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An Identification Method of Data-Specific GO Terms from a Microarray Data Set

Yoichi YAMADA, Ken-ichi HIROTANI, Kenji SATOU, Ken-ichiro MURAMOTO
2009 IEICE transactions on information and systems  
The identification of the differentially expressed genes and their commonly associated GO terms allows us to find stimulation-dependent or disease-related genes and biological events, etc.  ...  A preliminary step to extract any information from a microarray data set is to identify differentially expressed genes between microarray data.  ...  The simplest method for identifying the differentially expressed genes is based on fold change of gene expression between an object and a control sample or between microarray data.  ... 
doi:10.1587/transinf.e92.d.1093 fatcat:tztdn6h24vbkphfkh6i243xcxe

Whole-genome expression profiling through fragment display and combinatorial gene identification

A. Metsis
2004 Nucleic Acids Research  
Open systems such as differential display are capable of analyzing most of the expressed genome but are not quantitative and generally require manual identification of differentially expressed genes by  ...  By combinatorial analysis of three independent and complete DNA indexing profiles, each displaying the complete set of expressed transcripts on capillary electrophoresis, the method allows transcripts  ...  Recent work on expression profiling methods derived from differential display has focused on improving the gene identification step to avoid the laborious direct sequencing of excised fragments.  ... 
doi:10.1093/nar/gnh126 pmid:15356287 pmcid:PMC519127 fatcat:67lfo72ag5dgbjkvm26ta2x52e

Identification of immune landscape signatures associated with clinical and prognostic features of hepatocellular carcinoma

Hongmei Yan, Yuchuan Chen, Kai Wang, Lu Yu, Xixin Huang, Qianyu Li, Yuwen Xie, Jiayu Lin, Yueyun He, Xinyu Yi, Yanzhi Wang, Longhua Chen (+2 others)
2020 Aging  
Two independent prognostic indexes were established based on 6 immune-related genes and 17 differentially expressed genes associated with stromal cell content.  ...  These indexes were significantly correlated with tumor mutation burden, deficient DNA mismatch repair and microsatellite instability.  ...  Changes in TIME and prognosis based on differential immune-related genes Identification of HCC subtype-specific gene expression profiles We then used EdgeR to identify HCC subtype-specific gene expression  ... 
doi:10.18632/aging.103977 pmid:33049716 pmcid:PMC7732284 fatcat:3erpi5nvk5eexhvem3sz4tl3kq

Mapping and Identifying a Candidate Gene Plr4, a Recessive Gene Regulating Purple Leaf in Rice, by Using Bulked Segregant and Transcriptome Analysis with Next-Generation Sequencing

Ju Gao, Gaoxing Dai, Weiyong Zhou, Haifu Liang, Juan Huang, Dongjin Qing, Weiwei Chen, Hao Wu, Xinghai Yang, Danting Li, Lijun Gao, Guofu Deng
2019 International Journal of Molecular Sciences  
Subsequently, transcriptome sequencing (RNA-Seq) for pl3 and pl2 was used to analyze the differentially expressed genes in the localization interval, where 12 unigenes exhibited differential expression  ...  Mb on chromosome 4.  ...  Genes with an adjusted p < 0.05 based on DESeq were considered differentially expressed.  ... 
doi:10.3390/ijms20184335 fatcat:mcixgsa66vbhtlhabk6oktfah4

Identification of sepsis subtypes in critically ill adults using gene expression profiling

David M Maslove, Benjamin M Tang, Anthony S McLean
2012 Critical Care  
Results: We identified two sepsis subtypes based on gene expression patterns.  ...  Conclusions: Sepsis subtypes can be identified based on different gene expression patterns.  ...  Gene expression microarray data may be useful in identifying sepsis subtypes based on differential expression of key genes [4] .  ... 
doi:10.1186/cc11667 pmid:23036193 pmcid:PMC3682285 fatcat:lfzpqh3vvfd5dpkcw32i5hucly

Integrated analysis of methylation-driven genes and pretreatment prognostic factors in patients with hepatocellular carcinoma

