Table 1 List of publicly available de novo network enrichment methods in alphabetical order (February 7, 2016)

From: On the performance of de novo pathway enrichment

Tool

Method

Software

Reference

BioNet*

ASO

app

Ref. 25

ClustEx

Clust.

app

Ref. 32

cMonkey

Clust.

app

Ref. 33

COSINE*

SP

app

Ref. 26

GiGA*

SP

app

Ref. 34

GXNA*

SP

app

Ref. 29

HotNet

SP

app

Ref. 35

jActiveModules

ASO

C-PL

Ref. 36

KeyPathwayMiner*

MC

app, C-PL, WS

Ref. 30

DEGAS*

MC

app

Ref. 37

MEMCover

MC

app

Ref. 38

NetWalker

ASO

app

Ref. 16

NetworkTrail

ASO

WS

Ref. 39

PinnacleZ*

ASO

app, C-PL

Ref. 31

ReactomeViz-MCL

Clust.

C-PL

Ref. 40

RegMOD

SP

app

Ref. 41

ResponseNet

ASO

WS

Ref. 42

SubExtract

ASO

app

Ref. 43

TieDIE

SP

script (Python)

Ref. 44

  1. De novo methods capable of processing gene expression data are sub-divided into four categories, i.e. ASO aggregate score optimization, SP score propagation, MC module cover and Clust clustering based; see supplementary material for details. The availability of the tool as a stand-alone application (app), as Cytoscape plugin (C-PL), or as web service (WS) is further indicated.
  2. * Included in our quantitative study (see text for details)
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