bioconductor: TCGAbiolinks | Projects

10.18632/aging.103809

Landscape of transcription and expression regulated by DNA methylation related to age of donor and cell passage in adipose-derived mesenchymal stem cells
Cited by: 3
Author(s): Guan-Ming Lu, Yong-Xian Rong, Zheng Liang, Dong-Lin Hunag, Yuju Ma, Zhizhai Luo, Fengyao Wu, Xinheng Liu, Yu Liu, Steven Mo, Zhongquan Qi, Hong-Mian Li
Software Mentions: 5
Published: about 4 years ago

10.3389/fgene.2021.649619

Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer
Cited by: 21
Author(s): Anshika Chowdhary, Venkata Satagopam, Reinhard Schneider
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.670240

IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme
Cited by: 6
Author(s): Manasa Kalya, Alexander Kel, Darius Wlochowitz, Edgar Wingender, Tim Beißbarth
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.11321

Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis
Cited by: 5
Author(s): Di Zhang, Pengguang Yan, Tian Han, Xiaoyun Cheng, Jingnan Li
Software Mentions: 5
Published: over 3 years ago

10.1016/j.tranon.2021.101107

3D heterospecies spheroids of pancreatic stroma and cancer cells demonstrate key phenotypes of pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Xinyuan Liu, Beate Gündel, Xidan Li, Jianping Liu, Andrew N. Wright, Matthias Löhr, Gustav Arvidsson, Rainer Heuchel
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2020.00680

Identification of a Six-Immune-Related Long Non-coding RNA Signature for Predicting Survival and Immune Infiltrating Status in Breast Cancer
Cited by: 24
Author(s): Zheng Li, Yaming Li, Xiaolong Wang
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2020.610704

Investigation on Potential Correlation Between Small Nuclear Ribonucleoprotein Polypeptide A and Lung Cancer
Cited by: 6
Author(s): Maoxi Yuan, Chunxiao Yu, Xin Chen, Yubing Wu
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41419-021-03450-z

ECT2 overexpression promotes the polarization of tumor-associated macrophages in hepatocellular carcinoma via the ECT2/PLK1/PTEN pathway
Cited by: 26
Author(s): Dafeng Xu, Yu Wang, Junzhen Wu, Zhensheng Zhang, Jiacheng Chen, Mingwei Xie, Rong Tang, Cheng Chen, Liang Chen, Shaomin Lin, Xiangxiang Luo, Jinfang Zheng
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2021.663787

Integrated Analysis of Microarray and RNA-Seq Data for the Identification of Hub Genes and Networks Involved in the Pancreatic Cancer
Cited by: 10
Author(s): Maryum Nisar, Rehan Zafar Paracha, Iqra Arshad, Sidra Adil, Sabaoon Zeb, Rumeza Hanif, Mehak Rafiq, Zamir Hussain
Software Mentions: 5
Published: over 3 years ago

10.1186/s12920-021-00905-2

Bioinformatic analysis reveals an exosomal miRNA-mRNA network in colorectal cancer
Cited by: 17
Author(s): Jun Ma, Peilong Wang, Lei Huang, Jianxia Qiao, Jianhong Li
Software Mentions: 5
Published: over 3 years ago

10.3389/fonc.2019.01497

Identification of Distinct Immune Subtypes in Colorectal Cancer Based on the Stromal Compartment
Cited by: 27
Author(s): Rongfang Shen, Ping Li, Bing Li, Botao Zhang, Feng Li, Shujun Cheng
Software Mentions: 5
Published: almost 5 years ago

10.1093/bioinformatics/btx099

DeepBlueR: large-scale epigenomic analysis in R
Cited by: 6
Author(s): Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-34160-w

Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data
Cited by: 72
Author(s): Yin Li, Jie Gu, Fan Xu, Qinqing Zhu, Di Ge
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.63093

MITF reprograms the extracellular matrix and focal adhesion in melanoma
Cited by: 42
Author(s): Ramile Dilshat, Valerie Fock, Colin Kenny, Ilse Gerritsen, Romain Lasseur, Jana Trávníčková, Ossia M. Eichhoff, Philipp Cerny, Katrín Möller, Sara Sigurbjörnsdóttir, Kritika Kirty, Berglind O. Einarsdottir, Phil F. Cheng, Mitchell P. Levesque, Robert A. Cornell, E. Elizabeth Patton, Lionel Larue, Marie de Tayrac, Erna Magnúsdóttir, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 5
Published: almost 4 years ago

