This page accompanies the ongoing research of pathway maps as enablers of straightforward yet customized and semi-automated yet insightful analyses of omics data.
Network analyses are performed with GeneMANIA and matched against transcriptomes of a series of experiments, e.g. describing disease effects, in the Gene Expression Omnibus repository
with Cytoscape.
This website offers for each figure in the manuscript a representative graph for immediate inspection with CytoscapeJS.
Download the Cytoscape file cs_saspmarkers_kegg.cys for a detailed inspection of all attributes, P values and gene annotation. The gene lists contributing to these networks are offered in this Supplement File. In the graphs below, the colours are determined by the log Fold Change. The size maps to the GeneMania score.
Please activate JavaScript to interact with this web page. Tested on MacOS X, Linux and Windows with Firefox, Safari and Chrome.
The order of pathway maps reflects their presentation in the paper. The interpretation of these maps is aided with dynamic links for any selection of genes made in the graphs to the MEM (for interactions) and g:Profiler (for term enrichment) web services.
All code that contributed to this page is available from our public source code repository.
Figure 1: Canonical senescence pathway map, based on the SASP and the KEGG cellular senescence genes.
H. sapiens GSE19899 - senescence
Data derived from GEO GSE19899 dataset on the "retinoblastoma tumor suppressor during cellular senescence" by Cicas et al., 2010.
H. sapiens GSE61130 - senescence
Data derived from GEO GSE61130 dataset which contributed to Herranz et al., 2015 "mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype".
H. sapiens E-MTAB-5403 - senescence
Data derived from Hernandez-Segura et al., 2017 "Unmasking Transcriptional Heterogeneity in Senescent Cells", with observations 20 days after indruction of senescence in a HCA2 cell line.
Figure 2: Senescence in disease tissue
H. sapiens GSE46691 - prostate cancer
Data derived from GEO GSE46691 dataset on the "discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy" by Erho et al., 2013.
H. sapiens GSE81368 - pancreatic cancer
Data derived from GEO GSE81368 dataset on the "senescent carcinoma associated fibroblasts up-regulate interleukin 8 to enhance pancreatic cancer progression" by Wang et al., 2017.
H. sapiens GSE28155 - pancreatic cancer
Data derived from GEO GSE28155 dataset on the "loss of histone demethylase KDM6B enhances aggressiveness of pancreatic cancer through downregulation of C/EBPα" by Yamamoto et al., 2014.
Figure 3:
H. sapiens GSE22255 - stroke
Data derived from GEO GSE22255 dataset on the "blood genomic expression profile for ischemic stroke (IS)" by Krug et al., 2012.
H. sapiens GSE22255 - stroke, extended gene list
Data derived from GEO GSE22255 dataset on the "blood genomic expression profile for ischemic stroke (IS)" by Krug et al., 2012. Four genes of interest were added. No manual interferenc with the automated graph layout.
Human orthologues of mouse - mitochondrial heteroplasmy
Data derived from Hirose et al., 2018, describing effects of mitochondrial heteroplasmy in mice.
