Protein & Cell >

2024 , Vol. 15 >Issue 5: 385 - 392

DOI: https://doi.org/10.1093/procel/pwad066

Degeneration Directory: a multi-omics web resource for degenerative diseases

  • Haoteng Yan 1,2,3,4,5 ,
  • Changfa Lu 6 ,
  • Chenyang Lan 6 ,
  • Si Wang 4,5,7,8 ,
  • Weiqi Zhang 8,9,10,11 ,
  • Zan He 4,5 ,
  • Jinghao Hu 4,5 ,
  • Jiaqi Ai 4,5 ,
  • Guang-Hui Liu , 1,3,4,5,8,10,12,13 ,
  • Shuai Ma , 1,3,8,10,12,13 ,
  • Yuanchun Zhou , 6 ,
  • Jing Qu , 2,3,8,10,12,13
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  • 1. State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  • 2. State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  • 3. Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  • 4. Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
  • 5. Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
  • 6. Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
  • 7. The Fifth People’s Hospital of Chongqing, Chongqing 400062, China
  • 8. Aging Biomarker Consortium, Beijing 100101, China
  • 9. CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
  • 10. University of Chinese Academy of Sciences, Beijing 100049, China
  • 11. Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
  • 12. Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
  • 13. Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
ghliu@ioz.ac.cn
mashuai3ban@126.com
zyc@cnic.cn
qujing@ioz.ac.cn

Received date: 17 Sep 2023

Accepted date: 07 Dec 2023

Published date: 15 May 2024

Copyright

2023 The Author(s) 2023. Published by Oxford University Press on behalf of Higher Education Press.
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Cite this article

Haoteng Yan , Changfa Lu , Chenyang Lan , Si Wang , Weiqi Zhang , Zan He , Jinghao Hu , Jiaqi Ai , Guang-Hui Liu , Shuai Ma , Yuanchun Zhou , Jing Qu . Degeneration Directory: a multi-omics web resource for degenerative diseases[J]. Protein & Cell, 2024 , 15(5) : 385 -392 . DOI: 10.1093/procel/pwad066

References

Publishing order | Descend order by publishing year | Descend order by cited within
1
Abel O, Shatunov A, Jones AR et al. Development of a smart-phone app for a genetics website: the amyotrophic lateral sclerosis online genetics database (ALSoD). JMIR Mhealth Uhealth 2013; 1:e18.

DOI

2
Aging Atlas C. Aging Atlas: a multi-omics database for aging biology. Nucleic Acids Res 2021; 49:D825–30.

DOI

3
Aging Biomarker C, Bao H, Cao J et al. Biomarkers of aging. Sci China Life Sci 2023; 66:893–1066.

DOI

4
Aho VTE, Pereira PAB, Voutilainen S et al. Gut microbiota in Parkinson’s disease: temporal stability and relations to disease progression. EBioMedicine 2019; 44:691–707.

DOI

5
Bai B, Wang X, Li Y et al. Deep multilayer brain proteomics identifies molecular networks in Alzheimer’s disease progression. Neuron 2020; 105:975–991.e7.

DOI

6
Becker L, Nguyen L, Gill J et al. Age-dependent shift in macrophage polarisation causes inflammation-mediated degeneration of enteric nervous system. Gut 2018; 67: 827–36.

DOI

7
Cai Y, Song W, Li J et al. The landscape of aging. Sci China Life Sci 2022; 65:2354–454.

DOI

8
Carelock ME, Master RP, Kim M-C et al. Targeting intracellular proteins with cell type-specific functions for cancer immunotherapy. Life Med 2023; 2:1–24.lnad019.

DOI

9
Chen WT, Lu A, Craessaerts K et al. Spatial transcriptomics and in situ sequencing to study Alzheimer’s disease. Cell 2020; 182:976–991.e19.

DOI

10
Collaborators GBDN. Global, regional, and national burden of neurological disorders, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Neurol 2019; 18:459–80.

DOI

11
Cryan JF, O’Riordan KJ, Cowan CSM et al. The microbiota-gut-brain axis. Physiol Rev 2019; 99:1877–2013.

DOI

12
Dopazo J, Amadoz A, Bleda M et al. 267 Spanish exomes reveal population-specific differences in disease-related genetic variation. Mol Biol Evol 2016; 33:1205–18.

DOI

13
Greenwood AK, Montgomery KS, Kauer N et al. The AD knowledge portal: a repository for multi-omic data on Alzheimer’s disease and aging. Curr Protoc Hum Genet 2020; 108:e105.

DOI

14
Guo J, Huang X, Dou L et al. Aging and aging-related diseases: from molecular mechanisms to interventions and treatments. Signal Transduct Target Ther 2022; 7:391.

DOI

15
Hampel H, Nistico R, Seyfried NT et al. Alzheimer Precision Medicine Initiative (APMI). Omics sciences for systems biology in Alzheimer’s disease: state-of-the-art of the evidence. Ageing Res Rev 2021; 69:101346.