10.3389/fphar.2021.616529

Systematic Investigation of DNA Methylation Associated With Platinum Chemotherapy Resistance Across 13 Cancer Types
Cited by: 4
Author(s): Ruizheng Sun, Chao Du, Jiaxin Li, Yanhong Zhou, Xiong Wang, Juanjuan Xiang, Jiheng Liu, Zhifeng Xiao, Fang Li, Li Zheng
Software Mentions: 5
Published: over 3 years ago

10.1093/bioinformatics/btaa613

Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers
Cited by: 19
Author(s): Mingzhou Song, Hua Zhong
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-018-23195-8

Personalised drug repositioning for Clear Cell Renal Cell Carcinoma using gene expression
Cited by: 13
Author(s): Karel K.M. Koudijs, Anton G.T. Terwisscha van Scheltinga, Stefan Böhringer, Kirsten J. M. Schimmel, Henk‐Jan Guchelaar
Software Mentions: 5
Published: over 6 years ago

10.1186/s12935-020-01670-5

Development and validation of a VHL-associated immune prognostic signature for clear cell renal cell carcinoma
Cited by: 10
Author(s): Jin Zhang, Aiting Yan, Weimin Cao, Honglei Shi, Kai Cao, Xiaowu Liu
Software Mentions: 5
Published: almost 4 years ago

10.7150/jca.44436

DNA methylation profiling to predict overall survival risk in gastric cancer: development and validation of a nomogram to optimize clinical management
Cited by: 7
Author(s): Xianxiong Ma, Hengyu Chen, Guobin Wang, Lei Li, Kaixiong Tao
Software Mentions: 4
Published: almost 5 years ago

10.18632/aging.102766

Screening and identification of genes associated with cell proliferation in cholangiocarcinoma
Cited by: 1
Author(s): Li Guo, Yaodong Zhang, Zibo Yin, Yaya Ji, Guowei Yang, Bowen Qian, Sunjing Li, Jun Wang, Tingming Liang, Changxian Li, Xiangcheng Li
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12920-020-00749-2

Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression
Cited by: 6
Author(s): Damien Kaukonen, Riina Kaukonen, Lélia Polit, Bryan T. Hennessy, Riikka Lund, Stephen F. Madden
Software Mentions: 4
Published: over 4 years ago

10.1155/2019/5437531

Long Noncoding RNA ASB16-AS1 Promotes Proliferation, Migration, and Invasion in Glioma Cells
Cited by: 26
Author(s): Delong Zhang, Huanggui Zhou, Jun Liu, Jie Mao
Software Mentions: 4
Published: over 5 years ago

10.1002/cam4.3035

Develop a circular RNA–related regulatory network associated with prognosis of gastric cancer
Cited by: 9
Author(s): Shuxun Wei, Shang‐Hua Teng, Jun Yao, Wenchao Gao, Jiachen Zang, Guangyong Wang, Zhiqian Hu
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.6509

cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer
Cited by: 1
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1006938

Comparative transcriptomes of adenocarcinomas and squamous cell carcinomas reveal molecular similarities that span classical anatomic boundaries
Cited by: 37
Author(s): Eric W. Lin, Tatiana A. Karakasheva, Dong Jin Lee, Ju-Seog Lee, Qi Long, Adam J. Bass, Kwok Kin Wong, Anil K. Rustgi
Software Mentions: 4
Published: over 7 years ago

10.3390/cancers12092543

CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas
Cited by: 4
Author(s): Ju Won Ahn, Young Joon Park, Su Jung Kang, So Jung Hwang, Kyung Gi Cho, Jaejoon Lim, KyuBum Kwack
Software Mentions: 4
Published: about 4 years ago

10.3390/cancers12040963

Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington’s Disease
Cited by: 14
Author(s): Müge Yalçin, Rukeia El-Athman, Koliane Ouk, Josef Priller, Angela Relógio
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers12082210

Human FBXL8 Is a Novel E3 Ligase Which Promotes BRCA Metastasis by Stimulating Pro-Tumorigenic Cytokines and Inhibiting Tumor Suppressors
Cited by: 10
Author(s): Shu Chun Chang, Wei‐Hsiu Hsu, Emily Chia Yu Su, Chin Sheng Hung, Jeak Ling Ding
Software Mentions: 4
Published: over 4 years ago

