High-throughput sequencing data, pathways and reference networks to get trained with the R package SEMgraph. It includes:

Data:

• Amyotrophic Lateral Sclerosis (ALS) RNA-seq dataset of 139 cases and 21 healthy controls, from Tam O.H. et al., 2019 (GEO accession: GSE124439).
• Frontotemporal Dementia (FTD) DNA methylation dataset 150 cases and 150 healthy controls, from Li Y. et al., 2014 (GEO accession: GSE53740).
• COVID-19 RNA-seq dataset of 46 critical and 23 non-critical COVID-19 cases in young patients, from Carapito R. et al., 2022 (GEO accession: GSE172114.
• Breast Cancer RNA-seq dataset of 112 BRCA patients and 112 healthy controls from TCGA.
• Flow cytometry data and causal model from Sachs et al., 2005 available in SEMgraph.  

Pathways:

• KEGG pathways. A comprehensive list of igraph objects for 227 KEGG pathways (last update: November 2021).
• KEGG circuits. A comprehensvive list of igraph objects for 146 KEGG signalling pathways, which are subdivided into "effector" subpathays (i.e., a list 1868 subgraphs with many different input nodes and one output node), and "decomposed" subpathays (i.e., a list 8409 subgraphs with one input node and one output node) extracted from R package hipathia in Bioconductor project (last update: October, 2024).
• Reactome pathways. A comprehensive list of igraph objects for 1641 Reactome pathways (last update: April 2020).  

Reference networks:

• KEGG, an igraph object of 5007 nodes and 44755 edges (41122 directed and 3164/2 = 1582 bidirected) corresponding to the union of 225 KEGG pathways (update: Nov 2021).
• Reactome, an igraph object of 9762 nodes and 416128 edges (109268 directed and 306860/2 = 153430 bidirected) corresponding to the union of 1641 Reactome pathways (update: Apr 2020).
• DO, an igraph network object of 6576 nodes and 6923 directed edges, corresponding to the Disease Ontology terms (update: Feb, 2020).
• GOBP, an igraph network object of 27685 nodes and 58979 directed edges, corresponding to the Gene Ontology Biological Process terms (update: Feb, 2020).
• GOCC, an igraph network object of 3793 nodes and 7116 directed edges, corresponding to the Gene Ontology Cellular Component terms (update: Feb, 2020).
• GOMF, an igraph network object of 9933 nodes and 12114 directed edges, corresponding to the Gene Ontology Molecular Function terms (update: Feb, 2020)
• STRING, an igraph network object of 10829 nodes and 213445 edges (undirected), corresponding to the STRING interactome (version 10.5).  

Pathways and reference networks are freezed to benchmarked versions for SEMgraph. If you would like to get the latest version of your favourite database, you can use either the R package graphite in Bioconductor project, or the wrapper function loadPathways() available in SEMgraph v.1.2.4 or above.

SEMdata can be installed in R with the following line (it requires SEMgraph first):

devtools::install_github("fernandoPalluzzi/SEMgraph")

devtools::install_github("fernandoPalluzzi/SEMdata")