Material for the Genestigator hands on session (09-Nov 2012)
You will find here links and files that will be useful during the practical session and will allow you reproducing results presented in the slides.
[ Main_Page | Genevestigator_training ]
Contents
Today's main tools
Reminder: these tools need registration, access information will be provided during the session.
genevestigator: [https://www.genevestigator.com/gv/user/gvLogin.jsp]
Ingenuity: [https://apps.ingenuity.com/ingsso/login?]
Workspaces used during the presentation
You can download the following workspace files (in zip format) and expand them using your archiving application. After decompression, the file should have the extension .gv4 (tip: on mac, check that no additional hidden extension was added; on the BITS laptops, right-click on the file and choose '7zip' as expander)
REM: due to a content update just before the training, the saved plant .gv4 do not find the A.Th samples that were saved and load only gene lists. To fix this problem, you will need to reload 'all' A.thaliana data by using the sample NEW button after loading the plant .gv4 files.
example#1: 100 seed-specific markers in Arabidopsis thaliana (example1.gv4.zip)
example#2+3: 50 human liver-specific markers (example2.gv4.zip)
example#4: 50 Ath young flower markers (example4.gv4.zip)
example#5: 50 human liver neoplasm markers (example5.gv4.zip)
example#6: expression modules from a gene list (example6.gv4.zip)
example#7: genes correlated (+/-) with geneX (example7.gv4.zip)
all-merged_CD44_Co-Expression.xls (all-merged_CD44_Co-Expression.xls.zip)
IPA results (core-pos.pdf.zip core-neg.pdf.zip)
all examples bundled together (GV-Training_2012-11-09_files.zip)
Additional Resources
The list is obviously non-exhaustive, some tools also provide data for other species (prokaryotes, other small animal models...)
- multi-species
BIOMART: [http://www.biomart.org/biomart/martview/]
GSEA:MSigDB (email registration required): [http://www.broadinstitute.org/gsea/msigdb/index.jsp]
AmiGO: [http://amigo.geneontology.org/cgi-bin/amigo/go.cgi]
DAVID: [http://david.abcc.ncifcrf.gov/]
- focused on mammalian species
MiRWalk: [http://www.ma.uni-heidelberg.de/apps/zmf/mirwalk/]
Qiagen: [http://www.sabiosciences.com/ArrayList.php]
- additional tools for the plant kingdom
TAIR: http://www.arabidopsis.org/index.jsp
BAR: http://bar.utoronto.ca/welcome.htm
aramemnon: http://aramemnon.botanik.uni-koeln.de/request.ep
SUBA2: http://suba2.plantenergy.uwa.edu.au/index.php
AtPID: http://www.megabionet.org/atpid/webfile/
Gene Lists
These lists are given as a source of inspiration!
Using large lists will not always be possible because 'genevestigator' is limited to 400 probes import and most genes map to several probes.
Gene lists are built on experimental results that do not necessarily reflect co-expression of all list members.
What you can try is pick one or two genes from a list and search in genevestigator for more co-expressed genes (bottom-up approach from the data)
mitochondria markers (Qiagen)
human antifungal response markers (Qiagen)
cancer pathway finder (Qiagen)
Source: Qiagen PCR array lists
