Bias in microRNA functional enrichment analysis

Bioinformatics

Volumn 31, Issue 10, 2015, Pages 1592-1598

  Bleazard, Thomas ^a   Lamb, Janine A ^a   Griffiths Jones, Sam ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ALGORITHM; BIOLOGY; GENE EXPRESSION REGULATION; GENETICS; HUMAN; MOLECULAR GENETICS; PROCEDURES; SEQUENCE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, RNA;

EID: 84929649983     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv023     Document Type: Article

References (63)

1. Abrouk M., et al. (2012). Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication. Plant Cell, 24, 1776-1792
2. Arndt G.M., et al. (2009). Characterization of global microRNA expression reveals oncogenic potential of miR-145 in metastatic colorectal cancer. BMC Cancer, 9, 374
3. Ashburner M., et al. (2000). Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29
4. Bartel D.P. (2009). MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233
5. Benjamini Y. and Hochberg Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300
6. Chartoumpekis D.V., et al. (2012). Differential expression of microRNAs in adipose tissue after long-term high-fat diet-induced obesity in mice. PLoS One, 7, e34872
7. Chen G.-Q., et al. (2010). Systematic analysis of microRNA involved in resistance of the MCF-7 human breast cancer cell to doxorubicin. Med. Oncol., 27, 406-415
8. Chen M., et al. (2013a). High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation. PLoS One, 8, e76120
9. Chen W.-S., et al. (2013b). Co-modulated behavior and effects of differentially expressed miRNA in colorectal cancer. BMC Genomics, 14, S12
10. Cheng L.-C., et al. (2009). miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nat. Neurosci., 12, 399-408
11. Cho S., et al. (2013). MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. Nucleic Acids Res., 41, D252-D257
12. Collino F., et al. (2010). Microvesicles derived from adult human bone marrow and tissue specific mesenchymal stem cells shuttle selected pattern of miRNAs. PLoS One, 5, e11803
13. Dai X. and Zhao P.X. (2011). psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res., 39, W155-W159
14. Davidson M.R., et al. (2010). MicroRNA-218 is deleted and downregulated in lung squamous cell carcinoma. PLoS One, 5, e12560
15. Du Z., et al. (2010). agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res., 38, W64-W70
16. Enright A.J., et al. (2003). MicroRNA targets in Drosophila. Genome Biol., 5, R1
17. Flavin R.J., et al. (2009). Potentially important microRNA cluster on chromosome 17p13.1 in primary peritoneal carcinoma. Mod. Pathol., 22, 197-205
18. Friedman R. and Farh K. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105
19. Gusev Y., et al. (2007). Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer. BMC Bioinformatics, 8, S16
20. Gusev Y. (2008). Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. Methods, 44, 61-72
21. He X., et al. (2013). Identification and characterization of microRNAs by high through-put sequencing in mesenchymal stem cells and bone tissue from mice of age-related osteoporosis. PLoS One, 8, e71895
22. Hu Z., et al. (2014). miR-191 and miR-135 are required for long-lasting spine remodelling associated with synaptic long-term depression. Nat. Commun., 5, 3263
23. Huang D.W., et al. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57
24. Hunter M.P., et al. (2008). Detection of microRNA expression in human peripheral blood microvesicles. PLoS One, 3, e3694
25. Jiang J., et al. (2008). Association of MicroRNA expression in hepatocellular carcinomas with hepatitis infection, cirrhosis, and patient survival. Clin. Cancer Res., 14, 419-427
26. Kanehisa M. and Goto S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30
27. Keck-Wherley J., et al. (2011). Abnormal microRNA expression in Ts65Dn hippocampus and whole blood: contributions to Down syndrome phenotypes. Dev. Neurosci., 33, 451-467
28. Kertesz M., et al. (2007). The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278-1284
29. Kinsella R.J., et al. (2011). Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database, 2011, bar030
30. Kozomara A. and Griffiths-Jones S. (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157
31. Kraemer A., et al. (2013). UVA and UVB irradiation differentially regulate microRNA expression in human primary keratinocytes. PLoS One, 8, 1-11
32. Lee S.Y., et al. (2012). MicroRNA-centric measurement improves functional enrichment analysis of co-expressed and differentially expressed microRNA clusters. BMC Genomics, 13, S17
