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There is evidence that most CUPs are metastases of carcinomas whose primary site cannot be recognized. Driven by the hypothesis that the knowledge of primary cancer could improve patient's prognosis, we investigated microRNA expression profiling as a tool for identifying the tissue of origin of metastases. We assessed microRNA expression from 101 formalin-fixed, paraffin-embedded (FFPE) samples from primary cancers and metastasis samples by using a microarray platform. Forty samples representing ten different cancer types were used for defining a cancer-type-specific microRNA signature, which was used for predicting primary sites of metastatic cancers. A 47-miRNA signature was identified and used to estimate tissue-of-origin probabilities for each sample. Overall, accuracy reached 100% for primary cancers and 78% for metastases in our cohort of samples. When the signature was applied to an independent published dataset of 170 samples, accuracy remained high: correct prediction was found within the first two options in 86% of the metastasis cases (first prediction was correct in 68% of cases). This signature was also applied to predict 16 CUPs. In this group, first predictions exhibited probabilities higher than 90% in most of the cases. These results establish that FFPE samples can be used to reveal the tissue of origin of metastatic cancers by using microRNA expression profiling and suggest that the approach, if applied, could provide strong indications for CUPs, whose correct diagnosis is presently undefined. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.", "publicationTitle": "The Journal of Pathology", "publisher": "", "place": "", "date": "Apr 13, 2011", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Pathol", "DOI": "10.1002/path.2915", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21630269", "accessDate": "2011-06-02T15:57:15Z", "PMID": "", "PMCID": "", "ISSN": "1096-9896", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21630269", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-06-02T15:57:27Z", "dateModified": "2011-06-02T15:57:27Z" } }, { "key": "TPD8SS3G", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/TPD8SS3G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/TPD8SS3G", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/46360/items/8SRIWTFN", "type": "application/json" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "TPD8SS3G", "version": 1, "parentItem": "8SRIWTFN", "itemType": "attachment", "linkMode": "imported_url", "title": "van Jaarsveld et al. - 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Epithelial ovarian cancer is the most common cause of death from gynecological malignancies in the Western world. The overall 5-year survival is only 30% due to late diagnosis and development of resistance to chemotherapy. There is, therefore, a strong need for prognostic and predictive markers to help optimize and personalize treatment hence ameliorating the prognosis of ovarian cancer patients.
Since 2006, an increasing number of studies have indicated an essential role for microRNAs in ovarian cancer tumorigenesis. In this review, we provide an overview of the microRNAs that have been associated with different aspects of ovarian cancer, such as tumor subtype, stage, histological grade, germline mutations in BRCA genes, prognosis and therapy resistance. We highlight the role of the let-7 and miR-200 families, two major microRNA families that are frequently dysregulated in ovarian cancer and have been associated with poor prognosis. Interestingly, both have been implicated in the regulation of the epithelial-to-mesenchymal transition, a cellular transition associated with tumor aggressiveness, tumor invasion and chemoresistance. Furthermore, we discuss several other microRNAs that have been associated with chemotherapy resistance, such as miR-214, miR-130a, miR-27a and miR-451. In the final section, we speculate on the possibilities of microRNA-based therapies and the use of microRNAs as diagnostic tools.

", "publicationTitle": "The International Journal of Biochemistry & Cell Biology", "publisher": "", "place": "", "date": "August 2010", "volume": "42", "issue": "8", "section": "", "partNumber": "", "partTitle": "", "pages": "1282-1290", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.biocel.2010.01.014", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/B6TCH-4Y65SJP-3/2/7e347c48e0250628463f5c28af37d610", "accessDate": "2011-03-28T16:19:07Z", "PMID": "", "PMCID": "", "ISSN": "1357-2725", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Let-7 family", "type": 1 }, { "tag": "Ovarian cancer", "type": 1 }, { "tag": "Therapy resistance", "type": 1 }, { "tag": "miR-200 family", "type": 1 }, { "tag": "microRNA", "type": 1 }, { "tag": "toread" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T17:38:14Z", "dateModified": "2011-05-26T17:38:14Z" } }, { "key": "KZI7C65A", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/KZI7C65A", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/KZI7C65A", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/46360/items/WA2JT57K", "type": "application/json" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "KZI7C65A", "version": 1, "parentItem": "WA2JT57K", "itemType": "attachment", "linkMode": "imported_file", "title": "Mott et al. - 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Recently, Bcl-2 expression was shown to be regulated by microRNAs, small endogenous RNA molecules that regulate protein expression through sequence-specific interaction with messenger RNA. By analogy, we reasoned that Mcl-1 expression may also be regulated by microRNAs. We chose human immortalized, but non-malignant, H69 cholangiocyte and malignant KMCH cholangiocarcinoma cell lines for these studies, because Mcl-1 is dysregulated in