文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期,新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

因果CCC:一个用于探索细胞间通讯的细胞内因果途径的网络服务器。

CausalCCC: a web server to explore intracellular causal pathways enabling cell-cell communication.

作者信息

Dupuis Louise, Debeaupuis Orianne, Simon Franck, Isambert Hervé

机构信息

CNRS UMR168, Institut Curie, 75005 Paris, France.

Inserm U1163, Institut Imagine, 75005 Paris, France.

出版信息

Nucleic Acids Res. 2025 Jul 7;53(W1):W125-W131. doi: 10.1093/nar/gkaf404.


DOI:10.1093/nar/gkaf404
PMID:40366019
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12230657/
Abstract

Understanding cell-cell communication (CCC) pathways from single-cell or spatial transcriptomic data is key to unraveling biological processes. Recently, multiple CCC methods have been developed but primarily focus on refining ligand-receptor (L-R) interaction scores. A critical gap for a more comprehensive picture of cellular crosstalks lies in the integration of upstream and downstream intracellular pathways in the sender and receiver cells. We report here CausalCCC, https://miic.curie.fr/causalCCC.php, an interactive web server, which addresses this need by reconstructing gene-gene interaction pathways across two or more interacting cell types from single-cell or spatial transcriptomic data. CausalCCC includes a graphical introduction and a demo dataset within the workbench page as well as a comprehensive tutorial. CausalCCC methodology integrates a robust and scalable causal network reconstruction method, multivariate information-based inductive causation, with internally computed L-R pairs using LIANA+ (including CellphoneDBv5, SingleCellSignalR, Connectome, NATMI, and Log2FC). Alternatively, user-defined L-R pairs from any CCC methods can also be uploaded. We showcase here CausalCCC on different single-cell and spatial transcriptomic datasets from three original CCC methods (NicheNet, CellChat, and Misty). CausalCCC web server offers unique interactive visualization tools dedicated to single-cell data practitioners seeking to go beyond L-R scores and explore extended CCC pathways across multiple interacting cell types.

摘要

从单细胞或空间转录组数据中理解细胞间通信(CCC)途径是揭示生物学过程的关键。最近,已经开发了多种CCC方法,但主要集中在优化配体-受体(L-R)相互作用得分上。对于更全面了解细胞间串扰而言,一个关键差距在于整合发送细胞和接收细胞中上游和下游细胞内途径。我们在此报告CausalCCC,网址为https://miic.curie.fr/causalCCC.php,这是一个交互式网络服务器,它通过从单细胞或空间转录组数据中重建两种或更多相互作用细胞类型之间的基因-基因相互作用途径来满足这一需求。CausalCCC在工作台页面中包括图形介绍和演示数据集以及全面的教程。CausalCCC方法将一种强大且可扩展的因果网络重建方法——基于多变量信息的归纳因果关系,与使用LIANA+(包括CellphoneDBv5、SingleCellSignalR、Connectome、NATMI和Log2FC)内部计算的L-R对相结合。或者,也可以上传来自任何CCC方法的用户定义L-R对。我们在此展示了CausalCCC在来自三种原始CCC方法(NicheNet、CellChat和Misty)的不同单细胞和空间转录组数据集上的应用。CausalCCC网络服务器为寻求超越L-R得分并探索多种相互作用细胞类型之间扩展CCC途径的单细胞数据从业者提供了独特的交互式可视化工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/f8d122a44c61/gkaf404fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/9b830b855640/gkaf404figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/d345a326373d/gkaf404fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/fcfcc2f291d4/gkaf404fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/5355a46ad778/gkaf404fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/f8d122a44c61/gkaf404fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/9b830b855640/gkaf404figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/d345a326373d/gkaf404fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/fcfcc2f291d4/gkaf404fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/5355a46ad778/gkaf404fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a6e/12230657/f8d122a44c61/gkaf404fig4.jpg

相似文献

[1]
CausalCCC: a web server to explore intracellular causal pathways enabling cell-cell communication.

Nucleic Acids Res. 2025-7-7

[2]
Cost-effectiveness of using prognostic information to select women with breast cancer for adjuvant systemic therapy.

Health Technol Assess. 2006-9

[3]
Assessing the comparative effects of interventions in COPD: a tutorial on network meta-analysis for clinicians.

Respir Res. 2024-12-21

[4]
Comparison of Two Modern Survival Prediction Tools, SORG-MLA and METSSS, in Patients With Symptomatic Long-bone Metastases Who Underwent Local Treatment With Surgery Followed by Radiotherapy and With Radiotherapy Alone.

Clin Orthop Relat Res. 2024-12-1

[5]
Signs and symptoms to determine if a patient presenting in primary care or hospital outpatient settings has COVID-19.

Cochrane Database Syst Rev. 2022-5-20

[6]
Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data.

Nat Commun. 2025-7-1

[7]
Antidepressants for pain management in adults with chronic pain: a network meta-analysis.

Health Technol Assess. 2024-10

[8]
Technological aids for the rehabilitation of memory and executive functioning in children and adolescents with acquired brain injury.

Cochrane Database Syst Rev. 2016-7-1

[9]
Falls prevention interventions for community-dwelling older adults: systematic review and meta-analysis of benefits, harms, and patient values and preferences.

Syst Rev. 2024-11-26

[10]
A rapid and systematic review of the clinical effectiveness and cost-effectiveness of paclitaxel, docetaxel, gemcitabine and vinorelbine in non-small-cell lung cancer.

Health Technol Assess. 2001

本文引用的文献

[1]
collectNET: a web server for integrated inference of cell-cell communication network.

Database (Oxford). 2024-9-16

[2]
LIANA+ provides an all-in-one framework for cell-cell communication inference.

Nat Cell Biol. 2024-9

[3]
Learning interpretable causal networks from very large datasets, application to 400,000 medical records of breast cancer patients.

iScience. 2024-4-16

[4]
Adipose tissue-derived exosomes alleviate particulate matter-induced inflammatory response and skin barrier damage in atopic dermatitis-like triple-cell model.

PLoS One. 2024

[5]
The diversification of methods for studying cell-cell interactions and communication.

Nat Rev Genet. 2024-6

[6]
CellCommuNet: an atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states.

Nucleic Acids Res. 2024-1-5

[7]
TALKIEN: crossTALK IntEraction Network. A web-based tool for deciphering molecular communication through ligand-receptor interactions.

Mol Omics. 2023-10-30

[8]
exFINDER: identify external communication signals using single-cell transcriptomics data.

Nucleic Acids Res. 2023-6-9

[9]
Screening cell-cell communication in spatial transcriptomics via collective optimal transport.

Nat Methods. 2023-2

[10]
CommPath: An R package for inference and analysis of pathway-mediated cell-cell communication chain from single-cell transcriptomics.

Comput Struct Biotechnol J. 2022-10-26

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索