Lung fibrosis (Homo sapiens)

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Description

Lung fibrosis pathway linked to events (molecular initiating event, key events and associative events) in a putative Adverse Outcome Pathway for lung fibrosis.

Quality Tags

Ontology Terms

 

Bibliography

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  1. Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q; ''GeneMANIA: Fast gene network construction and function prediction for Cytoscape.''; http://www.ncbi.nlm.nih.gov/pubmed/25254104, 2014 PubMed
  2. Vietti G, Lison D, van den Brule S; ''Mechanisms of lung fibrosis induced by carbon nanotubes: towards an Adverse Outcome Pathway (AOP).''; http://www.ncbi.nlm.nih.gov/pubmed/26926090, 2016 PubMed
  3. Naumanen P, Lappalainen P, Hotulainen P; ''Mechanisms of actin stress fibre assembly''; J Microsc. 2008 Sep;231(3):446-54. doi: 10.1111/j.1365-2818.2008.02057.x., 2008 PubMed
  4. Todd NW, Luzina IG, Atamas SP; ''Molecular and cellular mechanisms of pulmonary fibrosis.''; http://www.ncbi.nlm.nih.gov/pubmed/22824096, 2012 PubMed
  5. Grebe A, Latz E; ''Cholesterol crystals and inflammation.''; Curr Rheumatol Rep, 2013 PubMed
  6. Labib S, Williams A, Yauk CL, Nikota JK, Wallin H, Vogel U, Halappanavar S; ''Nano-risk Science: application of toxicogenomics in an adverse outcome pathway framework for risk assessment of multi-walled carbon nanotubes''; http://www.ncbi.nlm.nih.gov/pubmed/26979667, 2016 PubMed
  7. Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D2, King BL, Wiegers TC2, Mattingly CJ; ''The Comparative Toxicogenomics Database's 10th year anniversary: update 2015''; http://www.ncbi.nlm.nih.gov/pubmed/25326323, 2015 PubMed
  8. Muir H.; ''The chondrocyte, architect of cartilage. Biomechanics, structure, function and molecular biology of cartilage matrix macromolecules.''; Bioessays. 1995 Dec;17(12):1039-48., 1995 PubMed

History

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CompareRevisionActionTimeUserComment
91475view12:07, 6 March 2017FehrhartAdded ID for Chemokine signaling
91457view12:32, 1 March 2017FehrhartDesign update
91456view11:57, 1 March 2017FehrhartFormat adjustments
91455view10:13, 1 March 2017FehrhartAdded AE3
91421view12:48, 22 February 2017FehrhartChanged shade of grey for AO
90900view11:37, 16 December 2016PennyRemoved "frustrated phagocytosis" since that is mainly related to high-aspect ratio materials and does not represent other types of fibrosis-inducing agents
90691view13:12, 9 December 2016PennyModified description
90684view11:24, 7 December 2016PennyLink to WP2666
90683view11:13, 7 December 2016PennyAdded link to WP474
90526view23:51, 21 November 2016Khanspersmoved pathway to improve scaling/readability
88994view12:05, 18 August 2016LindarieswijkConverted unknown node to label
88993view11:54, 18 August 2016LindarieswijkUpdate literature reference (double Vietti)
88992view11:51, 18 August 2016LindarieswijkUpdates references
88991view11:50, 18 August 2016LindarieswijkUpdates literature
88990view11:47, 18 August 2016LindarieswijkUpdates literature reference
88984view10:00, 18 August 2016LindarieswijkUpdated legend and coloring of the events
88974view08:57, 18 August 2016LindarieswijkChanged "ROS production" labels to metabolite nodes and added CHEBI ID
88972view07:59, 18 August 2016LindarieswijkUpdated literature
88923view15:24, 17 August 2016LindarieswijkChanged AE back to associative event (like in paper)
88922view15:19, 17 August 2016LindarieswijkCorrected the legend: added MIE and adjusted full name AE
88695view16:04, 12 August 2016JmeliusOntology Term : 'respiratory system disease pathway' added !
87393view11:05, 22 July 2016MaintBotadded missing graphids
86044view19:07, 28 June 2016MaintBotconnected interaction
85998view00:08, 24 June 2016KhanspersModified description
85992view08:34, 23 June 2016FehrhartConnected unconnected lines
85985view19:02, 22 June 2016KhanspersOntology Term : 'pulmonary fibrosis' added !
85070view10:30, 11 April 2016PennyAdded legend for AOP events
84887view14:15, 30 March 2016PennyPeriodical update, work in progress
84886view13:47, 30 March 2016PennyPeriodical update, work in progress
84881view20:33, 29 March 2016PennyPeriodical update, work in progress
84880view20:03, 29 March 2016PennyPeriodical update
84877view15:34, 29 March 2016PennySimplified connections with reference to MIEs, KEs and AEs associated with a putative AOP for lung fibrosis.
84873view11:29, 29 March 2016FehrhartAdded link to NDRP3 inflammasome pathway via IL1B
84792view12:33, 22 March 2016PennyUpdated links
84791view10:33, 22 March 2016PennyUpdated connections according to geneMANIA and CPDB induced network module.
84790view09:07, 22 March 2016PennyUpdated connections
84789view08:36, 22 March 2016PennyAdded gene connections
84787view15:28, 21 March 2016LindarieswijkUpdated Gene IDs
84775view14:33, 18 March 2016Penny
84774view14:13, 18 March 2016Penny
84773view14:06, 18 March 2016Penny
84772view12:38, 18 March 2016FehrhartModified description
84771view12:30, 18 March 2016FehrhartNew pathway