10.3390/cells10071821

Plasma Metabolome Profiling Identifies Metabolic Subtypes of Pancreatic Ductal Adenocarcinoma
Cited by: 8
Author(s): Ujjwal Mukund Mahajan, Ahmed Alnatsha, Qi Li, Bettina Oehrle, Florian Weiß, Matthias Sendler, Marius Distler, Waldemar Uhl, Tim Fahlbusch, Elisabetta Goni, Georg Beyer, Ansgar M. Chromik, M. Bahra, Fritz Klein, Christian Pilarsky, Robert Grützmann, Markus M. Lerch, Kirsten Lauber, Nicole Christiansen, Beate Kamlage, Ivonne Regel, Julia Mayerle
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-021-02499-y

Modeling the effects of EMT-immune dynamics on carcinoma disease progression
Cited by: 2
Author(s): Daniel Bergman, Matthew Karikomi, Min Yu, Qing Nie, Adam L. MacLean
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.659788

RNA-Associated Co-expression Network Identifies Novel Biomarkers for Digestive System Cancer
Cited by: 7
Author(s): Zheng Chen, Zijie Shen, Zilong Zhang, Zhao Da, Lei Xu, Lijun Zhang
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2018.00682

Embedding of Genes Using Cancer Gene Expression Data: Biological Relevance and Potential Application on Biomarker Discovery
Cited by: 26
Author(s): Chi Tung Choy, Chi Hang Wong, Stephen L. Chan
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2021.667875

TNF-Alpha Pathway Alternation Predicts Survival of Immune Checkpoint Inhibitors in Non-Small Cell Lung Cancer
Cited by: 9
Author(s): Anqi Lin, Hongman Zhang, Hua Meng, Ze Deng, Tianqi Gu, Peng Luo, Jian Zhang
Software Mentions: 4
Published: about 3 years ago

10.3389/fimmu.2021.676922

DNA Damage Repair Status Predicts Opposite Clinical Prognosis Immunotherapy and Non-Immunotherapy in Hepatocellular Carcinoma
Cited by: 11
Author(s): Yunfei Chen, Wei Xu, Xiaofang Deng, Yu Zhang, Rui Liao, Youzan Li, Hongji Yang, Kai Chen
Software Mentions: 4
Published: over 3 years ago

10.3389/fmolb.2021.706949

CD74 Correlated With Malignancies and Immune Microenvironment in Gliomas
Cited by: 11
Author(s): Shengchao Xu, Xizhe Li, Lu Tang, Zhixiong Liu, Kui Yang, Quan Cheng
Software Mentions: 4
Published: about 3 years ago

10.3389/fneur.2021.576382

Potential Molecular Mechanism of TNF Superfamily-Related Genes in Glioblastoma Multiforme Based on Transcriptome and Epigenome
Cited by: 6
Author(s): Hui Xie, Ce Yuan, Jinjiang Li, Zhaoyang Li, Wei-Cheng Lu
Software Mentions: 4
Published: almost 4 years ago

10.3389/fonc.2020.00846

LPAR1, Correlated With Immune Infiltrates, Is a Potential Prognostic Biomarker in Prostate Cancer
Cited by: 50
Author(s): Jingqi Shi, Duyin Jiang, Shuya Yang, Xiyang Zhang, Jing Wang, Yang Liu, Yuanjie Sun, You Lu, Kun Yang
Software Mentions: 4
Published: over 4 years ago

10.3389/fonc.2021.636461

Identification of Early Diagnostic and Prognostic Biomarkers via WGCNA in Stomach Adenocarcinoma
Cited by: 21
Author(s): Ruoyue Tan, Guanghui Zhang, Ruochen Liu, Jingyao Hou, Zhen Dong, Chaowei Deng, Sicheng Wan, Xiaodong Liu, Hongjuan Cui
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2021.744951

The Landscape of Immune Cells Indicates Prognosis and Applicability of Checkpoint Therapy in Hepatocellular Carcinoma
Cited by: 7
Author(s): Jiacheng Huang, Lele Zhang, Jianxiang Chen, Dalong Wan, Lin Zhou, Shusen Zheng, Yiting Qiao
Software Mentions: 4
Published: about 3 years ago

10.3389/fonc.2021.737867

Genomic Instability-Related LncRNA Signature Predicts the Prognosis and Highlights LINC01614 Is a Tumor Microenvironment-Related Oncogenic lncRNA of Papillary Thyroid Carcinoma
Cited by: 6
Author(s): Xubin Dong, Cong Jin, Danxiang Chen, Yizuo Chen, Zhiqiang Ye, Xiaohua Zhang, Xiaoli Huang, Wei Zhang, Di Gu
Software Mentions: 4
Published: about 3 years ago

