Literature DB >> 20089154

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes.

Andreas Ruepp1, Andreas Kowarsch, Daniel Schmidl, Felix Buggenthin, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Fabian J Theis.   

Abstract

In recent years, microRNAs have been shown to play important roles in physiological as well as malignant processes. The PhenomiR database http://mips.helmholtz-muenchen.de/phenomir provides data from 542 studies that investigate deregulation of microRNA expression in diseases and biological processes as a systematic, manually curated resource. Using the PhenomiR dataset, we could demonstrate that, depending on disease type, independent information from cell culture studies contrasts with conclusions drawn from patient studies.

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Year:  2010        PMID： 20089154      PMCID： PMC2847718          DOI： 10.1186/gb-2010-11-1-r6

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  40 in total

1.  microRNAs exhibit high frequency genomic alterations in human cancer.

Authors:  Lin Zhang; Jia Huang; Nuo Yang; Joel Greshock; Molly S Megraw; Antonis Giannakakis; Shun Liang; Tara L Naylor; Andrea Barchetti; Michelle R Ward; George Yao; Angelica Medina; Ann O'brien-Jenkins; Dionyssios Katsaros; Artemis Hatzigeorgiou; Phyllis A Gimotty; Barbara L Weber; George Coukos
Journal:  Proc Natl Acad Sci U S A       Date:  2006-06-05       Impact factor: 11.205

2.  The role of site accessibility in microRNA target recognition.

Authors:  Michael Kertesz; Nicola Iovino; Ulrich Unnerstall; Ulrike Gaul; Eran Segal
Journal:  Nat Genet       Date:  2007-09-23       Impact factor: 38.330

3.  The human disease network.

Authors:  Kwang-Il Goh; Michael E Cusick; David Valle; Barton Childs; Marc Vidal; Albert-László Barabási
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-14       Impact factor: 11.205

4.  Altered microRNA expression in human heart disease.

Authors:  Sadakatsu Ikeda; Sek Won Kong; Jun Lu; Egbert Bisping; Hao Zhang; Paul D Allen; Todd R Golub; Burkert Pieske; William T Pu
Journal:  Physiol Genomics       Date:  2007-08-21       Impact factor: 3.107

5.  Micro-RNA profiling in kidney and bladder cancers.

Authors:  Fedra Gottardo; Chang Gong Liu; Manuela Ferracin; George A Calin; Matteo Fassan; Pierfrancesco Bassi; Cinzia Sevignani; Dolores Byrne; Massimo Negrini; Francesco Pagano; Leonard G Gomella; Carlo M Croce; Raffaele Baffa
Journal:  Urol Oncol       Date:  2007 Sep-Oct       Impact factor: 3.498

6.  Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival.

Authors:  Junichi Takamizawa; Hiroyuki Konishi; Kiyoshi Yanagisawa; Shuta Tomida; Hirotaka Osada; Hideki Endoh; Tomoko Harano; Yasushi Yatabe; Masato Nagino; Yuji Nimura; Tetsuya Mitsudomi; Takashi Takahashi
Journal:  Cancer Res       Date:  2004-06-01       Impact factor: 12.701

7.  MicroRNAs accurately identify cancer tissue origin.

Authors:  Nitzan Rosenfeld; Ranit Aharonov; Eti Meiri; Shai Rosenwald; Yael Spector; Merav Zepeniuk; Hila Benjamin; Norberto Shabes; Sarit Tabak; Asaf Levy; Danit Lebanony; Yaron Goren; Erez Silberschein; Nurit Targan; Alex Ben-Ari; Shlomit Gilad; Netta Sion-Vardy; Ana Tobar; Meora Feinmesser; Oleg Kharenko; Ofer Nativ; Dvora Nass; Marina Perelman; Ady Yosepovich; Bruria Shalmon; Sylvie Polak-Charcon; Eddie Fridman; Amir Avniel; Isaac Bentwich; Zvi Bentwich; Dalia Cohen; Ayelet Chajut; Iris Barshack
Journal:  Nat Biotechnol       Date:  2008-03-23       Impact factor: 54.908

8.  Distinctive patterns of microRNA expression in primary muscular disorders.

Authors:  Iris Eisenberg; Alal Eran; Ichizo Nishino; Maurizio Moggio; Costanza Lamperti; Anthony A Amato; Hart G Lidov; Peter B Kang; Kathryn N North; Stella Mitrani-Rosenbaum; Kevin M Flanigan; Lori A Neely; Duncan Whitney; Alan H Beggs; Isaac S Kohane; Louis M Kunkel
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-17       Impact factor: 11.205

