Joint Analysis of Microbial and Immune Cell Abundance in Liver Cancer Tissue Using a Gene Expression Profile Deconvolution Algorithm Combined With Foreign Read Remapping

Recent transcriptomics and metagenomics studies showed that tissue-infiltrating immune cells and bacteria interact with cancer cells to shape oncogenesis. This interaction and its effects remain to be elucidated. However, it is technically difficult to co-quantify immune cells and bacteria in their...

Full description

Bibliographic Details
Main Authors:	Dongmei Ai, Yonglian Xing, Qingchuan Zhang, Yishu Wang, Xiuqin Liu, Gang Liu, Li C. Xia
Format:	Article
Language:	English
Published:	Frontiers Media S.A. 2022-04-01
Series:	Frontiers in Immunology
Subjects:	tumor microenvironment RNA-seq gene expression profiling support vector regression particle swarm algorithm
Online Access:	https://www.frontiersin.org/articles/10.3389/fimmu.2022.853213/full

Similar Items

REMAP
by: Mhishi, L, et al.
Published: (2022)

Deconvolution at the single-cell level reveals ovarian cell-type-specific transcriptomic changes in PCOS
by: Shumin Li, et al.
Published: (2024-02-01)

HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD)
by: Yen-Jung Chiu, et al.
Published: (2023-10-01)

Forward single‐cell sequencing into clinical application: Understanding of cancer microenvironment at single‐cell solution
by: Xuanqi Liu, et al.
Published: (2022-06-01)

Regularized survival learning and cross-database analysis enabled identification of colorectal cancer prognosis-related immune genes
by: Dongmei Ai, et al.
Published: (2023-02-01)

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
by: Francesca Finotello, et al.
Published: (2019-05-01)

Combining single-cell sequencing and spatial transcriptome sequencing to identify exosome-related features of glioblastoma and constructing a prognostic model to identify BARD1 as a potential therapeutic target for GBM patients
by: Songyun Zhao, et al.
Published: (2023-08-01)

Deconvolution of bulk RNA sequencing in activated phosphoinositide 3‐kinase δ syndrome
by: Xia Huang, et al.
Published: (2023-11-01)

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer
by: Kie Kyon Huang, et al.
Published: (2021-01-01)

Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas
by: Shaoshi Zhang, et al.
Published: (2022-12-01)

Saccadic Remapping in Hemianopia
by: K L Ritchie, et al.
Published: (2011-04-01)

Integrating Bulk and Single-Cell RNA Sequencing Reveals Heterogeneity, Tumor Microenvironment, and Immunotherapeutic Efficacy Based on Sialylation-Related Genes in Bladder Cancer
by: Tan Z, et al.
Published: (2023-08-01)

Blind Deconvolution Based on Correlation Spectral Negentropy for Bearing Fault
by: Tian Tian, et al.
Published: (2023-03-01)

Towards reproducible research in recurrent pregnancy loss immunology: Learning from cancer microenvironment deconvolution
by: Martina Betti, et al.
Published: (2023-02-01)

EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data
by: Andrew E. Teschendorff, et al.
Published: (2020-09-01)

HiTIMED: hierarchical tumor immune microenvironment epigenetic deconvolution for accurate cell type resolution in the tumor microenvironment using tumor-type-specific DNA methylation data
by: Ze Zhang, et al.
Published: (2022-11-01)

Unraveling the complexity: understanding the deconvolutions of RNA-seq data
by: Kavoos Momeni, et al.
Published: (2023-09-01)

The Application of Single-Cell RNA Sequencing in the Inflammatory Tumor Microenvironment
by: Jiayi Zhao, et al.
Published: (2023-02-01)

Advances in single-cell RNA sequencing and its applications in cancer research
by: Dezhi Huang, et al.
Published: (2023-08-01)

Integrating microarray-based spatial transcriptomics and single-cell RNA-sequencing reveals tissue architecture in esophageal squamous cell carcinoma
by: Wei Guo, et al.
Published: (2022-10-01)

Single-nucleus RNA sequencing reveals heterogenous microenvironments and specific drug response between cervical squamous cell carcinoma and adenocarcinomaResearch in context
by: Shitong Lin, et al.
Published: (2023-11-01)

Comparative immunological landscape between pre- and early-stage LUAD manifested as ground-glass nodules revealed by scRNA and scTCR integrated analysis
by: Ziqi Wang, et al.
Published: (2023-11-01)

Single-cell RNA-seq analysis and cell-cluster deconvolution of the human preovulatory follicular fluid cells provide insights into the pathophysiology of ovarian hyporesponse
by: Kristine Roos, et al.
Published: (2022-10-01)

Single-cell analyses reveal cannabidiol rewires tumor microenvironment via inhibiting alternative activation of macrophage and synergizes with anti-PD-1 in colon cancer
by: Xiaofan Sun, et al.
Published: (2023-07-01)

Single‐cell analyses reveal suppressive tumor microenvironment of human colorectal cancer
by: Yan Mei, et al.
Published: (2021-06-01)

Abundance, viability and diversity of the indigenous microbial populations at different depths of the NEEM Greenland ice core
by: Vanya Miteva, et al.
Published: (2015-02-01)

Students’ reading interest in biology learning model based on remap CIRC, GI and TGT
by: Nur Hayati, et al.
Published: (2020-10-01)

Deconvoluting virome-wide antibody epitope reactivity profiles
by: Daniel R. Monaco, et al.
Published: (2022-01-01)

Remapping the rise of the European novel
Published: (2017)

Architecture for wayfinding : remapping the city /
by: Naadiya Hani Mokhtar, 1986-, et al.
Published: (2010)

Beyond Topography: Remapping Appalachia
by: Koskey, Katherine
Published: (2023)

Sounds are remapped across saccades
by: Martin Szinte, et al.
Published: (2020-12-01)

Brain Circuit Remapping in Blind
by: Sonya Arshad, et al.
Published: (2018-10-01)

Remap Numbered Heads Together (Remap-NHT) Influence on Collaboration Skill of Students in Biology Lesson
by: Husna Nur Wanah, et al.
Published: (2020-06-01)

Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias
by: Shuhua Zhan, et al.
Published: (2021-04-01)

Alignment and mapping methodology influence transcript abundance estimation
by: Avi Srivastava, et al.
Published: (2020-09-01)

A Novel Fault Diagnosis Method of Gearbox Based on Maximum Kurtosis Spectral Entropy Deconvolution
by: Zhijian Wang, et al.
Published: (2019-01-01)

Single-cell RNA-sequencing data reveals the genetic source of extracellular vesicles in esophageal squamous cell carcinoma
by: Bolun Zhou, et al.
Published: (2023-06-01)

Forward single‐cell sequencing into clinical application: Understanding of ageing and rejuvenation from clinical observation to single‐cell solution
by: Furong Yan, et al.
Published: (2022-06-01)

Single-Cell Profiling of Tumor Microenvironment Heterogeneity in Osteosarcoma Identifies a Highly Invasive Subcluster for Predicting Prognosis
by: Junfeng Guo, et al.
Published: (2022-04-01)