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https://www.readbyqxmd.com/read/29045694/machine-learning-approaches-to-decipher-hormone-and-her2-receptor-status-phenotypes-in-breast-cancer
#1
Emmanuel S Adabor, George K Acquaah-Mensah
Breast cancer prognosis and administration of therapies are aided by knowledge of hormonal and HER2 receptor status. Breast cancer lacking estrogen receptors, progesterone receptors and HER2 receptors are difficult to treat. Regarding large data repositories such as The Cancer Genome Atlas, available wet-lab methods for establishing the presence of these receptors do not always conclusively cover all available samples. To this end, we introduce median-supplement methods to identify hormonal and HER2 receptor status phenotypes of breast cancer patients using gene expression profiles...
October 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29039552/prospective-lncrna-mirna-mrna-regulatory-network-of-long-non-coding-rna-linc00968-in-non-small-cell-lung-cancer-a549-cells-a-mirna-microarray-and-bioinformatics-investigation
#2
Dong-Yao Li, Wen-Jie Chen, Lei Luo, Yong-Kun Wang, Jun Shang, Yu Zhang, Gang Chen, Shi-Kang Li
Accumulating evidence suggests that the dysregulation of long non-coding RNAs (lncRNAs) serves vital roles in the incidence and progression of lung cancer. However, the molecular mechanisms of LINC00968, a recently identified lncRNA, remain unknown. The objective of present study was to investigate the role of a prospective lncRNA-miRNA‑mRNA network regulated by LINC00968 in non-small cell lung cancer cells. Following the transfection of lentiviruses carrying LINC00968 into A549 cells, the microRNA (miRNA) expression profile of the cells in response to the overexpression of LINC00968 was detected using an miRNA microarray...
October 12, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29039502/long-non%C3%A2-coding-rna-hottip-promotes-hepatocellular-carcinoma-tumorigenesis-and-development-a-comprehensive-investigation-based-on-bioinformatics-qrt%C3%A2-pcr-and-meta%C3%A2-analysis-of-393-cases
#3
Yu Zhang, Jia-Cheng Huang, Kai-Teng Cai, Xi-Bing Yu, You-Rong Chen, Wen-Ya Pan, Ze-Liang He, Jun Lv, Zhen-Bo Feng, Gang Chen
HOTTIP functions as an independent biomarker in multiple cancers. However, the role of HOTTIP in hepatocellular carcinoma (HCC) remains unclear. In this study, we sought to investigate the HOTTIP expression in HCC and normal liver. We combined quantitative reverse transcription-polymerase chain reactions (qRT‑PCR), Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), Multi Experiment Matrix (MEM) and Oncomine database to assess the clinical role and the potential molecular mechanism of HOTTIP in HCC...
October 16, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29038551/a-novel-machine-learning-approach-reveals-latent-vascular-phenotypes-predictive-of-renal-cancer-outcome
#4
Nathan Ing, Fangjin Huang, Andrew Conley, Sungyong You, Zhaoxuan Ma, Sergey Klimov, Chisato Ohe, Xiaopu Yuan, Mahul B Amin, Robert Figlin, Arkadiusz Gertych, Beatrice S Knudsen
Gene expression signatures are commonly used as predictive biomarkers, but do not capture structural features within the tissue architecture. Here we apply a 2-step machine learning framework for quantitative imaging of tumor vasculature to derive a spatially informed, prognostic gene signature. The trained algorithms classify endothelial cells and generate a vascular area mask (VAM) in H&E micrographs of clear cell renal cell carcinoma (ccRCC) cases from The Cancer Genome Atlas (TCGA). Quantification of VAMs led to the discovery of 9 vascular features (9VF) that predicted disease-free-survival in a discovery cohort (n = 64, HR = 2...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29038488/mcm2-regulated-functional-networks-in-lung-cancer-by-multi-dimensional-proteomic-approach
#5
Chantal Hoi Yin Cheung, Chia-Lang Hsu, Kai-Pu Chen, Siao-Ting Chong, Chang-Hsun Wu, Hsuan-Cheng Huang, Hsueh-Fen Juan
DNA replication control is vital for maintaining genome stability and the cell cycle, perhaps most notably during cell division. Malignancies often exhibit defective minichromosome maintenance protein 2 (MCM2), a cancer proliferation biomarker that serves as a licensing factor in the initiation of DNA replication. MCM2 is also known to be one of the ATPase active sites that facilitates conformational changes and drives DNA unwinding at the origin of DNA replication. However, the biological networks of MCM2 in lung cancer cells via protein phosphorylation remain unmapped...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29036590/tissgdb-tissue-specific-gene-database-in-cancer