Dongsheng He, Shengyin Liao, Lifang Cai, Weiming Huang, Xuehua Xie, Mengxing You
2021 BMC Cancer  
Methods The gene methylation, gene expression dataset and clinical information of HCC patients were downloaded from The Cancer Genome Atlas (TCGA) database.  ...  The C-index was superior to that from previous studies (0.75 vs 0.717, 0.676).  ...  Identification of differentially methylated and expressed genes The limma package was used to screen the differentially methylated genes, and the edgeR package was used to identify the differentially expressed  ... 
doi:10.1186/s12885-021-08314-5 pmid:34034705 fatcat:bidw4qnhqzb6hpvdyzitubids4

Differential Gene Expression Pipeline for Whole Transcriptome RNA-Seq Data using Personal Computer [article]

Rashid Saif, Aniqa Ejaz, Tania Mahmood, Saeeda Zia
2021 bioRxiv   pre-print
The steps include quality check, base filtration, quasi-mapping, quantification of samples, estimation and counting of transcript/gene expression abundances, identification and clustering of differentially  ...  An extension of this pipeline may also be formulated in future for the gene ontology enrichment analysis and functional annotation of the differential expression matrix to make this data biologically more  ...  We then quantified set of paired-end reads separately in mapping-based mode against the index generated using salmon quant feature. $ salmon quant -i output_index_dir-name -l A -1 trimmed1.fq -2 trimmed2  ... 
doi:10.1101/2021.01.26.428352 fatcat:hbruc3g4arg7hgupmwxnfay2p4

Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level

Yannick F. Fuchs, Virag Sharma, Anne Eugster, Gloria Kraus, Robert Morgenstern, Andreas Dahl, Susanne Reinhardt, Andreas Petzold, Annett Lindner, Doreen Löbel, Ezio Bonifacio
2019 Frontiers in Immunology  
These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors.  ...  Combined expression of TNFRSF9, XCL1, XCL2, and CRTAM was the most distinct marker of virus-responsive cells on a single-cell level.  ...  Table S4 | S4 Differentially expressed genes in cognate antigen-responsive CD8+ T cells from donors 4-6. Table S5 | S5 Separator index and ranking of separator genes.  ... 
doi:10.3389/fimmu.2019.02568 pmid:31781096 pmcid:PMC6851025 fatcat:y7gc4ze7kjaxrjf54oty4wjeiy

Prediction of severity and subtype of fibrosing disease using model informed by inflammation and extracellular matrix gene index

Amin M. Cheikhi, Zariel I. Johnson, Dana R. Julian, Sarah Wheeler, Carol Feghali-Bostwick, Yvette P. Conley, James Lyons-Weiler, Cecelia C. Yates, Minghua Wu
2020 PLoS ONE  
We have developed a multi-tiered method using Naïve Bayes modeling that is capable of predicting level of disease and clinical assessment of patients based on expression of a curated 60-gene panel that  ...  We refined this gene set to a 12-gene index that can accurately identify SSc patient disease state subsets and informs knowledge of the central regulatory pathways in disease progression.  ...  Summary scores were generated for each patient based on expression of the genes in our 60-gene predictive gene index.  ... 
doi:10.1371/journal.pone.0240986 pmid:33095822 fatcat:vdleywrmxvgqhpphho7hpgfmxq

A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis

H. Yang, H. Haddad, C. Tomas, K. Alsaker, E. T. Papoutsakis
2003 Proceedings of the National Academy of Sciences of the United States of America  
Genes with high differential expression are excluded from these calculations.  ...  Abbreviations: CHM, contour based on hierarchical modeling; ERM, expression-ratio mean; ERMD, expression-ratio median; ERPD, expression-ratio probability density; LER, logarithm of expression ratio; LERM  ...  Identification of Differentially Expressed Genes.  ... 
doi:10.1073/pnas.0237337100 pmid:12529501 pmcid:PMC298737 fatcat:ipez4mfnpndz3awevusagsh33e

Identification of long non-coding RNA signatures for specific disease-free prognosis in clear cell renal carcinoma