10.3389/fonc.2021.633899

High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma
Cited by: 7
Author(s): Xiaoqiang Du, Chen Zhang, Chuanzheng Yin, Wenjie Wang, Xueke Yan, Dawei Xie, Xichuan Zheng, Qi Zheng, Min Li, Zifang Song
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2021.552331

Computational Tumor Infiltration Phenotypes Enable the Spatial and Genomic Analysis of Immune Infiltration in Colorectal Cancer
Cited by: 1
Author(s): Henrik Failmezger, Natalie Zwing, Achim Tresch, Konstanty Korski, Fabian Schmich
Software Mentions: 4
Published: over 3 years ago

10.1186/s13073-021-00944-5

Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
Cited by: 10
Author(s): Emily F. Davis-Marcisak, Allison A. Fitzgerald, Michael Kessler, Ludmila Danilova, Elizabeth M. Jaffee, Neeha Zaidi, Louis M. Weiner, Elana J. Fertig
Software Mentions: 4
Published: over 3 years ago

10.1016/j.heliyon.2021.e06000

Unsupervised subtyping and methylation landscape of pancreatic ductal adenocarcinoma
Cited by: 9
Author(s): Shikha Roy, Amar Singh, Dinesh Gupta
Software Mentions: 4
Published: almost 4 years ago

10.1186/s41065-020-00165-7

Defining muscle-invasive bladder cancer immunotypes by introducing tumor mutation burden, CD8+ T cells, and molecular subtypes
Cited by: 9
Author(s): Zihao Chen, Guojun Liu, Mikhail A. Bolkov, Khyber Shinwari, Irina A. Tuzankina, V. А. Chereshnev, Zhifeng Wang
Software Mentions: 4
Published: almost 4 years ago

10.7150/jca.44413

Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration
Cited by: 17
Author(s): Pan Wang, Xinyu Zhang, Nan Sun, Zhihong Zhao, Jie He
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-018-36319-x

Low mutation and neoantigen burden and fewer effector tumor infiltrating lymphocytes correlate with breast cancer metastasization to lymph nodes
Cited by: 17
Author(s): Zhigang Wang, Wei Liu, Chong Chen, Xiaolin Yang, Yunping Luo, Bailin Zhang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13046-019-1403-9

IFN-gamma-induced PD-L1 expression in melanoma depends on p53 expression
Cited by: 93
Author(s): Alexander Thiem, Sonja Hesbacher, Hermann Kneitz, Teresa di Primio, Markus V. Heppt, Heike M. Hermanns, Matthias Goebeler, Svenja Meierjohann, Roland Houben, David Schrama
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms22031354

The Importance of Sex in the Discovery of Colorectal Cancer Prognostic Biomarkers
Cited by: 16
Author(s): Linnea Hases, Ahmed Atef Ibrahim, Xinsong Chen, Yanghong Liu, Johan Hartman, Cecilia Williams
Software Mentions: 4
Published: almost 4 years ago

10.3389/fphar.2021.645862

Catenin Alpha-2 Mutation Changes the Immune Microenvironment in Lung Adenocarcinoma Patients Receiving Immune Checkpoint Inhibitors
Cited by: 6
Author(s): Wen Yang, Anqi Lin, Wei Zhu, Ting Wei, Peng Luo, Linlang Guo, Jian Zhang
Software Mentions: 3
Published: over 3 years ago

10.15252/emmm.201911756

Cancer of Unknown Primary ( <scp>CUP</scp> ): genetic evidence for a novel nosological entity? A case report
Cited by: 8
Author(s): Silvia Benvenuti, Melissa Milan, Elena Geuna, Alberto Pisacane, Rebecca Senetta, Gennaro Gambardella, Giulia Maria Stella, Filippo Montemurro, Anna Sapino, Carla Boccaccio, Paolo M. Comoglio
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-96844-0

Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer
Cited by: 9
Author(s): Jean S. Fain, Axelle Loriot, Anna Diacofotaki, Aurélie Van Tongelen, Charles De Smet
Software Mentions: 3
Published: about 3 years ago

10.1038/s12276-021-00612-z

Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization
Cited by: 5
Author(s): Anders Berglund, Ryan M. Putney, Imène Hamaidi, Sungjune Kim
Software Mentions: 3
Published: over 3 years ago

10.3389/fmolb.2016.00078

The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer
Cited by: 32
Author(s): Mads Nygaard, Thilde Terkelsen, André Vidas Olsen, Valentina Sora, Juan Salamanca Viloria, Fabio Rizza, Sanne Bergstrand-Poulsen, Miriam Di Marco, Mette Vixø Vistesen, Matteo Tiberti, Matteo Lambrughi, Marja Jäättelä, Tuula Kallunki, Elena Papaleo
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13073-021-00888-w

