Towards a Pathway Inventory of the Human Brain for Modeling Disease Mechanisms Underlying Neurodegeneration

Journal of Alzheimer's Disease

Volumn 52, Issue 4, 2016, Pages 1343-1360

  Iyappan, Anandhi ^a,b   Gündel, Michaela ^a,b   Shahid, Mohammad ^c   Wang, Jiali ^d   Li, Hui ^h   Mevissen, Heinz Theodor ^a   Müller, Bernd ^e   Fluck, Juliane ^a   Jirsa, Viktor ^f   Domide, Lia ^g   Younesi, Erfan ^a,b   Hofmann Apitius, Martin ^a,b  

^a FRAUNHOFER INSTITUTE FOR ALGORITHMS AND SCIENTIFIC COMPUTING SCAI   (Germany)

^b UNIVERSITY OF BONN   (Germany)

^c GERMAN CENTER FOR NEURODEGENERATIVE DISEASES DZNE   (Germany)

^d UNIVERSITY OF LUXEMBOURG   (Luxembourg)

^e ZB MED Leibniz Information Centre for Life Sciences Department Digital Publishing GMS   (Germany)

^f AIX MARSEILLE UNIVERSITY   (France)

^g Str Petofi Sandor ^*  (Romania)

^h NONE

Author keywords

Alzheimer's disease; disease mechanism; disease modeling; neurodegeneration; pathway terminology

Indexed keywords

ALZHEIMER DISEASE; ARTICLE; BRAIN; BRAIN MAPPING; BRAIN REGION; BRAIN REGION AND CELL TYPE ONTOLOGY; DATA MINING; DISEASE ONTOLOGY; HUMAN; HUMAN BRAIN PHARMACOME; KNOWLEDGE BASE; NERVE DEGENERATION; NOMENCLATURE; PATHWAY TERMINOLOGY SYSTEM; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; BIOLOGICAL MODEL; DEGENERATIVE DISEASE; DRUG EFFECTS; FACTUAL DATABASE; METABOLISM; PATHOPHYSIOLOGY; PHYSIOLOGY;

BRAIN; DATABASES, FACTUAL; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, NEUROLOGICAL; NEURODEGENERATIVE DISEASES; SIGNAL TRANSDUCTION; TERMINOLOGY AS TOPIC;

EID: 84974530590     PISSN: 13872877     EISSN: 18758908     Source Type: Journal    
DOI: 10.3233/JAD-151178     Document Type: Article

References (66)

