Table 1 Key resources table

From: Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer

Resource

Source

Identifier

Deposited data

BRCA expression data 1

GEO

GSE12276

BRCA expression data 2

GEO

GSE16201

BRCA expression data 3

GEO

GSE20194

BRCA expression data 4

GEO

GSE20271

BRCA expression data 5

GEO

GSE20685

BRCA expression data 6

GEO

GSE21653

BRCA expression data 7

GEO

GSE22093

BRCA expression data 8

GEO

GSE22219

BRCA expression data 9

GEO

GSE22820

BRCA expression data 10

GEO

GSE24450

BRCA expression data 11

GEO

GSE25066

BRCA expression data 12

GEO

GSE25307

BRCA expression data 13

GEO

GSE26639

BRCA expression data 14

GEO

GSE2990

BRCA expression data 15

GEO

GSE30682

BRCA expression data 16

GEO

GSE31448

BRCA expression data 17

GEO

GSE3494

BRCA expression data 18

GEO

GSE36774

BRCA expression data 19

GEO

GSE45725

BRCA expression data 20

GEO

GSE4611

BRCA expression data 21

GEO

GSE48091

BRCA expression data 22

GEO

GSE4922

BRCA expression data 23

GEO

GSE54002

CRC expression data 1

GEO

GSE17536

CRC expression data 2

GEO

GSE17537

CRC expression data 3

GEO

GSE26682

CRC expression data 4

GEO

GSE26682

CRC expression data 5

GEO

GSE28722

CRC expression data 6

GEO

GSE37892

CRC expression data 7

GEO

GSE38832

CRC expression data 8

GEO

GSE39582

CRC expression data 9

GEO

GSE42284

CRC expression data 10

GEO

GSE44076

CRC expression data 11

GEO

GSE5206

CRC expression data 12

GEO

GSE68468

BRCA TCGA RNA-seq

TCGA Consortium

https://portal.gdc.cancer.gov/projects/TCGA-BRCA

BRCA TCGA Mutation

TCGA Consortium

https://portal.gdc.cancer.gov/projects/TCGA-BRCA

CRC TCGA RNA-seq

TCGA Consortium

https://portal.gdc.cancer.gov/projects/TCGA-COAD

CRC TCGA Mutation

TCGA Consortium

https://portal.gdc.cancer.gov/projects/TCGA-COAD

Software and Algorithms

Fast unfolding of communities in large networks (v0.3)

Blondel et al.19

https://sourceforge.net/projects/louvain/?source=navbar

GENE-E (v 3.0.21)

N/A

https://software.broadinstitute.org/GENE-E/

Gephi (v0.82)

Bastian et al.69

https://gephi.org/

Gephi sigma.js library

N/A

https://github.com/oxfordinternetinstitute/gephi-plugins/tree/sigmaexporter-plugin

MyGene.info

Xin et al.66

http://mygene.info

Python 2.7.1

N/A

https://www.anaconda.com/distribution/

R fastcluster package (v1.1.24)

Müllner68

https://cran.r-project.org/web/packages/fastcluster/index.html

R Limma package (v3.34.9)

Ritchie et al.67

http://bioconductor.org/packages/release/bioc/html/limma.html

R metafor package (v2.0.0)

Viechtbauer71

https://cran.r-project.org/web/packages/metafor/index.html

WGCNA (v1.66)

Langfelder and Horvath15

https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/

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