Lmst

March 2026 WikiPathways update: 45 edits by 5 contributors in the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/227

Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen. https://www.wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

February 2026 WikiPathways update: 95 edits by 9 contributorsin the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/221 Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen. https://www.wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

January 2026 WikiPathways update: 134 edits by 3 contributorsin the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/213 Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen. https://www.wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

December 2025 WikiPathways release: 840 edits by 8 contributors and 9 new pathways (4 in screenshots). Accessible via #webservices, #rstats, #pathvisio and #cytoscape.

https://www.wikipathways.org/#download

#bioinformatics #elixirnl

WikiPathways WP5609: Key metabolic pathways in melanoma, glycolytic pathway, TCA cycle, glutamine metabolism, and oxidative phosphorylation, with potential therapeutic targets and inhibitors. Inhibitors targeting critical metabolic nodes are outlined in teal. This pathway is based on Figure 1 in Shen et al.

WikiPathways WP5606: Cis- and trans-acting regulators shape gene expression within the β-globin cluster. The LDB1 complex (LDB1/LMO2/GATA1/TAL1) binds both the locus control region (LCR) and globin promoters, promoting chromatin looping to activate these genes—interactions that may be influenced by cis-acting variants linked to HbS haplotypes. Across the HBB gene cluster and its surrounding regions, BCL11A and ZBTB7A (LRF) binding sites are present, represented by red and blue stars. Each of these transcription factors recruits its own NuRD complex. MYB regulates HbF expression directly and also indirectly through KLF1 and BCL11A. Repression of the HbF genes is indicated by dashed lines. Inspired by figure 1 in Habara et al. (2017).

WikiPathways WP5604: This pathway shows the molecular pathophysiology of sickle cell disease. (A) A single–nucleotide variant in the β-globin gene replaces glutamic acid with valine at position 6 of the β-globin chain. Upon deoxygenation, the resulting hemoglobin S (HbS) molecules polymerize into rigid fibers, driving erythrocyte sickling (clockwise). (B) Sickled cells cause impaired blood rheology and enhanced adhesion of erythrocytes to neutrophils, platelets, and the endothelium, leading to slowed or obstructed microvascular flow – called vaso-occlusion. Vaso-occlusion in turn promotes ischemia-reperfusion (I-R) injury (clockwise). (C) HbS polymer formation also leads to red cell membrane damage and hemolysis (counterclockwise), releasing cell-free hemoglobin (Hb) into circulation. Oxygenated Hb (Fe²⁺) contributes to endothelial dysfunction by consuming nitric oxide (NO) and producing nitrate (NO₃⁻) and methemoglobin (Fe³⁺). Hb can also undergo Fenton chemistry with H₂O₂, generating hydroxyl radicals (•OH) and additional methemoglobin. Methemoglobin (Fe³⁺) can degrade and release cell-free heme (counterclockwise), a potent erythrocyte-derived DAMP. (D) ROS production, TLR4 activation, NET formation, release of tissue- or cell-derived DAMPs, extracellular DNA, and other yet-undefined mediators generated by cell-free heme or I-R injury can induce sterile inflammation by activating the inflammasome in vascular and immune cells, leading to IL-1β release.

WikiPathways WP5607: Erythroid lineage cell differentiation transitions from hematopoietic stem cells (HSCs) through successive erythroid progenitors – burst-forming unit–erythroid (BFU-E), colony-forming unit–erythroid (CFU-E) – then proerythroblasts (proEB), basophilic erythroblasts (basoEB), polychromatic erythroblasts (polyEB), and orthochromatic erythroblasts (orthoEB), then and ultimately to reticulocytes, pyrenocytes, and mature red blood cells (RBCs). Stage-specific transcription factors (GATA1, GATA2), surface markers (CD34, CD45, CD71, CD235a), the onset of hemoglobin expression, and other factors are also depicted.

November 2025 WikiPathways update: 686 edits by 6 contributors and 10 new pathways in the last month. Accessible via #webservices, #rstats, #pathvisio and #cytoscape.

Supported by #awsopen. https://www.wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

New pathway, Caffeine in blood vessels (WP5601). In vascular smooth muscle, caffeine promotes relaxation by inhibiting myosin light-chain kinase (MLCK) through cAMP elevation and activating myosin light-chain phosphatase (MLCP), reducing myosin–actin interaction. As a nonselective adenosine receptor antagonist, caffeine blocks A₁/A₃ receptors (which normally lower cAMP) and A₂A/A₂B receptors (which normally raise cAMP), thereby altering adenylate cyclase activity. In endothelial cells, caffeine increases intracellular Ca²⁺, activating eNOS to produce nitric oxide (NO), which diffuses to smooth muscle and stimulates cGMP signaling, further promoting vasodilation. Inspired by Figure 1 in Kumar and Lipshultz, 2019.

