PMID- 37439331
OWN - NLM
STAT- MEDLINE
DCOM- 20230911
LR  - 20231004
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 51
IP  - 16
DP  - 2023 Sep 8
TI  - iSMOD: an integrative browser for image-based single-cell multi-omics data.
PG  - 8348-8366
LID - 10.1093/nar/gkad580 [doi]
AB  - Genomic and transcriptomic image data, represented by DNA and RNA fluorescence in 
      situ hybridization (FISH), respectively, together with proteomic data, 
      particularly that related to nuclear proteins, can help elucidate gene regulation 
      in relation to the spatial positions of chromatins, messenger RNAs, and key 
      proteins. However, methods for image-based multi-omics data collection and 
      analysis are lacking. To this end, we aimed to develop the first integrative 
      browser called iSMOD (image-based Single-cell Multi-omics Database) to collect 
      and browse comprehensive FISH and nucleus proteomics data based on the title, 
      abstract, and related experimental figures, which integrates multi-omics studies 
      focusing on the key players in the cell nucleus from 20 000+ (still growing) 
      published papers. We have also provided several exemplar demonstrations to show 
      iSMOD's wide applications-profiling multi-omics research to reveal the molecular 
      target for diseases; exploring the working mechanism behind biological phenomena 
      using multi-omics interactions, and integrating the 3D multi-omics data in a 
      virtual cell nucleus. iSMOD is a cornerstone for delineating a global view of 
      relevant research to enable the integration of scattered data and thus provides 
      new insights regarding the missing components of molecular pathway mechanisms and 
      facilitates improved and efficient scientific research.
CI  - (c) The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic 
      Acids Research.
FAU - Zhang, Weihang
AU  - Zhang W
AUID- ORCID: 0000-0003-3717-9473
AD  - Department of Automation, Tsinghua University, Beijing 100084, China.
FAU - Suo, Jinli
AU  - Suo J
AD  - Department of Automation, Tsinghua University, Beijing 100084, China.
AD  - Institute of Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, 
      China.
AD  - Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China.
FAU - Yan, Yan
AU  - Yan Y
AD  - MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist; Center for 
      Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China.
AD  - School of Medicine, Tsinghua University, Beijing 100084, China.
FAU - Yang, Runzhao
AU  - Yang R
AD  - Department of Automation, Tsinghua University, Beijing 100084, China.
FAU - Lu, Yiming
AU  - Lu Y
AD  - Department of Automation, Tsinghua University, Beijing 100084, China.
FAU - Jin, Yiqi
AU  - Jin Y
AD  - Department of Automation, Tsinghua University, Beijing 100084, China.
FAU - Gao, Shuochen
AU  - Gao S
AD  - Department of Automation, Tsinghua University, Beijing 100084, China.
FAU - Li, Shao
AU  - Li S
AUID- ORCID: 0000-0002-8709-9167
AD  - Department of Automation, Tsinghua University, Beijing 100084, China.
AD  - MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist; Center for 
      Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China.
FAU - Gao, Juntao
AU  - Gao J
AD  - MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist; Center for 
      Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China.
AD  - School of Medicine, Tsinghua University, Beijing 100084, China.
FAU - Zhang, Michael
AU  - Zhang M
AD  - MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist; Center for 
      Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China.
AD  - School of Medicine, Tsinghua University, Beijing 100084, China.
FAU - Dai, Qionghai
AU  - Dai Q
AD  - Department of Automation, Tsinghua University, Beijing 100084, China.
AD  - Institute of Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, 
      China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
SB  - IM
MH  - *Proteomics
MH  - *Multiomics
MH  - In Situ Hybridization, Fluorescence
MH  - Genomics/methods
MH  - Gene Expression Profiling
PMC - PMC10484677
EDAT- 2023/07/13 12:31
MHDA- 2023/09/11 06:43
PMCR- 2023/07/13
CRDT- 2023/07/13 06:39
PHST- 2023/06/26 00:00 [accepted]
PHST- 2023/06/09 00:00 [revised]
PHST- 2022/11/23 00:00 [received]
PHST- 2023/09/11 06:43 [medline]
PHST- 2023/07/13 12:31 [pubmed]
PHST- 2023/07/13 06:39 [entrez]
PHST- 2023/07/13 00:00 [pmc-release]
AID - 7223586 [pii]
AID - gkad580 [pii]
AID - 10.1093/nar/gkad580 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2023 Sep 8;51(16):8348-8366. doi: 10.1093/nar/gkad580.