33. Leidinger P., et al. (2013). A blood based 12-miRNA signature of Alzheimer disease patients. Genome Biol., 14, R78
34. Li J.-H., et al. (2014). starBase v2.0: decoding miRNA-ceRNA, miRNAncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res., 42, D92-D97
35. Liang T., et al. (2013). Deep sequencing of small RNA repertoires in mice reveals metabolic disorders-associated hepatic miRNAs. PLoS One, 8, 1-9
36. Liu G., et al. (2010). Computational analysis of microRNA function in heart development. Acta Biochim Biophys Sin, 662-670
37. Lu T.-P., et al. (2012). miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PLoS One, 7, e42390
38. Ma J., et al. (2013). Intrinsic features inMicroRNA transcriptomes link porcine visceral rather than subcutaneous adipose tissues to metabolic risk. PLoS One, 8, e80041
39. Mizuguchi Y., et al. (2011). Sequencing and bioinformatics-based analyses of the microRNA transcriptome in hepatitis B-related hepatocellular carcinoma. PLoS One, 6, e15304
40. Munch E., et al. (2013). Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk. PLoS One, 8, 1-13
41. Peng T., et al. (2011). Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa). J. Exp. Bot., 62, 4943-4954
42. Presneau N. and Eskandarpour M. (2013). MicroRNA profiling of peripheral nerve sheath tumours identifies miR-29c as a tumour suppressor gene involved in tumour progression. Br. J. Cancer, 108, 964-972
43. Raponi M., et al. (2009). MicroRNA classifiers for predicting prognosis of squamous cell lung cancer. Cancer Res., 69, 5776-5783
44. Reczko M., et al. (2012). Functional microRNA targets in protein coding sequences. Bioinformatics, 28, 771-776
45. Ritchie W., et al. (2009). Predicting microRNA targets and functions: traps for the unwary. Nat. Methods, 6, 397-398
46. Romero-Cordoba S., et al. (2012). Identification and pathway analysis of microRNAs with no previous involvement in breast cancer. PLoS One, 7, e31904
47. Sanchez-Diaz P., et al. (2013). De-regulated microRNAs in pediatric cancer stem cells target pathways involved in cell proliferation, cell cycle and development. PLoS One, 8
48. Schonrock N., et al. (2010). Neuronal microRNA deregulation in response to Alzheimer's disease amyloid-beta. PLoS One, 5, e11070
49. Schratt G.M., et al. (2006). A brain-specific microRNA regulates dendritic spine development. Nature, 439, 283-289
50. Slowikowski K., et al. (2014). SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci. Bioinformatics, 30, 2496-2497
51. Soh J., et al. (2013). MicroRNA-30c reduces hyperlipidemia and atherosclerosis in mice by decreasing lipid synthesis and lipoprotein secretion. Nat. Med., 19, 892-900
52. Sokolov M., et al. (2012). Unraveling the global microRNAome responses to ionizing radiation in human embryonic stem cells. PLoS One, 7, e31028
53. Tanic M. and Andrés, E. (2013). MicroRNA-based molecular classification of non-BRCA1/2 hereditary breast tumours. Br. J. Cancer, 109, 2724-2734
54. Wei L.Q., et al. (2011). Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol., 12, R53
55. Wu C., et al. (2012a). Discrepant expression of microRNAs in transparent and cataractous human lenses. Invest. Ophthalmol. Vis. Sci., 53, 3906-3912
56. Wu X., et al. (2011). Genome-wide analysis of microRNA and mRNA expression signatures in hydroxycamptothecin-resistant gastric cancer cells. Acta Pharmacol. Sin., 32, 259-269
57. Wu Y.-Q., et al. (2012b). Pseudorabies virus infected porcine epithelial cell line generates a diverse set of host microRNAs and a special cluster of viral microRNAs. PLoS One, 7, e30988
58. Xie F., et al. (2013). High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress. Plant Biotechnol. J., 159, 1-13
59. Yan Z., et al. (2012). Identification of hsa-miR-335 as a prognostic signature in gastric cancer. PLoS One, 7, e40037
60. Yi R., et al. (2013). Identification and expression analysis of microRNAs at the grain filling stage in rice(Oryza sativa L.)via deep sequencing. PLoS One, 8, e57863
61. Yunta M., et al. (2012). MicroRNA dysregulation in the spinal cord following traumatic injury. PLoS One, 7, e34534
62. Zhang X., et al. (2013). MicroRNA expression profiling in HCV-infected human hepatoma cells identifies potential anti-viral targets induced by interferon-a. PLoS One, 8, e55733
63. Ziats M.N. and Rennert O.M. (2013). Identification of differentially expressed microRNAs across the developing human brain. Mol. Psychiatry, 1-5