New pathway, KCNQ2 and KCNQ3-related epilepsy (WP5599): Processes involved in KCNQ2 and KCNQ3-related epilepsies.

New pathways, GABA and glutamate signalling in epileptogenesis (WP5600): This pathway depicts the epileptogenic mechanisms involving GABA and glutamate signaling. It focuses on transporters and channel proteins that modulate action potential dynamics and their interacting partners, highlighting functional alterations that contribute to epilepsy pathogenesis.

October 2025 WikiPathways update: 129 edits by 10 contributors and 5 new pathways in the last month. Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen. https://www.wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

September 2025 WikiPathways update: 261 edits by 6 contributors and 13 new pathways in the last month. Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen. https://www.wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

October 2024 WikiPathways update: 167 edits by 4 contributors and 2 new pathways in the last month. Accessible via #webservices, #rstats, #pathvisio and #Cytoscape Supported by #AWSOpen

https://wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

Screenshot of a part of the "New Pathways" page, showing the two new pathways: "Transcriptional regulation of memory B cell differentiation" (WP5491), https://www.wikipathways.org/pathways/WP5491.html and "Regulation of cytotoxic T cell responses by Malat1 - miR-15/16 circuit" (WP5489), https://www.wikipathways.org/pathways/WP5489.html

September 2024 WikiPathways update: 179 edits by 6 contributors and 4 new pathways in the last month. Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen . https://wikipathways.org/index.php/Download_Pathways

#bioinformatics #openscience #opensource

I cannot help but wonder what if we had ported #PathVisio on top of #Bioclipse when I joined the group in 2012... https://chem-bla-ics.blogspot.com/2006/07/context-help-in-bioclipse.html

March 2024 WikiPathways release: 542 edits by 9 contributors and 10 new pathways. Accessible via #webservices and in #PathVisio, #Cytoscape. Supported by AWSOpen. https://wikipathways.org/#download #bioinformatics #openscience #opensource

my first #BioHackEU23 result: https://github.com/BiGCAT-UM/org.pathvisio.io.bioschemas #pathvisio #libGPML @wikipathways

cc @sneumann

July 2023 WikiPathways release: 232 edits by 32 contributors and 12 new pathways. Accessible via #webservices and in #PathVisio, #Cytoscape Supported by AWSOpen. https://wikipathways.org/#download #bioinformatics #openscience #opensource

I am attending the 4th #EpiLipidNET meeting in Toulouse tomorrow and Wednesday. Tomorrow I will demo @wikipathways @bridgedb and #pathvisio and on Wednesday I get to show some of the new things in these projects. I will cover the meeting from this account

June 2023 WikiPathways release: 137 edits by 22 contributors and 2 new pathways. Accessible via #webservices and in #PathVisio, #Cytoscape Supported by AWSOpen. https://wikipathways.org/#download
#bioinformatics #openscience #opensource

May 2023 WikiPathways release: 316 edits by 13 contributors and 15 new pathways. Accessible via #webservices and in #PathVisio, #Cytoscape. Supported by #AWSOpen. https://www.wikipathways.org/download.html
#bioinformatics #openscience #opensource #nomoa

April 2023 WikiPathways release: 276 edits by 32 contributors and 6 new pathways. Accessible via #webservices and in #PathVisio, #Cytoscape. Supported by #AWSOpen. https://www.wikipathways.org/download.html
#bioinformatics #openscience #opensource #nomoa

A molecular network map of orexin-orexin receptor signaling system. https://doi.org/10.1007/s12079-022-00700-3 #Orexin #Pathvisio #Sleep #Feeding #Hypothalamus

March 2023 WikiPathways release: 293 edits by 30 contributors and 22 new pathways. Accessible via #webservices and in #PathVisio, #Cytoscape. Supported by #AWSOpen. https://www.wikipathways.org/download.html
#bioinformatics #openscience #opensource #nomoa

February 2023 WikiPathways release: 283 edits by 32 contributors. Accessible via #webservices and in #PathVisio, #Cytoscape. Supported by #AWSOpen. https://wikipathways.org/index.php/Download_Pathways
#bioinformatics #openscience #opensource #nomoa

#Pathvisio

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