CIEC: Cross-tissue Immune Cell Type Enrichment and Expression Map Visualization for Cancer.

Autor:	He J; Central Laboratory, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China., Luo H; Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd, Shenzhen 518081, China., Wang W; Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd, Shenzhen 518081, China., Bu D; Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China., Zou Z; School of Management, Beijing University of Chinese Medicine, Beijing 100029, China., Wang H; School of Management, Beijing University of Chinese Medicine, Beijing 100029, China., Tang H; Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd, Shenzhen 518081, China., Han Z; Central Laboratory, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China., Luo W; Central Laboratory, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China., Shen J; Central Laboratory, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China., Xie F; Central Laboratory, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China., Zhao Y; Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China., Xiang Z; Central Laboratory, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China.
Jazyk:	angličtina
Zdroj:	Genomics, proteomics & bioinformatics [Genomics Proteomics Bioinformatics] 2024 Oct 03. Date of Electronic Publication: 2024 Oct 03.
DOI:	10.1093/gpbjnl/qzae067
Abstrakt:	Single-cell transcriptome sequencing technology has been applied to decode the cell types and functional states of immune cells, revealing their tissue-specific gene expression patterns and functions in cancer immunity. Comprehensive assessments of immune cells within and across tissues will provide us with a deeper understanding of the tumor immune system in general. Here, we present Cross-tissue Immune cell type or state Enrichment analysis of gene lists for Cancer (CIEC), the first web-based application that integrates database and enrichment analysis to estimate the cross-tissue immune cell type or state. CIEC version 1.0 consists of 480 samples covering primary tumor, adjacent normal tissue, lymph node, metastasis tissue, and peripheral blood from 323 cancer patients. By applying integrative analysis, we constructed an immune cell-type/state map for each context and adopted our previously developed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology Based Annotation System (KOBAS) algorithm to estimate the enrichment for context-specific immune cell type/state. In addition, CIEC also provides an easy-to-use online interface for users to comprehensively analyze the immune cell characteristics mapped across multiple tissues, including expression map, correlation, similar genes detection, signature score, and expression comparison. We believe that CIEC will be a valuable resource for exploring the intrinsic characteristics of immune cells in cancer patients and for potentially guiding novel cancer-immune biomarker development and immunotherapy strategies. CIEC is freely accessible at http://ciec.gene.ac/. (© The Author(s) 2024. Published by Oxford University Press and Science Press on behalf of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.)
Databáze:	MEDLINE
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