.2 | 0.452 |
gene3 | 120 | 10 | 0.785 |
gene4 | 30 | 1.1 | 0.234 |
gene5 | 801 | 4 | 0.01452 |
A zipped example can be downloaded: column.zip
Choose the menu point Open List in the File menu and navigate to a file in the format described in section 1a.
The export file format of the high-throughput GoMiner is now a single .gce file with a new column containing the false discovery rate (FDR).
The number of categories can be reduced with the interactive filtering panel.
The five parameters have to be adjusted until the number of filtered categories (field #filtered categories) is satisfying. The number of filtered categories and elements are immediately adjusted when changing the filter values.
Click on the Update button to start the simulation with the current filter settings. The Reset button sets the filter settings back to the currently shown diagram. Normally the filter dialog should react immediately when changing the filter parameters. If not press on the Filterbutton.
VennMaster allows the interactive exploration of the sets. When moving the mouse slowly over the polygon arrangement, the region under the mouse will be highlighted and the corresponding sets are shown in a small tool tip window. When a region is selected with the left mouse button the details of the selection are listed in the "Categories" tab of the information pane on the bottom. Right click on categories offers a menu for setting category labels and colors.
The upper panel shows the categories (for GoMiner files additional information is shown such as the TermID, nChanged, nTotal, pValue, and FDR). A double-click on a GO TermID opens a web browser with a direct link to www.geneontology.org. The lower pane shows a global information of the currently selected (intersection) set such as the number of involved groups and the number of elements in the intersection. Then all elements in the (intersection) set are listed in the lines below. With a double-click on a gene name a web browser is opened with a link to www.genecards.org. If a single polygon is selected it can be moved by drag and drop. When pressing the control button while selecting polygons, multiple regions can be selected and their corresponding elements are shown in the "Selection" region.
Set intersections for which no corresponding geometric intersection exists are listed in the "Inconsistencies" field of the information panel. Each entry consists of a list of categories { C1, C2 ..., Cn } : u with an integer u > 0 describing the number of elements in the shown intersection set.
VennMaster enables to copy and paste the contents of the category table and the gene list with the following key commands:
Wissenschaftlicher Mitarbeiter (m/w/d)
"Recent Trends and Future Challenges in Learning from Data" has been published with Springer.
Our paper "Permutation-invariant linear classifiers" has been published in Machine Learning.
Our paper "Prediction of resistance to bevacizumab plus FOLFOX in metastatic colorectal cancer-Results of the prospective multicenter PERMAD trial" has been published in PLoS One.
Our paper "Segmentation-based cardiomegaly detection based on semi-supervised estimation of cardiothoracic ratio" has been published in Scientific Reports.
"Prospective study validating a multidimensional treatment decision score predicting the 24-month outcome in untreated patients with clinically isolated syndrome and early relapsing–remitting multiple sclerosis, the ProVal-MS study" has been published in Neurological Research and Practice.
Our paper "GatekeepR: an R shiny application for the identification of nodes with high dynamic impact in boolean networks" has been published online first in Bioinformatics.
Our paper "The Necessity of Interoperability to Uncover the Full Potential of Digital Health Devices" has been published in JMIR Medical Informatics.
"Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients" has been published in npj Precision Oncology.
Our paper "AMBAR-interactive alteration annotations for molecular tumor boards" has been published in Computer Methods and Programs in Biomedicine.
"A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems" has been published in STAR Protocols.
Our paper "A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective" has been published in npj systems biology and applications.
"Supporting SURgery with GEriatric Co-Management and AI (SURGE-Ahead): A study protocol for the development of a digital geriatrician" has been published in PLoS One.
"Self-Assessment of Having COVID-19 With the Corona Check Mhealth App" has been published in IEEE Journal of Biomedical and Health Informatics.
Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.