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Mining gene expression datasets using density-based clustering

Seokkyung Chung, Jongeun Jun, Dennis McLeod
<span title="">2004</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6g37zvjwwrhv3dizi6ffue642m" style="color: black;">Proceedings of the Thirteenth ACM conference on Information and knowledge management - CIKM &#39;04</a> </i> &nbsp;
We propose a mining framework that supports the identication of useful patterns based on data clustering.  ...  Given the recent advancement of microarray technologies, we focus our attention on gene expression datasets mining. In particular, we are interested in mining a yeast cell cycle dataset.  ...  Recently, density-based clustering algorithms have been applied to gene expression datasets 17, 18 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1031171.1031198">doi:10.1145/1031171.1031198</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cikm/ChungJM04.html">dblp:conf/cikm/ChungJM04</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3sd2msyalneefkcmfbcbqurmum">fatcat:3sd2msyalneefkcmfbcbqurmum</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809093854/http://imsc-dmim.usc.edu/publications/cikm-gene-cluster.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/61/01/6101ebad4e6f044a014de3b874f1c412ca987088.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1031171.1031198"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Looking for chromosome spatial organization rules in microarray gene expression data

Teresa Szczepińska, Krzysztof Pawłowski
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
A graph-based data-mining approach efficiently identified frequent co-expression clusters in 105 assembled human microarray datasets [1] .  ...  In different expression datasets, different chromosomes do group within co-expression clusters. This has been observed for similar, medium gene-density, low density and acrocentric chromosomes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-s13-o6">doi:10.1186/1471-2105-10-s13-o6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/njrmzegwlrei7l4ffy5s7x7yui">fatcat:njrmzegwlrei7l4ffy5s7x7yui</a> </span>
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A performance analysis of clustering based algorithms for the microarray gene expression data

K Yuvaraj, D Manjula
<span title="2018-04-20">2018</span> <i title="Science Publishing Corporation"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/piy2nrvrjrfcfoz5nmre6zwa4i" style="color: black;">International Journal of Engineering &amp; Technology</a> </i> &nbsp;
Grouping the genes having identical expression patterns is known as gene clustering. A number of clustering algorithms have been applied for the analysis of microarray gene expression data.  ...  Clustering is a significant tool applied for analyzing such microarray gene expression data. It has developed into a greatest part of gene expression analysis.  ...  Density based clustering Density based clustering algorithms are created to determine arbitrary shaped clusters.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14419/ijet.v7i2.21.12172">doi:10.14419/ijet.v7i2.21.12172</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/77gmx44ix5fldmizv7zxiafcv4">fatcat:77gmx44ix5fldmizv7zxiafcv4</a> </span>
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Subspace clustering for high dimensional datasets

G.N.V.G. Sirisha, M. Shashi
<span title="2016-08-25">2016</span> <i title="Association of Computer, Communication and Education for National Triumph Social and Welfare Society (ACCENTS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/h6wni7yfjratfglwchnpmbf2iu" style="color: black;">International Journal of Advanced Computer Research</a> </i> &nbsp;
It mines coherent clusters along gene-sample-time (temporal) or gene-sample-region (spatial) dimensions.  ...  interesting subspace mine (SCHISM) and Density conscious subspace clustering (DENCOS) are grid based subspace clustering algorithms that use adaptive density thresholds.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.19101/ijacr.2016.625012">doi:10.19101/ijacr.2016.625012</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2jcwv5hwcvdw5ojoaznh2mv5gm">fatcat:2jcwv5hwcvdw5ojoaznh2mv5gm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180602185801/http://accentsjournals.org/PaperDirectory/Journal/IJACR/2016/9/4.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c3/25/c32597dbd2f84554127ec6f16ac5a9bc6e27360b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.19101/ijacr.2016.625012"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Massive Human Co-Expression Network and Its Medical Applications

Yaping Feng, Jonathan Hurst, Marcia Almeida-De-Macedo, Xi Chen, Ling Li, Nick Ransom, Eve Syrkin Wurtele
<span title="">2012</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lnsuzw7nnreyhg3rgzyjhviqj4" style="color: black;">Chemistry and Biodiversity</a> </i> &nbsp;
Regulons, groups of highly and consistently co-expressed genes, were obtained by partitioning the 18637Hu-co-expression-network using an MCL clustering algorithm.  ...  From this data, 18,637 chips encompassing over 500 experiments containing high quality data (18637Hu-dataset) were used to create a globally stable gene co-expression network (18637Hu-co-expressionnetwork  ...  We compared three major types: feature-based clustering (K-means), similarity matrix-based clustering (H-cluster), and graph-based clustering (MCL) (Fig. 1) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cbdv.201100355">doi:10.1002/cbdv.201100355</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22589089">pmid:22589089</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3711686/">pmcid:PMC3711686</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jvkreoyw3vcwfp26n4zxftp6x4">fatcat:jvkreoyw3vcwfp26n4zxftp6x4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722013228/https://lib.dr.iastate.edu/cgi/viewcontent.cgi?referer=&amp;httpsredir=1&amp;article=1079&amp;context=gdcb_las_pubs" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/13/33/13338287eeedd47943def987baeeec0c2278661d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cbdv.201100355"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711686" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Towards Framing an Integrated Model for Optimization and Clustering (IMOC) High-Dimensional Non-Linear DNA Data Processing using ACO and DENCLUE

<span title="2019-10-30">2019</span> <i title="Blue Eyes Intelligence Engineering and Sciences Engineering and Sciences Publication - BEIESP"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/h673cvfolnhl3mnbjxkhtxdtg4" style="color: black;">International Journal of Engineering and Advanced Technology</a> </i> &nbsp;
Two efficient algorithms are integrated in this work, Ant Colony Optimization for effectively determine the features of gene data and Density based Clustering (DENCLUE) is for clustering the DNA data based  ...  The Gene Expression data contains important information about the biological reactions that are carried out in creatures that are based on the surroundings.  ...  Here, for effective analysis of gene expression data, clustering model is incorporated. Figure 1: Model of DNA Microarray For clustering in this model, density based clustering model is used.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.35940/ijeat.a9753.109119">doi:10.35940/ijeat.a9753.109119</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3ncf3uggnredvojqjp2aoajj3y">fatcat:3ncf3uggnredvojqjp2aoajj3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209050535/https://www.ijeat.org/wp-content/uploads/papers/v9i1/A9753109119.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9b/4b/9b4b78e467873c7187937b18bd8c7dbb58d07c4c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.35940/ijeat.a9753.109119"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability

Jie Zhang, Kewei Lu, Yang Xiang, Muhtadi Islam, Shweta Kotian, Zeina Kais, Cindy Lee, Mansi Arora, Hui-wen Liu, Jeffrey D. Parvin, Kun Huang, Andrey Rzhetsky
<span title="2012-08-30">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
In this study, we used a network mining algorithm to identify tightly connected gene co-expression networks that are frequently present in microarray datasets from 33 types of cancer which were derived  ...  We tested 13 selected genes from this network for their involvement in genome maintenance using two cell-based assays.  ...  For example, Horvath's group has developed a series of weighted gene co-expression network analyses using a hierarchical clustering based approach [6, 10, [12] [13] [14] [15] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002656">doi:10.1371/journal.pcbi.1002656</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22956898">pmid:22956898</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3431293/">pmcid:PMC3431293</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/omy74u3virhntgc764lfenyi4y">fatcat:omy74u3virhntgc764lfenyi4y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015135746/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002656&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5f/8e/5f8e99fedcbcac5d987ccd1930fd2e0110fef367.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002656"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431293" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Frequent Pattern Discovery in Multiple Biological Networks: Patterns and Algorithms

Wenyuan Li, Haiyan Hu, Yu Huang, Haifeng Li, Michael R. Mehan, Juan Nunez-Iglesias, Min Xu, Xifeng Yan, Xianghong Jasmine Zhou
<span title="2011-12-29">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zpm2vqfkabhwbmjedzu7bm7o4u" style="color: black;">Statistics in Biosciences</a> </i> &nbsp;
We demonstrate these methods on gene co-expression networks, using the identified patterns to systematically annotate gene functions, map genome to phenome, and perform high-order cooperativity analysis  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided  ...  This term compliments the density and specificity objectives by comparing the average density of the cluster in the background datasets to its density in the phenotype datasets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12561-011-9047-0">doi:10.1007/s12561-011-9047-0</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dkpevwt6irgxfn7l3rpi4zcnnu">fatcat:dkpevwt6irgxfn7l3rpi4zcnnu</a> </span>
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Gene expression data clustering analysis: A survey

Sajid Nagi, Dhruba K. Bhattacharyya, Jugal K. Kalita
<span title="">2011</span> <i title="IEEE"> 2011 2nd National Conference on Emerging Trends and Applications in Computer Science </i> &nbsp;
In this survey, we address various approaches to gene expression data analysis using clustering techniques.  ...  The advent of DNA microarray technology has enabled biologists to monitor the expression levels (MRNA) of thousands of genes simultaneously.  ...  Discussion: Though partitioning based clustering algorithms can find separate clusters, in the context of gene expression data mining, it has the following disadvantages. i.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ncetacs.2011.5751377">doi:10.1109/ncetacs.2011.5751377</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hjywaja6qncynknoh6dq5fvbve">fatcat:hjywaja6qncynknoh6dq5fvbve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808195043/http://www.cs.uccs.edu/~jkalita/papers/2011/NagiSajidNCETACS2011.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/05/89/0589a25e7e9ddc4219144a7237e59248e2dfba41.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ncetacs.2011.5751377"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

A graph-based approach to systematically reconstruct human transcriptional regulatory modules

Xifeng Yan, Michael R. Mehan, Yu Huang, Michael S. Waterman, Philip S. Yu, Xianghong Jasmine Zhou
<span title="2007-07-01">2007</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Results: We propose a graph-based data-mining approach to efficiently and systematically identify frequent coexpression clusters.  ...  A commonly used approach for transcription module reconstruction is to derive coexpression clusters from a microarray dataset.  ...  In this article, we develop a graph-based approach to efficiently and systematically identify gene sets which form coexpression clusters across multiple datasets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm227">doi:10.1093/bioinformatics/btm227</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17646346">pmid:17646346</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vg4ds3xipzbyzfzzylprdofe6i">fatcat:vg4ds3xipzbyzfzzylprdofe6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729212533/https://watermark.silverchair.com/btm227.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAcAwggG8BgkqhkiG9w0BBwagggGtMIIBqQIBADCCAaIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMql48SUueCO95ArilAgEQgIIBc3skQJQvD9trzIk3sucyUdA9F7ZOvJNuNdp2igwPVmZfS3PFRegmTagm01dmWvPO-_lcVu2VeI7-tU-OV8HeNg9eR4CtN1dQIUb96IEE_cn6wTpt4UVKVkAvdH19uzEZ4npuGSzuxcEyGbTo5BccvpSRqInyhnJqPOn3xKCTzhWofmHbsaLh5484CC-K0y3Zn8aXY6zybpFow6O7tLqsShGrn9KRssf-Xou7-J3WKl6YbGE317xQIvqI6MOTMdUST91olibtj0GDx0LNXvkG2y07IIbX2Jb-jhAeTwCtdCr_0XaAe8mdmHgT5AT7xDSHYrs1MJoHPaRfDQmRbT8y79t0U_vYm6L3ATdUkKXPUiilnVFO_tZP01bbNm9eickYS3F0QLRDz6rlA_bxK_Tob63B6CDvy_XHOdGGOVCaQKi6sIZ9ZWo_cFgvd0c3sQIcSQILDwHf2T-kas6dq6m8mWBoeaK2iRSL1kkxYkmtIXvJJpBB" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/93/d1/93d148e7fe7b92c7cb21cdaa876782ef3a49c13d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm227"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Constraint-based Subspace Clustering [chapter]

Elisa Fromont, Adriana Prado, Celine Robardet
<span title="2009-04-30">2009</span> <i title="Society for Industrial and Applied Mathematics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/viwc2ys5x5a47ogpdlftfzj5fm" style="color: black;">Proceedings of the 2009 SIAM International Conference on Data Mining</a> </i> &nbsp;
We show how this new framework can be applied to both density and distancebased bottom-up subspace clustering techniques.  ...  Our experiments on real datasets show that instance-level constraints cannot only increase the efficiency of the clustering process but also the accuracy of the resultant clustering.  ...  This work has been partially supported by the BINGO2 project (ANR-07-MDCO 014-02), the GOA project 2003/8, "Inductive Knowledge bases" and the FWO project "Foundations for inductive databases".  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1137/1.9781611972795.3">doi:10.1137/1.9781611972795.3</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/sdm/FromontPR09.html">dblp:conf/sdm/FromontPR09</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dyjob5bwjrdvtfffoscoqhad3a">fatcat:dyjob5bwjrdvtfffoscoqhad3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705081111/http://perso.univ-st-etienne.fr/frel9915/datafiles/siam2008.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a5/fc/a5fcd32aaae67407353b6175de42499a2f543144.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1137/1.9781611972795.3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Integration of molecular features with clinical information for predicting outcomes for neuroblastoma patients

