Literature DB >> 25988189

Integrated miRNA and mRNA Analysis of Time Series Microarray Data.

Julian Dymacek1, Nancy Lan Guo2.   

Abstract

The dynamic temporal regulatory effects of microRNA are not well known. We introduce a technique for integrating miRNA and mRNA time series microarray data with known disease pathology. The integrated analysis includes identifying both mRNA and miRNA that are signi cantly similar to the quantitative pathology. Potential regulatory miRNA/mRNA target pairs are identi ed through databases of both predicted and validated pairs. Finally, potential target pairs are ltered by examining the second derivatives of the fold changes over time. Our system was used on genome-wide microarray expression data of mouse lungs (n = 160) following aspiration of multi-walled carbon nanotubes. This system shows promise of readily identifying miRNA for further study as potential biomarker use.

Entities:  

Year:  2014        PMID： 25988189      PMCID： PMC4433490          DOI： 10.1145/2649387.2649411

Source DB:  PubMed          Journal:  ACM BCB


  26 in total

1.  Learning the parts of objects by non-negative matrix factorization.

Authors:  D D Lee; H S Seung
Journal:  Nature       Date:  1999-10-21       Impact factor: 49.962

2.  Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.

Authors:  Benjamin P Lewis; Christopher B Burge; David P Bartel
Journal:  Cell       Date:  2005-01-14       Impact factor: 41.582

3.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs.

Authors:  Lee P Lim; Nelson C Lau; Philip Garrett-Engele; Andrew Grimson; Janell M Schelter; John Castle; David P Bartel; Peter S Linsley; Jason M Johnson
Journal:  Nature       Date:  2005-01-30       Impact factor: 49.962

4.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

5.  Systems Approach to Identifying Relevant Pathways from Phenotype Information in Dose-Dependent Time Series Microarray Data.

Authors:  Julian Dymacek; Nancy Lan Guo
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2011-11

6.  Mouse pulmonary dose- and time course-responses induced by exposure to multi-walled carbon nanotubes.

Authors:  Dale W Porter; Ann F Hubbs; Robert R Mercer; Nianqiang Wu; Michael G Wolfarth; Krishnan Sriram; Stephen Leonard; Lori Battelli; Diane Schwegler-Berry; Sherry Friend; Michael Andrew; Bean T Chen; Shuji Tsuruoka; Morinobu Endo; Vincent Castranova
Journal:  Toxicology       Date:  2009-10-24       Impact factor: 4.221

7.  System-based identification of toxicity pathways associated with multi-walled carbon nanotube-induced pathological responses.

Authors:  Brandi N Snyder-Talkington; Julian Dymacek; Dale W Porter; Michael G Wolfarth; Robert R Mercer; Maricica Pacurari; James Denvir; Vincent Castranova; Yong Qian; Nancy L Guo
Journal:  Toxicol Appl Pharmacol       Date:  2013-07-08       Impact factor: 4.219

8.  A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules.

Authors:  Shihua Zhang; Qingjiao Li; Juan Liu; Xianghong Jasmine Zhou
Journal:  Bioinformatics       Date:  2011-07-01       Impact factor: 6.937

9.  miRecords: an integrated resource for microRNA-target interactions.

Authors:  Feifei Xiao; Zhixiang Zuo; Guoshuai Cai; Shuli Kang; Xiaolian Gao; Tongbin Li
Journal:  Nucleic Acids Res       Date:  2008-11-07       Impact factor: 16.971

10.  miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions.

Authors:  Sheng-Da Hsu; Yu-Ting Tseng; Sirjana Shrestha; Yu-Ling Lin; Anas Khaleel; Chih-Hung Chou; Chao-Fang Chu; Hsi-Yuan Huang; Ching-Min Lin; Shu-Yi Ho; Ting-Yan Jian; Feng-Mao Lin; Tzu-Hao Chang; Shun-Long Weng; Kuang-Wen Liao; I-En Liao; Chun-Chi Liu; Hsien-Da Huang
Journal:  Nucleic Acids Res       Date:  2013-12-04       Impact factor: 16.971
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  3 in total

1.  mRNA and miRNA regulatory networks reflective of multi-walled carbon nanotube-induced lung inflammatory and fibrotic pathologies in mice.

Authors:  Julian Dymacek; Brandi N Snyder-Talkington; Dale W Porter; Robert R Mercer; Michael G Wolfarth; Vincent Castranova; Yong Qian; Nancy L Guo
Journal:  Toxicol Sci       Date:  2014-12-18       Impact factor: 4.849

2.  Nano-risk Science: application of toxicogenomics in an adverse outcome pathway framework for risk assessment of multi-walled carbon nanotubes.

Authors:  Sarah Labib; Andrew Williams; Carole L Yauk; Jake K Nikota; Håkan Wallin; Ulla Vogel; Sabina Halappanavar
Journal:  Part Fibre Toxicol       Date:  2016-03-15       Impact factor: 9.400

3.  Application of bi-clustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials.

Authors:  Andrew Williams; Sabina Halappanavar
Journal:  Data Brief       Date:  2017-10-26
  3 in total

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