Wujiao Wang, Jing Song, Wanfeng Zhang, Yongyao Tang, Ruihan Luo, Longke Ran, Fangzhou Song
2019 IEEE Access  
The expression data of GSE53757 (n = 144) and GSE66270 (n = 28) from Gene Expression Omnibus (GEO) were used to screen for ccRCC-related differentially expressed (DE) genes. 893 DE lncRNAs in common of  ...  The expression and clinical data of The Cancer Genome Atlas (TCGA, n = 603) and international cancer genomics consortium (ICGC, n = 392) were leveraged to identify long non-coding RNA (lncRNA)-based prognostic  ...  To identify lncRNAs that played a role in ccRCC, we performed differential expression analysis between ccRCC tumors and control samples based on TCGA dataset and GEO dataset separately. 789 genes were  ... 
doi:10.1109/access.2019.2929588 fatcat:a66f35fc6je5jjoouqky4dx3ru

Identification and Characterization of Poorly Differentiated Invasive Carcinomas in a Mouse Model of Pancreatic Neuroendocrine Tumorigenesis

Karen E. Hunter, Marsha L. Quick, Anguraj Sadanandam, Douglas Hanahan, Johanna A. Joyce, Matthew Bogyo
2013 PLoS ONE  
Interestingly, we identified expression of Id1, an inhibitor of DNA binding gene, and a regulator of differentiation, specifically in PDIC tumor cells by histological analysis.  ...  In addition, we found that these tumors exhibited a high mitotic index, resembling poorly differentiated (PD)-PanNETs in human patients.  ...  Robert Benezra and members of the Joyce lab for insightful discussion on this topic. We gratefully acknowledge Xiaoping Chen and Kenishana Simpson for excellent technical assistance.  ... 
doi:10.1371/journal.pone.0064472 pmid:23691228 pmcid:PMC3653861 fatcat:p7leynqiwvhzrf3mkun52ps6vm

Identification and validation of a four-miRNA(miRNA-21-5p, miRNA-9-5p, miR-149-5p, and miRNA-30b-5p) prognosis signature in clear cell renal cell carcinoma

Mingzhi Xie, Yufeng Lv, Zhihui Liu, Jingyan Zhang, Chaoyong Liang, Xiaoli Liao, Rong Liang, Yan Lin, Yongqiang Li
2018 Cancer Management and Research  
The miRNAs differentially expressed between ccRCCs and matched normal tissues were analyzed using the "limma" package.  ...  A miRNA-based signature was constructed using the multivariate Cox regression model with prognosis index (PI) formula.  ...  Construction and validation of the miRNA-based prognostic signature for ccRCC In the training set, the patients were separated into high-and low-level groups based on the median value of the differential  ... 
doi:10.2147/cmar.s187109 pmid:30532596 pmcid:PMC6245347 fatcat:st7hsslax5gyvawsik2n4exiuq

Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification

Michael Gormley, Aydin Tozeren
2008 BMC Bioinformatics  
Use of a model-based clustering algorithm accurately classified more than 400 microarray samples into 19 different tissue types on the basis of bimodal gene expression.  ...  Bimodal expression patterns were also highly effective in differentiating between infectious diseases in model-based clustering of microarray data.  ...  A set of 300 bimodal genes expressed on the extracellular matrix or the plasma membrane is sufficient to accurately differentiate between nineteen different tissue types in model-based clustering even  ... 
doi:10.1186/1471-2105-9-486 pmid:19014681 pmcid:PMC2620272 fatcat:yuwhfkvdyfdunahib7tuvet4gy

Identification of an independent immune-genes prognostic index for renal cell carcinoma

Guangyao Li, Xiyi Wei, Shifeng Su, Shangqian Wang, Wei Wang, Yichun Wang, Xianghu Meng, Jiadong Xia, Ninghong Song, Chao Qin
2021 BMC Cancer  
Results Via differential analysis, we found that 556 immune-related genes were expressed differentially between tumor and normal tissues (p < 0. 05).  ...  Through Lasso-Cox regression analysis, we established an immune genetic risk scoring model based on 18 immune-related genes. The high-risk group showed a bad prognosis in K-M analysis. (p < 0.001).  ...  A The volcano plot showed 540 differential expressions of genes in ccRCC and normal tissues based on TCGA data-base.  ... 
doi:10.1186/s12885-021-08367-6 pmid:34187413 fatcat:3prgwdxrw5azrketaxdm7rkf6e
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