1. Yuryev A (2008) Pathway Analysis for Drug Discovery: Computational Infrastructure and Applications. JohnWiley & Sons, Hoboken, NJ.
2. Kyoto Encylopedia of Genes and Genomes, http://www. genome. jp/kegg/, Accessed on December 9, 2015.
3. BioCarta, http://www. genecarta. com/, Accessed on December 9, 2015.
4. WikiPathways, http://www. wikipathways. org/index. php/ WikiPathways, Accessed on December 9, 2015.
5. Adriaens ME, Jaillard M, Waagmeester A, Coort SL, Pico AR, Evelo CT (2008) The public road to high-quality curated biological pathways. Drug Discov Today 13, 856-862.
6. Khatri P, Sirota M, Butte AJ (2012) Ten years of pathway analysis: Current approaches and outstanding challenges. PLoS Comput Biol 8, e1002375.
7. Pathway Ontology, https://bioportal. bioontology. org/onto logies/PW, Last updated on October 27, 2015.
8. Rat Genome Database, http://rgd. mcw. edu/, Last accessed on December 9, 2015.
9. Petri V, Jayaraman P, Tutaj M, Hayman G, Smith JR, De Pons J, Laulederkind SJ, Lowry TF, Nigam R, Wang S-J, Shimoyama M, Dwinell MR, Munzenmaier DH, Worthey EA, Jacob HJ (2014) The pathway ontology - updates and applications. J Biomed Semantics 5, 7.
10. Kodamullil AT, Younesi E, Naz M, Bagewadi S, Hofmann-Apitius M (2015) Computable cause-and-effect models of healthy and Alzheimer's disease states and their mechanistic differential analysis. Alzheimers Dement 11, 1329-1339.
11. Neuroscience Information Framework (NIF) Standard Ontology, https://bioportal. bioontology. org/ontologies/ NIFSTD, Last updated on October 9, 2015.
12. The Virtual Brain, http://www. Thevirtualbrain. org/, Last accessed on December 9, 2015.
13. Miller JA, Woltjer RL, Goodenbour JM, Horvath S, Geschwind DH (2013) Genes and pathways underlying regional and cell type changes in Alzheimer's disease. Genome Med 5, 48.
14. Hodges A (2006) Regional and cellular gene expression changes in human Huntington's disease brain. Hum Mol Genet 15, 965-977.
15. INOH Ontology, http://www. berkeleybop. org/ontologies/ iev. owl, Last accessed on December 9, 2015.
16. Grenon P, Smith B (2004) SNAP and SPAN: Towards dynamic spatial ontology. Spat Cogn Comput 1, 69-103.
17. Tenenbaum D (2013) KEGGREST: Client-side REST access to KEGG. R package version, 1(1).
18. Reactome Database, http://www. reactome. org/, Last accessed on December 9, 2015.
19. Pathway Interaction Database, http://pid. nci. nih. gov/, Last accessed on December 9, 2015.
20. Hanisch D, Fundel K, Mevissen H-T, Zimmer R, Fluck J (2005) ProMiner: Rule-based protein and gene entity recognition. BMC Bioinformatics 6(Suppl 1), S14.
21. Lipscomb CE (2000) Medical subject headings (MeSH). Bull Med Libr Assoc 88, 265-266.
22. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS (2011) DrugBank 3. 0: A comprehensive resource for 'Omics' research on drugs. Nucleic Acids Res 39, D1035-D1041.
23. Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ (2013) The Comparative Toxicogenomics Database: Update 2013. Nucleic Acids Res 41, D1104-D1114.
24. Zhu F, Shi Z, Qin C, Tao L, Liu X, Xu F, Zhang L, Song Y, Liu X, Zhang J, Han B, Zhang P, ChenY(2012) Therapeutic target database update 2012: A resource for facilitating target-oriented drug discovery. Nucleic Acids Res 40, 1-9.
25. Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P (2012) STITCH 3: Zooming in on protein-chemical interactions. Nucleic Acids Res 40, D876-D880.
26. Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P (2010) Aside effect resource to capture phenotypic effects of drugs. Mol Syst Biol 6, 1-6.
27. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) ChEMBL: A large-scale bioactivity database for drug discovery. Nucleic Acids Res 40, D1100-D1107.
28. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK (2007) BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 35, D198-D201.
29. Roth BL, Lopez E, Patel S, Kroeze WK (2000) The multiplicity of serotonin receptors: Uselessly diverse molecules or an embarrassment of riches? Neuroscientist 6, 252-262.
30. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopaedia of Genes and Genomes. Nucl Acids Res 28, 27-30.
31. Groth P, Pavlova N, Kalev I, Tonov S, Georgiev G, Pohlenz H-D, Weiss B (2007) PhenomicDB: A new cross-species genotype/phenotype resource. Nucleic Acids Res 35, D696-D699.
32. European Prevention of Alzheimer's Dementia Consortium (EPAD), http://www. imi. europa. eu/content/epad, Last accessed on December 9, 2015.
33. Aetionomy, http://www. Aetionomy. org/, Last accessed on December 9, 2015.
34. Gardner D, Bowden DM (2009) NIH Public Access. Neuroinformatics 6, 149-160.
35. Bowden DM, Song E, Kosheleva J, Dubach MF (2012) NeuroNames: An ontology for the BrainInfo portal to neuroscience on the web. Neuroinformatics 10, 97-114.
36. Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, Schomburg D (2011) The BRENDA Tissue Ontology (BTO): The first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res 39, D507-D513.
37. Bodenreider O (2004) The Unified Medical Language System (UMLS): Integrating biomedical terminology. Nucleic Acids Res 32, D267-D270.