Evaluating the transcriptional fidelity of cancer models
Cited by: 23
Author(s): Da Peng, Rachel Gleyzer, Wen Hsin Tai, Pavithra Kumar, Qin Bian, Bradley Isaacs, Edroaldo Lummertz da Rocha, Stephanie Cai, Kathleen T. DiNapoli, Franklin W. Huang, Patrick Cahan
Software Mentions: 3
Published: over 3 years ago

10.3389/fmolb.2020.565383

The Significance of Secreted Phosphoprotein 1 in Multiple Human Cancers
Cited by: 26
Author(s): Tengteng Wei, Guoshu Bi, Yunyi Bian, Suhong Ruan, Guangda Yuan, Haifeng Xie, Mengnan Zhao, Rongming Shen, Yimeng Zhu, Qun Wang, Yong Yang, Donglin Zhu
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers13040681

Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue
Cited by: 12
Author(s): Sara Terreri, Sara Mancinelli, Matteo Ferro, Maria Concetta Vitale, Sisto Perdoná, Luigi Castaldo, Vincenzo Gigantino, Vincenzo Mercadante, Rossella De Cecio, Gabriella Aquino, Marco Montella, Claudia Angelini, Eugenio Del Prete, Marianna Aprile, Angelo Ciaramella, Giovanna L. Liguori, Valerio Costa, George A. Calin, Evelina La Civita, Daniela Terracciano, Ferdinando Febbraio, Amelia Cimmino
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12967-020-02436-3

Presence of a 34-gene signature is a favorable prognostic marker in squamous non-small cell lung carcinoma
Cited by: 8
Author(s): Wendy Theelen, Oscar Krijgsman, Kim Monkhorst, Thomas Kuilman, Dennis Peters, Sten Cornelissen, Maarten A. Ligtenberg, Stefan M. Willems, J. L. G. Blaauwgeers, Carel J. M. van Noesel, Daniel S. Peeper, Michel M. van den Heuvel, Katja Schulze
Software Mentions: 3
Published: over 4 years ago

10.1042/BSR20204062

Exploring the mechanism of aidi injection for lung cancer by network pharmacology approach and molecular docking validation
Cited by: 4
Author(s): Zhenjie Zhuang, Tong Lin, Lixia Luo, Weixin Zhou, Junping Wen, Huayi Huang, Zhanhua Liu, Lizhu Lin
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12967-018-1535-2

In silico identification of drug target pathways in breast cancer subtypes using pathway cross-talk inhibition
Cited by: 22
Author(s): Claudia Cava, Gloria Bertoli, Isabella Castiglioni
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-71527-4

A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy
Cited by: 17
Author(s): Mukesh Kumar, Elena Papaleo
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1007485

Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level
Cited by: 38
Author(s): Simon Mathis Kønig, Vendela Rissler, Thilde Terkelsen, Matteo Lambrughi, Elena Papaleo
Software Mentions: 3
Published: almost 5 years ago

10.1186/s10020-020-00261-4

Inhibition of mitochondrial carrier homolog 2 (MTCH2) suppresses tumor invasion and enhances sensitivity to temozolomide in malignant glioma
Cited by: 6
Author(s): Qiuyun Yuan, Wanchun Yang, Shuxin Zhang, Tengfei Li, Mingrong Zuo, Xingwang Zhou, Junhong Li, Mao Li, Xiaoqiang Xia, Mina Chen, Yan‐Hui Liu
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers10110397

DNA Methylation Predicts the Response of Triple-Negative Breast Cancers to All-Trans Retinoic Acid
Cited by: 19
Author(s): Krysta M. Coyle, Cheryl A. Dean, Margaret Lois Thomas, Dejan Vidovic, Carman A. Giacomantonio, Lucy Helyer, Paola Marcato
Software Mentions: 3
Published: about 6 years ago

10.1038/s41416-020-01145-4

A balance score between immune stimulatory and suppressive microenvironments identifies mediators of tumour immunity and predicts pan-cancer survival
Cited by: 12
Author(s): Tolga Turan, Sarah Kongpachith, Kyle Halliwill, Jessica Roelands, Wouter Hendrickx, Francesco M. Marincola, Thomas J. Hudson, Howard J. Jacob, Davide Bedognetti, Josue Samayoa, Michele Ceccarelli
Software Mentions: 3
Published: about 4 years ago