#6
Pora Kim, Aekyung Park, Guangchun Han, Hua Sun, Peilin Jia, Zhongming Zhao
Tissue-specific gene expression is critical in understanding biological processes, physiological conditions, and disease. The identification and appropriate use of tissue-specific genes (TissGenes) will provide important insights into disease mechanisms and organ-specific therapeutic targets. To better understand the tissue-specific features for each cancer type and to advance the discovery of clinically relevant genes or mutations, we built TissGDB (Tissue specific Gene DataBase in cancer) available at http://zhaobioinfo...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036324/pancanqtl-systematic-identification-of-cis-eqtls-and-trans-eqtls-in-33-cancer-types
#7
Jing Gong, Shufang Mei, Chunjie Liu, Yu Xiang, Youqiong Ye, Zhao Zhang, Jing Feng, Renyan Liu, Lixia Diao, An-Yuan Guo, Xiaoping Miao, Leng Han
Expression quantitative trait locus (eQTL) analysis, which links variations in gene expression to genotypes, is essential to understanding gene regulation and to interpreting disease-associated loci. Currently identified eQTLs are mainly in samples of blood and other normal tissues. However, no database comprehensively provides eQTLs in large number of cancer samples. Using the genotype and expression data of 9196 tumor samples in 33 cancer types from The Cancer Genome Atlas (TCGA), we identified 5 606 570 eQTL-gene pairs in the cis-eQTL analysis and 231 210 eQTL-gene pairs in the trans-eQTL analysis...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036320/detect-differentially-methylated-regions-using-non-homogeneous-hidden-markov-model-for-methylation-array-data
#8
Linghao Shen, Jun Zhu, Shuo-Yen Robert Li, Xiaodan Fan
Motivation: DNA methylation is an important epigenetic mechanism in gene regulation and the detection of differentially methylated regions (DMRs) is enthralling for many disease studies. There are several aspects that we can improve over existing DMR detection methods: (i) methylation statuses of nearby CpG sites are highly correlated, but this fact has seldom been modelled rigorously due to the uneven spacing; (ii) it is practically important to be able to handle both paired and unpaired samples; and (iii) the capability to detect DMRs from a single pair of samples is demanded...
July 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29034516/identifying-gene-gene-interactions-using-penalized-tensor-regression
#9
Mengyun Wu, Jian Huang, Shuangge Ma
Gene-gene (G×G) interactions have been shown to be critical for the fundamental mechanisms and development of complex diseases beyond main genetic effects. The commonly adopted marginal analysis is limited by considering only a small number of G factors at a time. With the "main effects, interactions" hierarchical constraint, many of the existing joint analysis methods suffer from prohibitively high computational cost. In this study, we propose a new method for identifying important G×G interactions under joint modeling...
October 16, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/29033587/dna-hypermethylated-status-and-gene-expression-of-pax1-sox1-in-patients-with-colorectal-carcinoma
#10
Jin Huang, Zhi-Rong Tan, Jing Yu, He Li, Qiao-Li Lv, Ying-Ying Shao, Hong-Hao Zhou
BACKGROUND: Colorectal cancer (CRC) is a widespread and aggressive carcinoma with poor prognosis. Hypermethylation of specific gene promoters is an important mechanism of CRC. In this study, we investigated the hypermethylation of paired boxed gene 1 (PAX1) and sex-determining region Y-related high-mobility group box 1 (SOX1) genes in CRC tissues. METHODS: DNA methylation at cg2,09,07,471 PAX1 and cg0,66,75,478 SOX1 from 166 cancer tissues and 37 normal tissues from CRC patients were compared using datasets downloaded from The Cancer Genome Atlas...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29033218/early-onset-colorectal-cancer-is-distinct-from-traditional-colorectal-cancer
#11
Heather Yeo, Doron Betel, Jonathan S Abelson, Xi E Zheng, Rhonda Yantiss, Manish A Shah
BACKGROUND: Early-onset colorectal cancer (E-CRC) is increasing in incidence, unlike traditional CRC (T-CRC). We sought to characterize differences between E-CRC and T-CRC. MATERIALS AND METHODS: Data sources included the Surveillance, Epidemiology, and End Results database, the Behavioral Risk Factor Surveillance Survey, and The Cancer Genome Atlas (TCGA). We compared demographics, tumor characteristics, and incidence of CRC in subjects aged 20 to 49 years (E-CRC) with those aged ≥ 50 years (T-CRC)...
