1 von 15 MapMan Help 1 Short Introduction 1.1 View data included in the package 1.2 Display options 1.3 Print 1.4 Save 1.5 Search Functions 1.6 Statistics (Wilcoxon Rank Sum Test) 2 View your own Arabidopsis 22KAffymetrix data 2.1 Data format 2.2 Create an experiment folder 2.3 Add data files to your new folder 2.4 Visualise your data 3 Use MapMan to visualise any gene expression, metabolite or other data 3.1 Creation of a mapping file 3.2 Create your own pathway (Annotation of an image file) 3.3 Histogram frequency chart 4 Structure of MapMan 5 Available Pathways Overview 6 Contact information 1 Short introduction index MapMan is a user-driven tool that displays large datasets, e.g. from gene expression experiments onto diagrams of metabolic pathways or other processes. You can not only use the provided diagrams, but also generate your own ones and let the software display yours and others data onto your diagrams. There are three different types of files needed to use MapMan. They are located in three different folders inside the directory of example data. (i) data files: contain experimental results (.xls or .txtfile format) (ii) pathways: diagrams ( .bmp file format) which serve as context (iii) mapping files: connects gene/metabolite/protein identifiers to BINs (“functional categories”) which are displayed (. xls or .txt file format)
15
Embed
MapMan Help - GabiPDgabipd.org/projects/MapMan/help/MapMan_Help.pdf · 1.6 Statistics (Wilcoxon Rank Sum Test) 2 View your own Arabidopsis 22KAffymetrix data 2.1 Data format 2.2 Create
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
1 von 15
MapMan Help
1 Short Introduction
1.1 View data included in the package
1.2 Display options
1.3 Print
1.4 Save
1.5 Search Functions
1.6 Statistics (Wilcoxon Rank Sum Test)
2 View your own Arabidopsis 22KAffymetrix data
2.1 Data format
2.2 Create an experiment folder
2.3 Add data files to your new folder
2.4 Visualise your data
3 Use MapMan to visualise any gene expression, metabolite or other data
3.1 Creation of a mapping file
3.2 Create your own pathway (Annotation of an image file)
3.3 Histogram frequency chart
4 Structure of MapMan
5 Available Pathways Overview
6 Contact information
1 Short introduction index
MapMan is a user-driven tool that displays large datasets, e.g. from gene expression experiments onto
diagrams of metabolic pathways or other processes.
You can not only use the provided diagrams, but also generate your own ones and let the software display
yours and others data onto your diagrams.
There are three different types of files needed to use MapMan. They are located in three different folders
inside the directory of example data.
(i) data files: contain experimental results (.xls or .txtfile format)
(ii) pathways: diagrams (.bmp file format) which serve as context
(iii) mapping files: connects gene/metabolite/protein identifiers to BINs (“functional categories”) which are
displayed (.xls or .txt file format)
2 von 15
1.1 View data included in the package index
The MapMan download provides example.
After starting the MapMan software you will find data files in the Experiments folder, pathway image files
in the Pathways(overview of available predefined pathways)folder and mapping files in the Mappings
folder of the selection directory on the left.
You can view the included datasets in context of different metabolic pathways
(i)Double click an image file from the folder "Pathways",
e.g. "Metabolism_overview" or "Glycolysis".
Choose a mapping file from the pop-up box
and click "OK".
Choose "AFFY2005" in combination with "Metabolism_overview"
with all maps showing biological processes (This is most often
right).
Hint: Images need different mapping files (table 1).
Response_images need an Response_mapping file. (In fact, if you
don’t care about the statistics you can combine both files).
(ii) A simple click activates experiment files from the folder
"Experiment:DiurnalCycle (or other) one by one.
All data files from one experiment can now be
viewed in sequence. Each file is called up after
loaded the first time by mouse click in a fraction of
a second.
Each gene is symbolised by a box,
the gene expression level is colour-encoded
(red = down-, blue = upregulation).
A simple mouse-over action on an individual box will call up the gene annotation beneath your mouse,
while a click will copy the information to the text window below pathway.
Right clicking on an individual box brings up further options, such as opening a webbrowser (link out) with
additional information about the particular spot from the GABI website (http://gabi.rzpd.de) which will also
get you to further information ressources.
You can get unigene information, and information how good a spot reflects a given transcripts.
3 von 15
Number Filename Description/Keywords Visualization Data Standard/
Response
1 photosynthesis Light reaction, Calvin cycle, photorespiration P T S
2 cell functions overview cellular functions H T S
3 Cell Wall precursors NDP sugar pathways (used for the cell wall) P T S
4Cellular reponse
overviewstresses, redox, development, cell cycle and division P T S
5 Glycolysis glycolysis P T S
6 Large enzyme families Large enzyme families like oxidases, GDSL lipases, etc P T S
7 Lignin Monolignol pathway starting from Phenylalanine P T S
8 metabolism overview overview of metabolic reactions P T S
9mitochondrial
e-transportmitochondriol overview including transporters P T S
10 N-metabolism Nitrogen metabolism P T S
11 RNA-Protein SynthesisProtein Synthesis, targeting and degradation as well as
RNA processingP/H T S
12 Sucrose Starch Sucrose and Starch Degradation and Synthesis P T S
13Transcription
RegulationPotential Transcription factors and regulators of transcription P T S
14 Transport Overview different transporters P T S
15 Proteasome Ubiquitin dependent protein degradation pathway P T S
16 Regulation overviewTFs, Protein modification and degradation,
hormone regulation, receptor kinases, G proteins, MAPKs etc.P T S
17 TCA TCA Cycle including mitochondrial genes P T S
18 Glycolysis-TCA Combination of Glycolysis, TCA, and mitochondrial genes P T S
19 Secondary metabolism Secondary metabolism like flavenols, chalcones, lignins, etc P T S
20 Pentose phosphate Pentose phosphate pathway, Warburg way, Shunt P T S
21 Metabolites
most metabolites that can be measured, for a conversion
of your metabolite name to the canonical MM one see: