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The limits of p-values for biological data mining

James D Malley, Abhijit Dasgupta, Jason H Moore
2013 BioData Mining  
Acknowledgements This research was supported in part by the Intramural Research Programs of the Center for Information Technology and the National Institute of Arthritis and Musculoskeletal and Skin Diseases  ...  , both part of the National Institutes of Health.  ...  Beyond p-values, FDR, ROC, and AUC, are there more efficient uses of the same data? What is truly predictive rather than being merely significant?  ... 
doi:10.1186/1756-0381-6-10 pmid:23663551 pmcid:PMC3668262 fatcat:ty6g7cxjcfc4fmzzkf2vm5o5ha

Efficient mining gapped sequential patterns for motifs in biological sequences

Vance Liao, Ming-Syan Chen
2013 BMC Systems Biology  
Biological data mining yield impact in diverse biological fields, such as discovery of co-occurring biosequences, which is important for biological data analyses.  ...  The approach is the Depth-First Spelling algorithm for mining sequential patterns of biological sequences with Gap constraints (termed DFSG).  ...  In general, the problem of mining gapped motifs does not confine any categories of biological sequences. Definition 4. We denote a motif p = {p 1 p 2 p 3 ...p m }, where p m is an item.  ... 
doi:10.1186/1752-0509-7-s4-s7 pmid:24565366 pmcid:PMC3854651 fatcat:piag3qx4jvbkfcfpk7nerptx6q

Assessing relationships between human land uses and the decline of native mussels, fish, and macroinvertebrates in the Clinch and Powell river watershed, USA

Jerome M. Diamond, David W. Bressler, Victor B. Serveiss
2002 Environmental Toxicology and Chemistry  
Sites less than 2 km downstream of urban areas, major highways, or coal mine activities had a significantly lower mean IBI value than those more than 2 km away (ANOVA, p Ͻ .05).  ...  Based on land uses within a riparian corridor of 200 m ϫ 2 km for each biological site in the watershed, fish IBI was inversely related to percent cropland and urban area and positively related to pasture  ...  Acknowledgement-We wish to thank Don Gowan, Roberta Hylton, and other members of the Clinch Watershed Ecological Risk Work-group, who provided extensive information and reviews of earlier reports.  ... 
doi:10.1002/etc.5620210606 pmid:12069297 fatcat:ncissmcsgjenvon6bwzumxylqe

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Da Wei Huang, Brad T. Sherman, Richard A. Lempicki
2008 Nucleic Acids Research  
The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study.  ...  Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the  ...  ACKNOWLEDGEMENTS Thanks go to Dr Xin Zheng and Ms Jun Yang in the Laboratory of Immunopathogenesis and Bioinformatics (LIB) group for biological and bioinformatics discussion.  ... 
doi:10.1093/nar/gkn923 pmid:19033363 pmcid:PMC2615629 fatcat:gwatxne6hng23gtydhc4puem6a

Estimation of inter-laboratory reference change values from external quality assessment data

Michael Paal, Katharina Habler, Michael Vogeser
2021 Biochemia Medica  
As a proof-of-concept study, we aimed at estimating the inter-laboratory reference change value (IL-RCV) for exemplary analytes from publicly available data on external quality assessment (EQA) and biological  ...  External quality assessment data together with data on the biological variation - both freely available - allow the estimation of inter-laboratory RCVs.  ...  , has fuelled the mining of lab data (3) .  ... 
doi:10.11613/bm.2021.030902 pmid:34393596 pmcid:PMC8340502 fatcat:42sndgfulzd3ffop7gzgzfgtaa

Assigning Schema Labels Using Ontology And Hueristics

Xuan Zhang, Ruoming Jin, Gagan Agrawal
2006 Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06)  
Detailed experimental results from three datasets demonstrate the effectiveness of the use of data mining for biological applications.  ...  As a result, manually written parsers are widely used to extract data from them. This has limited the readiness of the data for data consuming programs, such as integration systems.  ...  This has limited the readiness of the data for data consuming programs, such as integration systems.  ... 
doi:10.1109/bibe.2006.253344 dblp:conf/bibe/ZhangJA06 fatcat:m6ankxl5uzhhblw3hlcpwoqxd4

Analyzing Large Biological Datasets with an Improved Algorithm for MIC [article]

Shuliang Wang, Yiping Zhao
2014 arXiv   pre-print
A computational framework utilizes the traditional similarity measures for mining the significant relationships in biological annotations is recently proposed by Tatiana V. Karpinets et al. [2].  ...  Further, IAMIC is the enhanced algorithm for approximating a novel similarity coefficient MIC with generality and equitability, which makes it more appropriate for data exploration.  ...  MINEING BIOLOGICAL DATASETS WITH IAMIC Here we are going to describe the main steps of mining biological annotations with an improved algorithm for calculating MIC named IAMIC.  ... 
arXiv:1403.3495v1 fatcat:xccvfw7asfavdim7f35zei5bte

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction

Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li
2009 BMC Bioinformatics  
Moreover, GEOGLE summarizes the signature genes from a subset of GDSes and estimates the correlation between gene expression and the phenotypic distinction with an integrated p value.  ...  In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing  ...  However most of these tools for retrieving data from the GEO repository paid little attention to mining further information about the gene expression signatures, such as linking to the biological functions  ... 
doi:10.1186/1471-2105-10-264 pmid:19703314 pmcid:PMC2745391 fatcat:vgdubrketfgy7judhixtmofrza

STREAM RECONSTRUCTION UNDER SMCRA BURNING STAR #4: A CASE STUDY

William G. O'Leary, Jack R. Nawrot
2012 Journal American Society of Mining and Reclamation  
Important hydrologic and biologic functions were successfully restored following surface mining for coal through two large streams by reconstruction of the stream systems.  ...  Stream water sulfate concentration was identified as the biggest difference between the pre-mining and post-mining stream environments with a tenfold increase as a result of mining.  ...  Acknowledgements Consolidation Coal Company is to be commended for the fine quality of reclamation work completed at the Burning Star #4 site, as are the many employees of that company who dedicated their  ... 
doi:10.21000/jasmr12010406 fatcat:wj63zdn3frfs5jo55wklaalqpe

Mining co-regulated gene profiles for the detection of functional associations in gene expression data

A. Gyenesei, U. Wagner, S. Barkow-Oesterreicher, E. Stolte, R. Schlapbach
2007 Bioinformatics  
Our experimental results show that the Mining Attribute Profile (MAP) method is an efficient tool for the analysis of gene expression data and competitive with bi-clustering techniques.  ...  Our implementation mined the data effectively and discovered patterns of co-regulated genes that are hidden to traditional APD methods.  ...  ACKNOWLEDGEMENTS The authors thank Sarah Rodgers for fruitful discussions regarding the MAP algorithm and Katalin Fu¨lo¨p and Mike Scott for helpful advices and comments on the manuscript. A.  ... 
doi:10.1093/bioinformatics/btm276 pmid:17537754 fatcat:qfagwrpdjjfmzlrkhp5vdr2hky

Querying Biological Sequences Docking Using Different Constraint Programming's: a Survey
English

B.Mallikarjuna Reddy, P Chandrasekhar, M.Ramakrishna Reddy
2015 International Journal of Computer Trends and Technology  
the data mining tool with soft computing.  ...  These domains related techniques are providing the data rich environment solutions. Consider the mixed biological data transactions and we select the different number of approaches.  ...  That's why in this paper we concentrate on biologic data sequence for preparation of drugs. Biological data sequence preparation possible with different data mining techniques.  ... 
doi:10.14445/22312803/ijctt-v22p110 fatcat:ag36qn6m4jdkhlakxvrbbisyma

Downstream effects of mountaintop coal mining: comparing biological conditions using family- and genus-level macroinvertebrate bioassessment tools

Gregory J. Pond, Margaret E. Passmore, Frank A. Borsuk, Lou Reynolds, Carole J. Rose
2008 Journal of The North American Benthological Society  
Four lines of evidence indicate that mining activities impair biological condition of streams: shift in species assemblages, loss of Ephemeroptera taxa, changes in individual metrics and indices, and differences  ...  the assessment results using family-and genus-level taxonomic data.  ...  Green (retired) for field and laboratory support, analysts at the Office of Analytical Services and Quality Assurance in Fort Meade, Maryland, for chemical analyses, and J. Forren for reviews.  ... 
doi:10.1899/08-015.1 fatcat:fe3s5335nvakjabgb4j2dzwzty

Functional diversity of microorganisms in metal- and alkali-contaminated soils of Central and North-eastern Slovakia

Juraj Fazekaš, Danica Fazekašová, Peter Adamišin, Petra Huličová, Eva Benková
2019 Soil and Water Research  
The examined area of Central Spiš showed extremely high values of Hg and Cu and the values of Zn, Cd, Pb and Cr exceeding the permissible limit were determined.  ...  The values of Cr, Mn, and Mg exceeding the permissible limit were measured there. The results indicate harmful and even toxic contamination.  ...  The assessed values of heavy metals in soils were compared with the limit values of Slovak soils (Act No. 220/2004).  ... 
doi:10.17221/37/2018-swr fatcat:lrtqch6b2ncybm76rwvn3nzhdq

Discovery of error-tolerant biclusters from noisy gene expression data

Rohit Gupta, Navneet Rao, Vipin Kumar
2011 BMC Bioinformatics  
However, traditional association mining only finds exact biclusters, which limits its applicability in reallife data sets where the biclusters may be fragmented due to random noise/errors.  ...  of some of the approaches to find overlapping biclusters, which is crucial as many genes participate in multiple biological processes.  ...  The full contents of the supplement are available online at http://www. biomedcentral.com/1471-2458/11/S5.  ... 
doi:10.1186/1471-2105-12-s12-s1 pmid:22168285 pmcid:PMC3247082 fatcat:wqnv5ef4sfg27fwodhu5w3vbeu

CARIBIAM: Constrained Association Rules using Interactive Biological IncrementAl Mining

Imad Rahal, Riad Rahhal, Baoying Wang, William Perrizo
2008 International Journal of Bioinformatics Research and Applications  
This paper analyses annotated genome data by applying a very central data-mining technique known as Association Rule Mining (ARM) with the aim of discovering rules and hypotheses capable of yielding deeper  ...  In the literature, ARM has been noted for producing an overwhelming number of rules.  ...  Introduction Understanding biological data and unravelling its hidden patterns pose many challenges for biological researchers and require intelligent data mining and analysis techniques.  ... 
doi:10.1504/ijbra.2008.017162 pmid:18283027 fatcat:no4g2ni4xfczbesvbgou5mhi4i
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