38. Tsarkov D, Horrocks I (2006) FaCT++ Description Logic Reasoner: System description. In Proceedings of the Third International Joint Conference (IJCAR 2006), pp. 292-297.
39. Brain Region and Cell Type Terminology (BRCT), http://bioportal. bioontology. org/ontologies/BRCT, Last updated on November 3, 2014.
40. Hofmann-Apitius M, Fluck J, Furlong L, Fornes O, Kolárik C, Hanser S, Boeker M, Schulz S, Sanz F, Klinger R, Mevissen T, Gattermayer T, Oliva B, Friedrich CM (2008) Knowledge environments representing molecular entities for the virtual physiological human. Philos Trans A Math Phys Eng Sci 366, 3091-3110.
41. SCAIView Academia, http://www. scaiview. com/scaiviewacademia. html, Last accessed on December 9, 2015.
42. Knowtator, http://knowtator. sourceforge. net/, Last accessed on December 9, 2015.
43. Ogren PV (2006) Knowtator: A Protégé plug-in for annotated corpus construction. Proc 2006 Conf North Am Chapter Assoc Comput Linguist Hum Lang Technol companion Vol. Demonstr., pp. 273-275.
44. Wu Z, Palmer M (1994) Verbs semantics and lexical selection. ACL '94 Proceedings of the 32nd annual meeting on Association for Computational Linguistics, pp. 133-138.
45. PatBase, https://www. patbase. com/login. Asp, Last updated on December 9, 2015.
46. ChemoCR, http://www. scai. fraunhofer. de/en/businessresearch-areas/bioinformatics/products/chemocr. html, Last accessed on December 9, 2015.
47. PDFBox, https://pdfbox. Apache. org/, Last accessed on December 9, 2015.
48. Ogren PV, Bethard SJ (2009) Building test suites for UIMA components. Proc Work Softw Eng Testing Qual Assur Nat Lang Process (SETQA-NLP 2009) Proceeding, pp. 1-4.
49. Count-Text Tool, http://textmechanic. com/Count-Text. html, Last accessed on December 9, 2015.
50. Sanz Leon P, Knock SA, Woodman MM, Domide L, Mersmann J, McIntosh AR, Jirsa V (2013) The Virtual Brain: A simulator of primate brain network dynamics. Front Neuroinform 7, 10.
51. Gregori-Puigjane E, Setola V, Hert J, Crews BA, Irwin JJ, Lounkine E, Marnett L, Roth BL, Shoichet BK (2012) Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A 109, 11178-11183.
52. Ghavami S, Shojaei S, Yeganeh B, Ande SR, Jangamreddy JR, Mehrpour M, Christoffersson J, Chaabane W, Moghadam AR, Kashani HH, Hashemi M, Owji AA, ?os MJ (2014) Autophagy and apoptosis dysfunction in neurodegenerative disorders. Prog Neurobiol 112, 24-49.
53. Naoi M, Maruyama W, Akao Y, Yi H, Yamaoka Y (2006) Involvement of type A monoamine oxidase in neurodegeneration: Regulation of mitochondrial signaling leading to cell death or neuroprotection. In Oxidative Stress and Neuroprotection, Editors: Parvez SH, Riederer P, eds. Springer, Vienna, pp. 67-77.
54. Weinreb O, Amit T, Bar-Am O, Youdim MB (2007) Induction of neurotrophic factors GDNF and BDNF associated with the mechanism of neurorescue action of rasagiline and ladostigil. Ann N Y Acad Sci 1122, 155-168.
55. Choi C, Kim S, Park Y (2007) A patent-based cross impact analysis for quantitative estimation of technological impact: The case of information and communication technology. Technol Forecast Soc Change 74, 1296-1314.
56. Jessop DM, Adams SE, Murray-Rust P (2011) Mining chemical information from open patents. J Cheminform 3, 40.
57. Grandjean N, Charpiot B, Pena CA, Peitsch MC (2005) Competitive intelligence and patent analysis in drug discovery. Mining the competitive knowledge bases and patents. Drug Discov. Today Technol 2, 211-215.
58. Liang WS, Reiman EM, Valla J, Dunckley T, Beach TG, Grover A, Niedzielko TL, Schneider LE, Mastroeni D, Caselli R, KukullW, Morris JC, Hulette CM, Schmechel D, Rogers J, Stephan DA (2008) Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc Natl Acad Sci U S A 105, 4441-4446.
59. Campos-Peña V, Meraz-Ríos MA (2014) Alzheimer disease: The role of A- in the glutamatergic system. In Neurochemistry, Heinbockel T, ed. ISBN: 978-953-51-1237-2, InTech, doi: 10. 5772/57367
60. Marwarha G, Ghribi O (2012) Leptin signaling and Alzheimer's disease. Am J Neurodegener Dis 1, 245-265.
61. Younesi E, Hofmann-Apitius M (2013) A network model of genomic hormone interactions underlying dementia and its translational validation through serendipitous off-target effect. J Transl Med 11, 177.
62. Korolainen M, Goldsteins G, Nyman T, Alafuzoff I, Koistinaho J, Pirttil T (2006) Oxidative modification of proteins in the frontal cortex of Alzheimer's disease brain. Neurobiol Aging 27, 42-53.
63. Zaroff S, Leone P, Markov V, Francis JS (2015) Transcriptional regulation of N-acetylaspartate metabolism in the 5xFAD model of Alzheimer's disease: Evidence for neuron-glia communication during energetic crisis. Mol Cell Neurosci 65, 143-152.
64. Malhotra A, Younesi E, Gurulingappa H, Hofmann-Apitius M (2013) HypothesisFinder: A strategy for the detection of speculative statements in scientific text. PLoS Comput Biol 9, e1003117.
65. Human Connectome Project, http://www. humanconnec tomeproject. org/, Last accessed on December 9, 2015.
66. European Medical Information Framework (EMIF-AD), http://www. emif. eu/emif-ad/about-emif-alzheimersdisease, Last accessed on December 9, 2015.