June 23, 2017: Clinical Colorectal Cancer
https://www.readbyqxmd.com/read/29033189/mir-375-a-prospective-regulator-in-medullary-thyroid-cancer-based-on-microarray-data-and-bioinformatics-analyses
#12
Lin Shi, Shi-Mei Zhao, Yu Luo, An-Wen Zhang, Li-Hua Wei, Zheng-Yi Xie, Yuan-Yuan Li, Wei Ma
BACKGROUND: This research aims to investigate the prospective molecular mechanism of miR-375 in Medullary Thyroid Cancer (MTC). MATERIAL AND METHODS: The expression level of miR-375 in MTC was explored with microarray data from Gene Expression Omnibus (GEO). To gather the putative target genes of miR-375, we selected eligible datasets in GEO, in which antagomir-375 and premir-375 were transfected to provide the miR-375-related genes. Subsequently, we attained the intersection of the results of GEO microarray data and 12 online target genes prediction database as the prospective target genes...
September 27, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/29031853/co-expression-modules-construction-by-wgcna-and-identify-potential-prognostic-markers-of-uveal-melanoma
#13
Qi Wan, Jing Tang, Yu Han, Dan Wang
Uveal melanoma is an aggressive cancer which has a high percentage recurrence and with a worse prognosis. Identify the potential prognostic markers of uveal melanoma may provide information for early detection of recurrence and treatment. RNA sequence data of uveal melanoma and patient clinic traits were obtained from The Cancer Genome Atlas (TCGA) database. Co-expression modules were built by weighted gene co -expression network analysis (WGCNA) and applied to investigate the relationship underlying modules and clinic traits...
October 12, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/29031505/-histological-and-molecular-classification-of-endometrial-carcinoma-and-therapeutical-implications
#14
REVIEW
Catherine Genestie, Alexandra Leary, Mojgan Devassoux-Shisheboran, Aurélie Auguste
Endometrial cancer is the fourth cause of cancer in women in France and is the second most common cancer of the gynecologic cancer after breast cancer with 7275 new cases in 2012. The incidence of this neoplasm tends to increase with population aging, diabetes and obesity's augmentation. In rare cases, a hereditary factor has been described: Lynch's syndrome. The therapeutic management of the patient depends on the endometrial biopsy which specifies the histological type and the histo-prognostic grade as well as the MRI which allow the tumor staging...
October 11, 2017: Bulletin du Cancer
https://www.readbyqxmd.com/read/29030773/outcome-prediction-with-the-revised-american-joint-committee-on-cancer-staging-system-and-american-thyroid-association-guidelines-for-thyroid-cancer
#15
Sunghwan Suh, Yun Hak Kim, Tae Sik Goh, Jin Lee, Dae Cheon Jeong, Sae-Ock Oh, Jong Chul Hong, Seong Jang Kim, In Joo Kim, Kyoungjune Pak
BACKGROUND: Several staging systems have been developed to predict the risk of mortality in patients with differentiated thyroid cancer (DTC). However, none of them have been shown to be clearly superior to the other. METHODS: We compared the patient outcome predictability of recently revised staging systems predictability of patient outcome using data from The Cancer Genome Atlas. To set a comparison among American Joint Committee on Cancer (AJCC)/Union for International Cancer Control (UICC) staging 7th, 8th editions, American Thyroid Association guidelines 2009 and 2015, concordance index (c-index), Akaike information criterion (AIC), Bayesian information criterion (BIC), and Brier score were applied to quantify the predictive ability of a survival model, to select the statistical model, and to measure the accuracy of probabilistic predictions...