10.1186/s40170-020-00225-6

Body mass index-associated molecular characteristics involved in tumor immune and metabolic pathways
Cited by: 3
Author(s): Chao Hu, Xiong Chen, Chengyun Yao, Yu Liu, Haojun Xu, Guoren Zhou, Hongping Xia, Jinglin Xia
Software Mentions: 3
Published: about 4 years ago

10.3390/cancers13010105

Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma Are Molecularly Distinct
Cited by: 6
Author(s): Alana Sorgini, Hugh Andrew Jinwook Kim, Peter YF. Zeng, M.A.Q. Shaikh, Neil Mundi, Farhad Ghasemi, Eric Di Gravio, Halema Khan, Danielle MacNeil, Michael A. Khan, Adrian Mendez, John Yoo, Kevin Fung, Pencilla Lang, Joe S. Mymryk, John W. Barrett, Krupal Patel, Paul C. Boutros, Anthony C. Nichols
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-06741-8

Porcine familial adenomatous polyposis model enables systematic analysis of early events in adenoma progression
Cited by: 22
Author(s): Tatiana Flisikowska, Monika Stachowiak, Hongen Xu, Alexandra Wagner, Alejandra Hernandez-Caceres, Christine Wurmser, Carolin Perleberg, Hubert Pausch, Anna Perkowska, Konrad Fischer, Dmitrij Frishman, R. Fries, M. Świtoński, Alexander Kind, Dieter Saur, Angelika Schnieke, Krzysztof Flisikowski
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-18132-0

IFNγ induces PD-L1 overexpression by JAK2/STAT1/IRF-1 signaling in EBV-positive gastric carcinoma
Cited by: 85
Author(s): Ji Wook Moon, Su Kang Kong, Byung Soo Kim, Hyun Ji Kim, Hyangsoon Lim, Kyeonga Noh, Younghye Kim, Jung Woo Choi, Ju Han Lee, Young Sik Kim
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-22771-2

Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A
Cited by: 12
Author(s): Muhammad Shahid, Nicole Gull, Austin Yeon, Eunho Cho, Jooeun Bae, Hee Yoon, Sungyong You, Hana Yoon, Minjung Kim, Benjamin P. Berman, Jayoung Kim
Software Mentions: 3
Published: over 6 years ago

10.1002/cam4.2833

Identification of three m6A‐related mRNAs signature and risk score for the prognostication of hepatocellular carcinoma
Cited by: 50
Author(s): Zedong Li, Fazhan Li, Pei Yu, Jianyu Fang, Jun Zhou
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-39891-y

The impact of estimated tumour purity on gene expression-based drug repositioning of Clear Cell Renal Cell Carcinoma samples
Cited by: 6
Author(s): Karel K.M. Koudijs, Anton G.T. Terwisscha van Scheltinga, Stefan Böhringer, Kirsten J. M. Schimmel, Henk‐Jan Guchelaar
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22052553

Comprehensive Analysis of Correlations in the Expression of miRNA Genes and Immune Checkpoint Genes in Bladder Cancer Cells
Cited by: 3
Author(s): Przemyslaw Stempor, Dror Avni, Raya Leibowitz, Yechezkel Sidi, Maria Stępień, Tomasz Dzieciątkowski, Paula Dobosz
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers12092713

Hormonal Receptor Status Determines Prognostic Significance of FGFR2 in Invasive Breast Carcinoma
Cited by: 9
Author(s): Marcin Braun, Dominika Piasecka, Bartłomiej Tomasik, Kamil Mieczkowski, Konrad Stawiski, Aleksandra Zielińska, Janusz Kopczyński, Dariusz Nejc, Radzisław Kordek, Rafał Sądej, Hanna Romańska
Software Mentions: 3
Published: about 4 years ago

10.1186/s12920-020-0658-5

DeepTRIAGE: interpretable and individualised biomarker scores using attention mechanism for the classification of breast cancer sub-types
Cited by: 20
Author(s): Adham Beykikhoshk, Thomas P. Quinn, Samuel C. Lee, Truyen Tran, Svetha Venkatesh
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12885-021-08777-6

ER expression associates with poor prognosis in male lung squamous carcinoma after radical resection
Cited by: 2
Author(s): Xue Yang, Xiangfeng Jin, Rongjian Xu, Zhuang Yu, Ning An
Software Mentions: 3
Published: about 3 years ago

10.1186/s12920-019-0501-z

Genes CEP55, FOXD3, FOXF2, GNAO1, GRIA4, and KCNA5 as potential diagnostic biomarkers in colorectal cancer
Cited by: 32
Author(s): Nina Hauptman, Daša Jevšinek Skok, Elena Spasovska, Emanuela Boštjančič, Damjan Glavač
Software Mentions: 3
Published: over 5 years ago

