GeneMANIA query runner
How to download the tool or source code including installation and usage instructions as well as any source code that might be associated with the executable. This should also include a listing of any dependencies for this tool or script.
Minimum system requirements
- Java 1.5+ JVM
- Queries that use more than ~1.5 GB of RAM require Cytoscape to be launched with a 64-bit JVM
- 2 GB RAM
- Installation Instructions
The GeneMANIA plugin is distributed as a JAR file. Available through Cytoscape's main
plugin repository under the Network Inference category
http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=GeneMANIA
A complete list of networks currently in the GeneMANIA system are available at
http://www.genemania.org/pages/networkList.jsf. Network data can be downloaded from within GeneMANIA plugin
Required version of the program necessary to perform the desired task
- Version: 2.0
Release Date: 2010-12-01
Verified to work in: Cytoscape2.6,2.7,2.8
Sample dataset and expected results to be output
USAGE (32-bit JVM):
java -Xmx1800M -cp GeneMANIA.jar org.genemania.plugin.apps.QueryRunneroptions query-file-1 [ query-file-2 ... ]
USAGE (64-bit JVM):
java -d64 -Xmx3G -cp GeneMANIA.jar org.genemania.plugin.apps.QueryRunneroptions query-file-1 [ query-file-2 ... ]
Query file should contain the gene list and other parameters, tab delimited flat file.
Flat Query File Format:
organism name
query-gene-1 [ \t query-gene-2 ... ]
networks
related-gene-limit
weighing method
- Organism options
Organism name Taxonomy ID
A. Thaliana 3702
C. Elegans 6239
D. Melanogaster 7227
H. Sapiens 9606
M. Musculus 10090
S. Cerevisiae 4932
- Available network types
coexp co-expression
coloc Co-localization
gi Genetic interactions
pi physical interactions
predict predicted
spd Shared protein domains
other Networks that don't belong to any of the above types.
all all available networks
preferred shorthand for coexp gi pi
- weighing methods
automatic The networks are weighted such that the query genes interact as much as possible(Default).
average All networks are weighted equally.
average_category Networks are weighted such that each type of network has the same overall weight.
For Organisms With GO Annotations:
bp Networks are weighted in an attempt to reproduce Gene Ontology Biological Process co-annotation patterns.
mf Networks are weighted in an attempt to reproduce Gene Ontology Molecular Function co-annotation patterns.
cc Networks are weighted in an attempt to reproduce Gene Ontology Cellular Component co-annotation patterns.
Example Query file: Query1.txt
A. thaliana
HY5 ELF3 PHYB PHYA
coexp
50
bp
Excerpt from the out put file query1.txt-results.report -
Gene Score Description
ELF3 ELF3 (EARLY FLOWERING 3); protein C-terminus binding / transcription factor
PHYB PHYB (PHYTOCHROME B); G-protein coupled photoreceptor/ protein histidine kinase/ red or far-red light photoreceptor/ signal transducer
HY5 HY5 (ELONGATED HYPOCOTYL 5); DNA binding / double-stranded DNA binding / transcription factor
PHYA PHYA (PHYTOCHROME A); G-protein coupled photoreceptor/ protein histidine kinase/ red or far-red light photoreceptor/ signal transducer
ATBETAFRUCT4 0.18 ATBETAFRUCT4; beta-fructofuranosidase/ hydrolase, hydrolyzing O-glycosyl compounds
TOC1 0.12 TOC1 (TIMING OF CAB EXPRESSION 1); transcription regulator/ two-component response regulator
SCL3 0.12 SCL3; transcription factor
F3H 0.12 F3H (FLAVANONE 3-HYDROXYLASE); naringenin 3-dioxygenase
AKIN11 0.11 AKIN11 (Arabidopsis SNF1 kinase homolog 11); protein binding / protein kinase
AtMYB32 0.11 AtMYB32 (myb domain protein 32); DNA binding / transcription factor
GA3 0.11 GA3 (GA REQUIRING 3); ent-kaurene oxidase/ oxygen binding
AT3G19100 0.09 calcium-dependent protein kinase, putative / CDPK, putative
COL9 0.09 COL9 (CONSTANS-LIKE 9); transcription factor/ zinc ion binding