October 13, 2017: Endocrine
https://www.readbyqxmd.com/read/29029488/integrated-analysis-of-competing-endogenous-rna-network-revealing-lncrnas-as-potential-prognostic-biomarkers-in-human-lung-squamous-cell-carcinoma
#16
Jing Sui, Si-Yi Xu, Jiali Han, Song-Ru Yang, Cheng-Yun Li, Li-Hong Yin, Yue-Pu Pu, Ge-Yu Liang
Accumulating evidence shows the important role of long non-coding RNAs (lncRNAs) in competing endogenous RNA (ceRNA) networks for predicting survival in tumor patients. However, prognostic biomarkers for lung squamous cell carcinoma (LUSC) are still lacking. The objective of this study is to identify a lncRNA signature for evaluation of overall survival (OS) in 474 LUSC patients from The Cancer Genome Atlas (TCGA) database. A total of 474 RNA sequencing profiles in LUSC patients with clinical data were obtained, providing a large sample of RNA sequencing data, and 83 LUSC-specific lncRNAs, 26 miRNAs, and 85 mRNAs were identified to construct the ceRNA network (fold change>2, P<0...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29029429/twist1-is-highly-expressed-in-cancer-associated-fibroblasts-of-esophageal-squamous-cell-carcinoma-with-a-prognostic-significance
#17
So-Young Yeo, Sang-Yun Ha, Keun-Woo Lee, Yan Cui, Zhao-Ting Yang, Yan-Hua Xuan, Seok-Hyung Kim
Cancer-associated fibroblasts (CAFs) play important roles in cancer progression. Twist1 was recently reported to be a key regulator of CAFs in gastric cancer, but its role in other types of cancer remains unclear, especially for esophageal squamous cell carcinoma (ESCC). We assessed the Twist1 expression on stromal fibroblasts using immunohistochemistry in 169 tissue specimens from ESCC patients, and performed in vitro and in vivo experiments to confirm the role of Twist1 in CAFs of ESCC. And we investigated the biological pathways that are activated in Twist1-high ESCC using The Cancer Genome Atlas (TCGA) data...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29028907/oncomir-an-online-resource-for-exploring-pan-cancer-microrna-dysregulation
#18
Nathan W Wong, Yuhao Chen, Shuai Chen, Xiaowei Wang
Summary: Dysregulation of microRNAs (miRNAs) is extensively associated with cancer development and progression. miRNAs have been shown to be biomarkers for predicting tumor formation and outcome. However, identification of the relationships between miRNA expression and tumor characteristics can be difficult and time-consuming without appropriate bioinformatics expertise. To address this issue, we present OncomiR, an online resource for exploring miRNA dysregulation in cancer. Using combined miRNA-seq, RNA-seq, and clinical data from The Cancer Genome Atlas, we systematically performed statistical analyses to identify dysregulated miRNAs that are associated with tumor development and progression in most major cancer types...
October 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29027401/identification-of-dna-methylation-associated-gene-signatures-in-endometrial-cancer-via-integrated-analysis-of-dna-methylation-and-gene-expression-systematically
#19
Chuandi Men, Hongjuan Chai, Xumin Song, Yue Li, Huawen Du, Qing Ren
OBJECTIVE: Endometrial cancer (EC) is a common gynecologic cancer worldwide. However, the pathogenesis of EC has not been epigenetically elucidated. Here, this study aims to describe the DNA methylation profile and identify favorable gene signatures highly associated with aberrant DNA methylation changes in EC. METHODS: The data regarding DNA methylation and gene expression were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially methylated CpG sites (DMCs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs) were identified, and the relationship between the 2 omics was further analyzed...
November 2017: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/29027393/down-regulated-serum-microrna-101-is-associated-with-aggressive-progression-and-poor-prognosis-of-cervical-cancer
#20
Wei Jiang, Jia Jia Pan, Ying Hui Deng, Mei Rong Liang, Li Hua Yao
OBJECTIVE: MicroRNAs (miRNAs) play a vital role in pathogenesis and progression of many cancers, including cervical cancer. However, importance of serum level of miR-101 in cervical cancer has rarely been studied. In the present study, clinical significance and prognostic value of serum miR-101 for cervical cancer was investigated. METHODS: Association between miR-101 level in cervical cancer tissues and prognosis of patients was analyzed by using data retrieved from The Cancer Genome Atlas (TCGA) database, which was followed with our clinical study in which miR-101 serum level comparison between cervical cancer patients and healthy controls was conducted by real-time quantitative polymerase chain reaction (PCR)...
November 2017: Journal of Gynecologic Oncology
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