External references

Datanodes

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NameTypeDatabase referenceComment
ATP11AGeneProductENSG00000068650 (Ensembl)
ApoptosisPathwayWP254 (WikiPathways)
BMP7GeneProductENSG00000101144 (Ensembl)
CALCAGeneProductENSG00000110680 (Ensembl)
CCL11GeneProductENSG00000172156 (Ensembl)
CCL2GeneProductENSG00000108691 (Ensembl)
CCL3GeneProductENSG00000277632 (Ensembl)
CCL4GeneProductENSG00000275302 (Ensembl)
CCL5GeneProductENSG00000271503 (Ensembl)
CCR2GeneProductENSG00000121807 (Ensembl)
CCR3GeneProductENSG00000183625 (Ensembl)
CEBPBGeneProductENSG00000172216 (Ensembl)
CMA1GeneProductENSG00000092009 (Ensembl)
CSF2GeneProductENSG00000164400 (Ensembl)
CSF3GeneProductENSG00000108342 (Ensembl)
CTGFGeneProductENSG00000118523 (Ensembl)
CXCL2GeneProductENSG00000081041 (Ensembl)
CXCL8GeneProductENSG00000169429 (Ensembl)
CYSLTR2GeneProductENSG00000152207 (Ensembl)
Chemokine signalingPathwayWP3929 (WikiPathways)
Chondrocyte differentiationPathwayWP474 (WikiPathways) Link to the pathway Endochondrial ossification describing chondrocyte differentiation. Chondrocytes produce and maintain cartilage consisting mainly of collagen and proteoglycans.
Coagulation disturbancesPathwayWP558 (WikiPathways)
Collagen productonPathwayWP2798 (WikiPathways)
Cytokines

and inflammatory

response
PathwayWP530 (WikiPathways)
DPP9GeneProductENSG00000142002 (Ensembl)
DSPGeneProductENSG00000096696 (Ensembl)
Differentiation PathwayPathwayWP2848 (WikiPathways)
EDN1GeneProductENSG00000078401 (Ensembl)
EGFGeneProductENSG00000138798 (Ensembl)
ELMOD2GeneProductENSG00000179387 (Ensembl)
ELNGeneProductENSG00000049540 (Ensembl)
FAM13AGeneProductENSG00000138640 (Ensembl)
FGF1GeneProductENSG00000113578 (Ensembl)
FGF2GeneProductENSG00000138685 (Ensembl)
FGF7GeneProductENSG00000140285 (Ensembl)
GREM1GeneProductENSG00000166923 (Ensembl)
HGFGeneProductENSG00000019991 (Ensembl)
HMOX1GeneProductENSG00000100292 (Ensembl)
IGF1GeneProductENSG00000017427 (Ensembl)
IL12BGeneProductENSG00000113302 (Ensembl)
IL13GeneProductENSG00000169194 (Ensembl)
IL1BGeneProductENSG00000125538 (Ensembl)
IL4GeneProductENSG00000113520 (Ensembl)
IL5GeneProductENSG00000113525 (Ensembl)
IL6GeneProductENSG00000136244 (Ensembl)
Inflammasome activationPathwayWP288 (WikiPathways)
InflammationPathwayWP453 (WikiPathways)
MAPK signalingPathwayWP382 (WikiPathways)
MECP2GeneProductENSG00000169057 (Ensembl)
MIE - Molecular Initiating Event
MMP2GeneProductENSG00000087245 (Ensembl)
MMP9GeneProductENSG00000100985 (Ensembl)
MT2AGeneProductENSG00000125148 (Ensembl)
MUC5BGeneProductENSG00000117983 (Ensembl)
Matrix metalloproteinasesPathwayWP129 (WikiPathways)
NADPH oxidasePathwayWP3396 (WikiPathways)
NF-KBPathwayhsa04064 (KEGG Pathway)
NFE2L2GeneProductENSG00000116044 (Ensembl)
NRF2 signalingPathwayWP2884 (WikiPathways)
OBFC1GeneProductENSG00000107960 (Ensembl)
Oxidative StressPathwayWP408 (WikiPathways)
PARNGeneProductENSG00000140694 (Ensembl)
PDGFAGeneProductENSG00000197461 (Ensembl)
PDGFBGeneProductENSG00000100311 (Ensembl)
PLAUGeneProductENSG00000122861 (Ensembl)
PTX3GeneProductENSG00000163661 (Ensembl)
ROS productionMetaboliteCHEBI:26523 (ChEBI)
RTEL1GeneProductENSG00000258366 (Ensembl)
SERPINA1GeneProductENSG00000197249 (Ensembl)
SFTPA1GeneProductENSG00000122852 (Ensembl)
SFTPA2GeneProductENSG00000185303 (Ensembl)
SFTPCGeneProductENSG00000168484 (Ensembl)
SKILGeneProductENSG00000136603 (Ensembl)
SMAD7GeneProductENSG00000101665 (Ensembl)
SPP1GeneProductENSG00000118785 (Ensembl)
Stress fibre assemblyPathwayWP2666 (WikiPathways) Link to Elastic fibre formation, which describes the dynamic connective tissues such as large arteries and lung parenchyma. The stress fibre assembly related gene ELN is involved in this pathway.
TERCGeneProductENSG00000270141 (Ensembl)
TERTGeneProductENSG00000164362 (Ensembl)
TGF beta signalingPathwayWP560 (WikiPathways)
TGFAGeneProductENSG00000163235 (Ensembl)
TGFB1GeneProductENSG00000105329 (Ensembl)
TIMP1GeneProductENSG00000102265 (Ensembl)
TNFGeneProductENSG00000232810 (Ensembl)
Toll-like receptor signalingPathwayWP75 (WikiPathways)
p38 MAPKPathwayWP400 (WikiPathways)

Annotated Interactions

No annotated interactions

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