10.1136/jitc-2020-002115

MUC1-C integrates activation of the IFN-γ pathway with suppression of the tumor immune microenvironment in triple-negative breast cancer
Cited by: 35
Author(s): Nami Yamashita, Mark D. Long, Atsushi Fushimi, Masaaki Yamamoto, Tsuyoshi Hata, Masaru Hagiwara, Atrayee Bhattacharya, Qiang Hu, Kwok-Kin Wong, Song Liu, Donald Küfe
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-019-2739-z

Extracting predictors for lung adenocarcinoma based on Granger causality test and stepwise character selection
Cited by: 4
Author(s): Xuemeng Fan, Yaolai Wang, Xu-Qing Tang
Software Mentions: 3
Published: over 5 years ago

10.1186/s40360-020-00444-z

A protein interaction map identifies existing drugs targeting SARS-CoV-2
Cited by: 16
Author(s): Claudia Cava, Gloria Bertoli, Isabella Castiglioni
Software Mentions: 3
Published: about 4 years ago

10.1111/1759-7714.13497

Integrated analysis of <scp>miRNAs</scp> and <scp>DNA</scp> methylation identifies <scp>miR‐132‐3p</scp> as a tumor suppressor in lung adenocarcinoma
Cited by: 7
Author(s): Yun Su, Amol Shetty, Feng Jiang
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2021.630773

Effect of NCOR1 Mutations on Immune Microenvironment and Efficacy of Immune Checkpoint Inhibitors in Patient with Bladder Cancer
Cited by: 21
Author(s): Anqi Lin, Zhengang Qiu, Jian Zhang, Peng Luo
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.625452

A Glycolysis-Related Five-Gene Signature Predicts Biochemical Recurrence-Free Survival in Patients With Prostate Adenocarcinoma
Cited by: 13
Author(s): Zi‐jun Xu, Lijuan Xu, Liping Liu, Hai Li, Jiewen Jin, Miaoguan Peng, Yanrui Huang, Hang Xiao, Yanbing Li, Hongyu Guan
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.657531

Genomic Analysis of Glioblastoma Multiforme Reveals a Key Transcription Factor Signature Relevant to Prognosis and the Immune Processes
Cited by: 6
Author(s): Zhen-Hang Li, Yanlei Guan, Guobin Zhang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0255168

FFPE samples from cavitational ultrasonic surgical aspirates are suitable for RNA profiling of gliomas
Cited by: 2
Author(s): Cristina Alenda, Estefanía Rojas, Luis M. Valor
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.719355

Identification of a Prognostic Model Based on 2-Gene Signature and Analysis of Corresponding Tumor Microenvironment in Alcohol-Related Hepatocellular Carcinoma
Cited by: 1
Author(s): Yong Guo, Jie‐Jun Hu, Zhibo Zhang, Guo‐Chao Zhong, Jianping Gong, Dong Cai
Software Mentions: 3
Published: about 3 years ago

10.3390/cancers13112589

DNA Methylation Signatures and the Contribution of Age-Associated Methylomic Drift to Carcinogenesis in Early-Onset Colorectal Cancer
Cited by: 14
Author(s): Jihoon E. Joo, Mark Clendenning, Ee Ming Wong, Christophe Rosty, Khalid Mahmood, Peter Georgeson, Ingrid Winship, Susan Preston, Aung Ko Win, Pierre Antoine Dugué, Harindra Jayasekara, Dallas R. English, Finlay Macrae, John L. Hopper, Mark A. Jenkins, Roger L. Milne, Graham G. Giles, Melissa C. Southey, Daniel D. Buchanan
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.00418

Construction and Analysis of a ceRNA Network Reveals Potential Prognostic Markers in Colorectal Cancer
Cited by: 12
Author(s): Li Guo, Guowei Yang, Yihao Kang, Sunjing Li, Rui Duan, Lulu Shen, Wenwen Jiang, Bowen Qian, Zibo Yin, Tingming Liang
Software Mentions: 3
Published: over 4 years ago

10.3389/fonc.2020.00979

High Expression of FAP in Colorectal Cancer Is Associated With Angiogenesis and Immunoregulation Processes
Cited by: 42
Author(s): Mairene Coto‐Llerena, Caner Ercan, Venkatesh Kancherla, Stephanie Taha‐Mehlitz, Serenella Eppenberger‐Castori, Savas D. Soysal, Charlotte K.Y. Ng, Martin Bolli, Markus von Flüe, Guillaume Nicolas, Luigi Terracciano, Melpomeni Fani, Salvatore Piscuoglio
Software Mentions: 3
Published: over 4 years ago