ELIP2 0.09 ELIP2 (EARLY LIGHT-INDUCIBLE PROTEIN 2); chlorophyll binding
SPL7 0.09 SPL7 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 7); DNA binding / transcription factor
AT2G25730 0.09 hypothetical protein
ATMRP4 0.09 ATMRP4 (ARABIDOPSIS THALIANA MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 4); ATPase, coupled to transmembrane movement of substances / folic acid transporter
AT5G48250 0.09 zinc finger (B-box type) family protein
AAE17 0.09 AAE17 (ACYL-ACTIVATING ENZYME 17); catalytic/ ligase
RHA2B 0.08 RHA2B (RING-H2 FINGER PROTEIN 2B); protein binding / ubiquitin-protein ligase/ zinc ion binding
MP 0.08 MP (MONOPTEROS); transcription factor
FLS 0.08 FLS (FLAVONOL SYNTHASE); flavonol synthase
AT3G61580 0.08 delta-8 sphingolipid desaturase (SLD1)
AT4G37180 0.08 myb family transcription factor
RPL23AA 0.08 RPL23AA (RIBOSOMAL PROTEIN L23AA); RNA binding / nucleotide binding / structural constituent of ribosome
POP1 0.08 POP1; transporter
GDH1 0.08 GDH1 (GLUTAMATE DEHYDROGENASE 1); ATP binding / glutamate dehydrogenase NAD(P)+/ oxidoreductase
DRT102 0.08 DRT102 (DNA-DAMAGE-REPAIR/TOLERATION 2)
ACC1 0.08 ACC1 (ACETYL-COENZYME A CARBOXYLASE 1); acetyl-CoA carboxylase
PHV 0.08 PHV (PHAVOLUTA); DNA binding / protein binding / transcription factor
- One prediction report per query file.
Set of parameters and command line switches that match the expected execution of the tool including the possible command line definitions according to the occurrence of optional parameters. Also, validation instructions for parameters are requested.
actual command-line parameter |
name and brief description of the parameter |
required |
default value |
text, number, or name of file |
description of validation rules |
|---|---|---|---|---|---|
--data |
directory of geneMANIA dataset; file path |
yes |
|
text |
|
|
|
|
|||
--in |
input-format; format of the query file |
optional |
flat (tab delimited) |
text |
|
--out |
output-format; format of the output files |
optional |
genes |
text |
|
--scoring-method |
method used to compute the gene scores |
optional |
disciminant |
text |
Discriminant |
--ids |
gene identifier types.A comma separated file of gene identifier types in descending order of preference. |
optional |
|
text |
Ensembl Gene Name |
--results |
output file directory.Path to where the prediction result files will be created (one per input query file) |
optional |
working directory |
text |
|
--threads |
The maximum number of parallel predictions. Ideally this should be set to the number of processing cores. |
optional |
1 |
number |
|
--verbose |
print more details about what's happening. |
optional |
|
text |
|
--list_networks organism name |
Lists the available networks for the given organism. Put quotes around the organism name. |
optional |
|
text |
|
--list-genes organism name |
Lists the genes that are recognized for the given organism. Put quotes around the organism name. Each line in the output contains a gene and all its synonyms, if any. |
optional |
|
text |
|
|
|
|
|
|
|
Example invocation of the command line application and its associated parameters such that it can perform an analysis.
java -Xmx1800M -cp GeneMANIA.jar org.genemania.plugin.apps.QueryRunner --data /users/usename/genemania_plugin/gmdata-2010-12-01 --out flat query1.txt
Reference
J. Montojo, K. Zuberi, H. Rodriguez, F. Kazi, G. Wright, S. L. Donaldson, Q. Morris and G. D. Bader. (2010).GeneMANIA Cytoscape plugin: fast gene function predictions on
the desktop. Bioinformatics,26 (22):2927-2928.
Mostafavi,S. et al. (2008) GeneMANIA: a real-time multiple association network integration algorithm for prediction gene function. Genome Biol., 9, S4.
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q(2010).The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.Nucleic Acids Res. 38 Suppl:W214-20.
[http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_2/W214] |