FANMOD statistics

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Protocols

FANMOD specifications

Information


Unique identifier OMICS_05013
Name FANMOD
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Publication for FANMOD

FANMOD citations

 (55)
library_books

Network Based Methods for Identifying Key Active Proteins in the Extracellular Electron Transfer Process in Shewanella oneidensis MR 1

2018
Genes
PMCID: 5793192
PMID: 29337910
DOI: 10.3390/genes9010041

[…] than the un-interacted proteins, both of the biological motifs and modules play an important role in understanding complex biological processes. The identification of motifs was carried out with the FANMOD tool [], with the conventional parameters (p value < 0.05, z score > 2, etc.). The functional modules were extracted using the NetCarto program, which maximized the network modularity M by a si […]

library_books

A causal mediation model of ischemia reperfusion injury in the retina

2017
PLoS One
PMCID: 5679526
PMID: 29121052
DOI: 10.1371/journal.pone.0187426

[…] rstand network biology at each time point. Therefore, the MT, MM, and MTM class loops at 24h and 7d were searched for statistically significant functional network motifs via the motif detection tools FANMOD []. While the computational problem of finding three and four node motifs is tractable, exhaustive enumeration becomes problematic for larger values of nodes, making such analysis impossible [] […]

call_split

NemoProfile as an efficient approach to network motif analysis with instance collection

2017
BMC Bioinformatics
PMCID: 5657038
PMID: 29072139
DOI: 10.1186/s12859-017-1822-6
call_split See protocol

[…] f motifs, therefore even listing them is intractable. As an example, there are 11,716,571 patterns for motif size 10, as shown in Table  Many motif search programs are also available []: MFinder [], FANMOD [], Kavosh [], Mavisto [], and NeMoFinder [] follow the network-centric methods. Motif-centric methods are available with Grochow’s [], and MODA []. However, most of them provide only frequency […]

library_books

Modular Organization of Residue Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

2017
Genome Biol Evol
PMCID: 5388290
PMID: 28338825
DOI: 10.1093/gbe/evx036

[…] amino acid (k) varies between 1 and 12. We collate the entire network into isomorphic patterns (subgraphs), where one amino acid contacts ≥1 nucleotides, but internucleotide contacts are disregarded. FANMOD standalone tool () is used to identify these subgraphs. The number of occurrences of each subgraph is enumerated in the input network. For example, we find 35 subgraphs with k = 7 (). Next, we […]

library_books

The Multilayer Connectome of Caenorhabditis elegans

2016
PLoS Comput Biol
PMCID: 5215746
PMID: 27984591
DOI: 10.1371/journal.pcbi.1005283

[…] g method []. Hive plots were generated using the custom hiveplotter function written in Python (Python Software Foundation. Python Language Reference, v3.5). 3-node network motifs were computed using FANMOD []. Additional network visualisations were created using Cytoscape [] and Dia (https://wiki.gnome.org/Apps/Dia/). […]

call_split

Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach

2016
Sci Rep
PMCID: 4932630
PMID: 27378055
DOI: 10.1038/srep29043
call_split See protocol

[…] locks. A network motif was defined based on the criterion that the number of occurrences must be at least five, and also must be significantly higher than that used in randomized networks. We applied FANMOD on the complete network, to select network motifs. The significance test was carried out on 1000 randomized networks, and a pattern with P < 0.05 was considered statistically significant. Clust […]

Citations

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FANMOD institution(s)
Institut für Informatik, Friedrich-Schiller-Universität Jena Ernst-Abbe- Jena, Germany

FANMOD reviews

 (2)
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li yan

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Desktop
I have not used the software yet, but I have found that the software has very little knowledge, it is difficult to find relevant information, I hope to buy books related to the software on some websites.
Anonymous user #951's avatar image No country

Anonymous user #951

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Desktop
I think the standalone tool (and hence the code associated with that) has a lot of limitations when used with a network of 20 or 30 million nodes. The tool easily crashes and even for subgraphs of size 6 or 7, it is not able to handle even 50000 nodes and a dense network.