10.1093/database/baz060

ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer
Cited by: 10
Author(s): Judith Pérez-Granado, Janet Piñero, Laura I. Furlong
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0241924

Identification of a 6-gene signature for the survival prediction of breast cancer patients based on integrated multi-omics data analysis
Cited by: 7
Author(s): Wenju Mo, Yuqin Ding, Shuai Zhao, Dayang Zou, Xiaowen Ding
Software Mentions: 3
Published: about 4 years ago

10.3390/cancers13092044

Multiregional Sequencing of IDH-WT Glioblastoma Reveals High Genetic Heterogeneity and a Dynamic Evolutionary History
Cited by: 4
Author(s): Sara Franceschi, Prospero Civita, Francesco Pasqualetti, Francesca Lessi, Martina Modena, Serena Barachini, Maria Sole Morelli, Orazio Santonocito, Riccardo Vannozzi, Geoffrey J. Pilkington, Valerio Ortenzi, Antonio Giuseppe Naccarato, Paolo Aretini, Chiara Maria Mazzanti
Software Mentions: 3
Published: over 3 years ago

10.3389/fphar.2020.572627

Identification of Mutations Related to Cisplatin-Resistance and Prognosis of Patients With Lung Adenocarcinoma
Cited by: 9
Author(s): Rui Li, Junfang Liu, Ze-Kui Fang, Zhenyu Liang, Xin Chen
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-021-97102-z

A ferroptosis-associated gene signature for the prediction of prognosis and therapeutic response in luminal-type breast carcinoma
Cited by: 3
Author(s): Yang Peng, Haochen Yu, Yingzi Zhang, Fanli Qu, Zhenrong Tang, Chi Qu, Jiao Tian, Beige Zong, Yu Wang, Haoyu Ren, Shengchun Liu
Software Mentions: 3
Published: about 3 years ago

10.3389/fgene.2020.555537

Screening and Identification of Potential Biomarkers in Hepatitis B Virus-Related Hepatocellular Carcinoma by Bioinformatics Analysis
Cited by: 10
Author(s): Xianchang Zeng, Lu Zhang, Wenjun Liao, Lu Ao, Zeman Lin, Wen Kong, Wan-Nan Chen, Xu Lin
Software Mentions: 3
Published: about 4 years ago

10.3390/cancers13040783

TAp73β Can Promote Hepatocellular Carcinoma Dedifferentiation
Cited by: 10
Author(s): Evin İşcan, Umut Ekin, Gökhan Yıldız, Özden Öz, Umur Keles, Aslı Süner, Gulcin Cakan-Akdogan, Günes Özhan, Marta Nekulová, Bořivoj Vojtěšek, Hamdiye Uzuner, Gökhan Karakülah, Hani Alotaibi, Mehmet Öztürk
Software Mentions: 2
Published: almost 4 years ago

10.3390/cancers13123045

Genome-Wide Transcriptomic Analysis of Non-Tumorigenic Tissues Reveals Aging-Related Prognostic Markers and Drug Targets in Renal Cell Carcinoma
Cited by: 7
Author(s): Euiyoung Oh, Jun-Hyeong Kim, JungIn Um, Dawoon Jung, Darren R. Williams, Hyunju Lee
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers13010126

Mutation of the Cell Cycle Regulator p27kip1 Drives Pseudohypoxic Pheochromocytoma Development
Cited by: 7
Author(s): Hermine Mohr, Simone Ballke, Nicole Bechmann, Sebastian Gulde, Jaber Malekzadeh-Najafabadi, Mirko Peitzsch, Vasilis Ntziachristos, Katja Steiger, Tobias Wiedemann, Natalia S. Pellegata
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms21218025

The P72R Polymorphism in R248Q/W p53 Mutants Modifies the Mutant Effect on Epithelial to Mesenchymal Transition Phenotype and Cell Invasion via CXCL1 Expression
Cited by: 4
Author(s): Cristabelle De Souza, Jill A. Madden, Dennis Minn, Vigneshwari Easwar Kumar, Dennis Montoya, R Nambiar, Zheng Zhu, Wenwu Xiao, Neeki Tahmassebi, Harikumara Kathi, Nina Nelson, Anthony N. Karnezis, Jeremy Chien
Software Mentions: 2
Published: about 4 years ago

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Papers Mentioning TCGAbiolinks 276