9.  A mammalian microRNA expression atlas based on small RNA library sequencing.

Authors:  Pablo Landgraf; Mirabela Rusu; Robert Sheridan; Alain Sewer; Nicola Iovino; Alexei Aravin; Sébastien Pfeffer; Amanda Rice; Alice O Kamphorst; Markus Landthaler; Carolina Lin; Nicholas D Socci; Leandro Hermida; Valerio Fulci; Sabina Chiaretti; Robin Foà; Julia Schliwka; Uta Fuchs; Astrid Novosel; Roman-Ulrich Müller; Bernhard Schermer; Ute Bissels; Jason Inman; Quang Phan; Minchen Chien; David B Weir; Ruchi Choksi; Gabriella De Vita; Daniela Frezzetti; Hans-Ingo Trompeter; Veit Hornung; Grace Teng; Gunther Hartmann; Miklos Palkovits; Roberto Di Lauro; Peter Wernet; Giuseppe Macino; Charles E Rogler; James W Nagle; Jingyue Ju; F Nina Papavasiliou; Thomas Benzing; Peter Lichter; Wayne Tam; Michael J Brownstein; Andreas Bosio; Arndt Borkhardt; James J Russo; Chris Sander; Mihaela Zavolan; Thomas Tuschl
Journal:  Cell       Date:  2007-06-29       Impact factor: 41.582

10.  miRBase: tools for microRNA genomics.

Authors:  Sam Griffiths-Jones; Harpreet Kaur Saini; Stijn van Dongen; Anton J Enright
Journal:  Nucleic Acids Res       Date:  2007-11-08       Impact factor: 16.971
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  103 in total

1.  Systematic analysis of genomic organization and heterogeneities of miRNA cluster in vertebrates.

Authors:  Jie Sun; Hai-Ping Liu; Jia-En Deng; Meng Zhou
Journal:  Mol Biol Rep       Date:  2011-12-11       Impact factor: 2.316

2.  Integration of MicroRNA databases to study MicroRNAs associated with multiple sclerosis.

Authors:  Charlotte Angerstein; Michael Hecker; Brigitte Katrin Paap; Dirk Koczan; Madhan Thamilarasan; Hans-Jürgen Thiesen; Uwe Klaus Zettl
Journal:  Mol Neurobiol       Date:  2012-05-02       Impact factor: 5.590

3.  Transcriptional regulation of microRNA-100, -146a, and -150 genes by p53 and NFκB p65/RelA in mouse striatal STHdh(Q7)/ Hdh(Q7) cells and human cervical carcinoma HeLa cells.

Authors:  Jayeeta Ghose; N P Bhattacharyya
Journal:  RNA Biol       Date:  2015       Impact factor: 4.652

4.  miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs.

Authors:  Andreas Kowarsch; Martin Preusse; Carsten Marr; Fabian J Theis
Journal:  RNA       Date:  2011-03-25       Impact factor: 4.942

5.  RSCMDA: Prediction of Potential miRNA-Disease Associations Based on a Robust Similarity Constraint Learning Method.

Authors:  Yu ShengPeng; Wang Hong
Journal:  Interdiscip Sci       Date:  2021-07-10       Impact factor: 2.233

6.  A non-negative matrix factorization based method for predicting disease-associated miRNAs in miRNA-disease bilayer network.

Authors:  Yingli Zhong; Ping Xuan; Xiao Wang; Tiangang Zhang; Jianzhong Li; Yong Liu; Weixiong Zhang
Journal:  Bioinformatics       Date:  2018-01-15       Impact factor: 6.937

7.  Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device.

Authors:  Maggie R Williams; Robert D Stedtfeld; Tiffany M Stedtfeld; James M Tiedje; Syed A Hashsham
Journal:  Biomed Microdevices       Date:  2017-09       Impact factor: 2.838

8.  miR-125b promotes cell death by targeting spindle assembly checkpoint gene MAD1 and modulating mitotic progression.

Authors:  S Bhattacharjya; S Nath; J Ghose; G P Maiti; N Biswas; S Bandyopadhyay; C K Panda; N P Bhattacharyya; S Roychoudhury
Journal:  Cell Death Differ       Date:  2012-10-26       Impact factor: 15.828

9.  Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways.

Authors:  Andreas Kowarsch; Carsten Marr; Daniel Schmidl; Andreas Ruepp; Fabian J Theis
Journal:  PLoS One       Date:  2010-06-30       Impact factor: 3.240

10.  MicroRNA-196a2 Biomarker and Targetome Network Analysis in Solid Tumors.

Authors:  Eman A Toraih; Manal S Fawzy; Eman A Mohammed; Mohammad H Hussein; Mohamad M El-Labban
Journal:  Mol Diagn Ther       Date:  2016-12       Impact factor: 4.074
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