Yatong Han, Xiufen Ye, Chao Wang, Yusong Liu, Siyuan Zhang, Weixing Feng, Kun Huang, Jie Zhang
<span title="2019-08-23">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m5tyg6kdofe7db2hdtm2zxndi4" style="color: black;">Biology Direct</a> </i> &nbsp;
To remove any further batch effect within a dataset, we further converted gene expression values into z-score values within each dataset for further gene co-expression network mining and data integration  ...  Gene co-expression network mining and eigengene summarization We applied our previously developed weighted network mining algorithm lmQCM [6] for gene co-expression module mining.  ...  Based on Methods, the FPKM values for RNA-seq gene expression were downloaded and used for further analysis. The FPKM values are not normally distributed, so t-test is not appropriate here.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13062-019-0244-y">doi:10.1186/s13062-019-0244-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31443736">pmid:31443736</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6706887/">pmcid:PMC6706887</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jqaijgx5dnbjldkioeesl7c6hu">fatcat:jqaijgx5dnbjldkioeesl7c6hu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200310055840/https://scholarworks.iupui.edu/bitstream/handle/1805/21155/13062_2019_Article_244.pdf;jsessionid=44DA8A4B63312619CEF6B20A12021CAE?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/b1/25b1a748c65276986c18c3249c1fa6c31f46b6ca.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13062-019-0244-y"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706887" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Analyzing miRNA co-expression networks to explore TF-miRNA regulation

Sanghamitra Bandyopadhyay, Malay Bhattacharyya
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
However, there remains a basic difference between the mining method and a clustering approach.  ...  Conclusion: A heuristic mining methodology that resembles a clustering motivation is proposed in this paper.  ...  Moreover, they employ clustering tools commonly used for gene expression analysis though, as mentioned earlier, the scalability and the other characteristics of miRNA expression data are somewhat different  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-163">doi:10.1186/1471-2105-10-163</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19476620">pmid:19476620</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2707367/">pmcid:PMC2707367</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eolbddsmmfdr7lttx2sbauuqjm">fatcat:eolbddsmmfdr7lttx2sbauuqjm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829215650/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-163?site=http://bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ea/4e/ea4e9eef394ed9022b3818e28b644528417d4d44.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-163"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2707367" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Clustering Algorithms: Their Application to Gene Expression Data

Jelili Oyelade, Itunuoluwa Isewon, Funke Oladipupo, Olufemi Aromolaran, Efosa Uwoghiren, Faridah Ameh, Moses Achas, Ezekiel Adebiyi
<span title="">2016</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/i7e77v75qbe7rbbcdp63ijxhza" style="color: black;">Bioinformatics and Biology Insights</a> </i> &nbsp;
of cells, mining useful information from noisy data, and understanding gene regulation.  ...  The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes  ...  a model-based clustering strategy based on CRP for clustering gene expression data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/bbi.s38316">doi:10.4137/bbi.s38316</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27932867">pmid:27932867</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5135122/">pmcid:PMC5135122</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5iammdivhrbdnn3jsscvb3oss4">fatcat:5iammdivhrbdnn3jsscvb3oss4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720081058/http://insights.sagepub.com/redirect_file.php?fileId=8031&amp;filename=6054-BBI-Clustering-Algorithms:-Their-Application-to-Gene-Expression-Data.pdf&amp;fileType=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/82/1c/821cf1442bd44a559359f73b0b9d62dc77c9356f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/bbi.s38316"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135122" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Mining the tissue-tissue gene co-expression network for tumor microenvironment study and biomarker prediction

Yang Xiang, Jie Zhang, Kun Huang
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
The tumor and stroma gene expression data are modeled as a weighted bipartite network (tumor-stroma coexpression network) where the weight of an edge indicates the correlation between the expression profiles  ...  in nearly all types of breast cancer subtypes we used in this study.  ...  In contrast, the clustering based approaches do not allow shared genes between two clusters and the clusters identified are often too large to find small gene networks with subtle functions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-14-s5-s4">doi:10.1186/1471-2164-14-s5-s4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24564578">pmid:24564578</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3852209/">pmcid:PMC3852209</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aiwj2elxafckhp3dr7u37asqm4">fatcat:aiwj2elxafckhp3dr7u37asqm4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809153947/https://translational-medicine.biomedcentral.com/track/pdf/10.1186/1471-2164-14-S5-S4?site=translational-medicine.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ae/49/ae496e921c7ad647d4e56da5c822035743f10359.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-14-s5-s4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852209" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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