DOI

16
Hao Y, Hao S, Andersen-Nissen E et al. Integrated analysis of multimodal single-cell data. Cell 2021; 184:3573–3587.e29.

DOI

17
Huang D, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2008; 37(1):1-13.

DOI

18
Jiang J, Wang C, Qi R et al. scREAD: a single-cell RNA-seq database for Alzheimer’s disease. iScience 2020; 23:101769.

DOI

19
Jing Y, Zuo Y, Sun L et al. SESN1 is a FOXO3 effector that counteracts human skeletal muscle ageing. Cell Proliferation 2023; 56:e13455.

DOI

20
Kang W, Jin T, Zhang T et al. Regeneration roadmap: database resources for regenerative biology. Nucleic Acids Res 2022; 50:D1085–90.

21
Kuchroo M, DiStasio M, Song E et al. Single-cell analysis reveals inflammatory interactions driving macular degeneration. Nat Commun 2023; 14:2589.

DOI

22
Leng SX, Pawelec G. Single-cell immune atlas for human aging and frailty. Life Med 2022; 1:67–70.

DOI

23
Li B, Zhao G, Zhou Q et al. Gene4PD: a comprehensive genetic database of Parkinson’s disease. Front Neurosci 2021; 15:679568.

DOI

24
Liu P, Wu L, Peng G et al. Altered microbiomes distinguish Alzheimer’s disease from amnestic mild cognitive impairment and health in a Chinese cohort. Brain Behav Immun 2019; 80:633–43.

DOI

25
Liu C, Yang M, Liu L et al. Molecular basis of degenerative spinal disorders from a proteomic perspective (Review). Mol Med Rep 2020; 21:9–19.

DOI

26
Liu Z, Belmonte JCI, Zhang W et al. Deciphering aging at three-dimensional genomic resolution. Cell Insight 2022; 1(3):1.

DOI

27
Nativio R, Lan Y, Donahue G et al. An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease. Nat Genet 2020; 52:1024–35.

DOI

28
Navarro JF, Croteau DL, Jurek A et al. Spatial transcriptomics reveals genes associated with dysregulated mitochondrial functions and stress signaling in Alzheimer disease. iScience 2020; 23:101556.

DOI

29
Pandey S, Shen K, Lee SH et al. Disease-associated oligodendrocyte responses across neurodegenerative diseases. Cell Rep 2022; 40:111189.

DOI

30
Petersen RC, Aisen PS, Beckett LA et al. Alzheimer’s disease neuroimaging initiative (ADNI): clinical characterization. Neurology 2010; 74:201–9.

DOI

31
Rickner HD, Jiang L, Hong R et al. Single cell transcriptomic profiling of a neuron-astrocyte assembloid tauopathy model. Nat Commun 2022; 13:6275.

DOI

32
Risbud MV, Shapiro IM. Role of cytokines in intervertebral disc degeneration: pain and disc content. Nat Rev Rheumatol 2014; 10:44–56.

DOI

33
Rubinsztein DC, Marino G, Kroemer G. Autophagy and aging. Cell 2011; 146:682–95.

DOI

34
Stevnsner T, Thorslund T, de Souza-Pinto NC et al. Mitochondrial repair of 8-oxoguanine and changes with aging. Exp Gerontol 2002; 37:1189–96.

DOI

35
Stockwell BR, Jiang X, Gu W. Emerging mechanisms and disease relevance of ferroptosis. Trends Cell Biol 2020; 30:478–90.

DOI

36
Sun G, Zheng Y, Fu X et al. Single-cell transcriptomic Atlas of mouse cochlear aging. Protein Cell 2022; 14:180–201.

DOI

37
Sun H, Wen X, Li H et al. Single-cell RNA-seq analysis identifies meniscus progenitors and reveals the progression of meniscus degeneration. Ann Rheum Dis 2020; 79:408–17.

DOI

38
Tiklova K, Nolbrant S, Fiorenzano A et al. Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson’s disease. Nat Commun 2020; 11:2434.

DOI

39
Wolters FJ, Chibnik LB, Waziry R et al. Twenty-seven-year time trends in dementia incidence in Europe and the United States: the Alzheimer cohorts consortium. Neurology 2020; 95:e519–31.

DOI

40
Yan H, Wang R, Ma S et al. Lineage Landscape: a comprehensive database that records lineage commitment across species. Nucleic Acids Res 2023; 51:D1061–6.

DOI

41
Yan P, Ren J, Zhang W et al. Protein quality control of cell stemness. Cell Regeneration 2021; 9:22.

DOI

42
Zhang F, Yue L, Fang X et al. Altered gut microbiota in Parkinson’s disease patients/healthy spouses and its association with clinical features. Parkinsonism Relat Disord 2020; 81:84–8.

DOI

43
Zhou T, Kiran M, Lui KO et al. Decoding liver fibrogenesis with single-cell technologies. Life Med 2022; 1:333–44.

DOI

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