cells with the malignant phenotype. By in silico analysis, we identified a putative target site in the Mcl-1 mRNA for the mir-29 family, and found that mir-29b was highly expressed in cholangiocytes. Interestingly, mir-29b was downregulated in malignant cells, consistent with Mcl-1 protein upregulation. Enforced mir-29b expression reduced Mcl-1 protein expression in KMCH cells. This effect was direct, as mir-29b negatively regulated the expression of an Mcl-1 3' untranslated region (UTR)-based reporter construct. Enforced mir-29b expression reduced Mcl-1 cellular protein levels and sensitized the cancer cells to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) cytotoxicity. Transfection of non-malignant cells (that express high levels of mir-29) with a locked-nucleic acid antagonist of mir-29b increased Mcl-1 levels and reduced TRAIL-mediated apoptosis. Thus mir-29 is an endogenous regulator of Mcl-1 protein expression, and thereby, apoptosis.", "publicationTitle": "Oncogene", "publisher": "", "place": "", "date": "Sep 13, 2007", "volume": "26", "issue": "42", "section": "", "partNumber": "", "partTitle": "", "pages": "6133-6140", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Oncogene", "DOI": "10.1038/sj.onc.1210436", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/17404574", "accessDate": "2011-04-04T02:01:05Z", "PMID": "", "PMCID": "", "ISSN": "0950-9232", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 17404574", "tags": [ { "tag": "Apoptosis", "type": 1 }, { "tag": "Cell Line, Transformed", "type": 1 }, { "tag": "Cell Line, Tumor", "type": 1 }, { "tag": "Gene Expression Regulation, Neoplastic", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "MicroRNAs", "type": 1 }, { "tag": "Neoplasm Proteins", "type": 1 }, { "tag": "Proto-Oncogene Proteins c-bcl-2", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T17:37:13Z", "dateModified": "2011-05-26T17:37:13Z" } }, { "key": "WT82U7DW", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/WT82U7DW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/WT82U7DW", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Sandhu et al.", "parsedDate": "2011", "numChildren": 0 }, "data": { "key": "WT82U7DW", "version": 1, "itemType": "journalArticle", "title": "Micro-RNA Expression and Function in Lymphomas", "creators": [ { "creatorType": "author", "firstName": "Sukhinder K", "lastName": "Sandhu" }, { "creatorType": "author", "firstName": "Carlo M", "lastName": "Croce" }, { "creatorType": "author", "firstName": "Ramiro", "lastName": "Garzon" } ], "abstractNote": "The recent discovery of microRNAs (miRNAs) has introduced a new layer of complexity to the process of gene regulation. MiRNAs are essential for cellular function, and their dysregulation often results in disease. Study of miRNA expression and function in animal models and human lymphomas has improved our knowledge of the pathogenesis of this heterogeneous disease. In this paper, we attempt to describe the expression of miRNAs and their function in lymphomas and discuss potential miRNA-based therapies in the diagnosis and treatment of lymphomas.", "publicationTitle": "Advances in Hematology", "publisher": "", "place": "", "date": "2011", "volume": "2011", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "347137", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Adv Hematol", "DOI": "10.1155/2011/347137", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21461378", "accessDate": "2011-04-06T15:52:34Z", "PMID": "", "PMCID": "", "ISSN": "1687-9112", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21461378", "tags": [ { "tag": "lymphoma" }, { "tag": "mirna" }, { "tag": "review" }, { "tag": "toget" }, { "tag": "toskim" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T17:37:05Z", "dateModified": "2011-05-26T17:37:05Z" } }, { "key": "CDITNHPW", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/CDITNHPW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/CDITNHPW", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Vogt et al.", "parsedDate": "2011-03", "numChildren": 1 }, "data": { "key": "CDITNHPW", "version": 1, "itemType": "journalArticle", "title": "Frequent concomitant inactivation of miR-34a and miR-34b/c by CpG methylation in colorectal, pancreatic, mammary, ovarian, urothelial, and renal cell carcinomas and soft tissue sarcomas", "creators": [ { "creatorType": "author", "firstName": "Markus", "lastName": "Vogt" }, { "creatorType": "author", "firstName": "Johanna", "lastName": "Munding" }, { "creatorType": "author", "firstName": "Martha", "lastName": "Grüner" }, { "creatorType": "author", "firstName": "Sven-Thorsten", "lastName": "Liffers" }, { "creatorType": "author", "firstName": "Berlinda", "lastName": "Verdoodt" }, { "creatorType": "author", "firstName": "Jennifer", "lastName": "Hauk" }, { "creatorType": "author", "firstName": "Lars", "lastName": "Steinstraesser" }, { "creatorType": "author", "firstName": "Andrea", "lastName": "Tannapfel" }, { "creatorType": "author", "firstName": "Heiko", "lastName": "Hermeking" } ], "abstractNote": "The microRNA encoding genes miR-34a and miR-34b/c represent direct p53 target genes and possess tumor suppressive properties as they mediate apoptosis, cell cycle arrest, and senescence. We previously reported that the miR-34a gene is subject to epigenetic inactivation by CpG methylation of its promoter region in primary prostate cancer and melanomas, and in 110 different cancer cell lines of diverse origin. Here we analyzed the methylation status of miR-34a and miR-34b/c in additional primary tumors of divergent sites. We found methylation of miR-34a or miR-34b/c in formalin-fixed, paraffin-embedded (FFPE) tumor samples from 178 patients with the following frequencies: colorectal cancer (74% miR-34a, 99% miR-34b/c; n = 114), pancreatic cancer (64%, 100%; n = 11), mammary cancer (60%, 90%; n = 10), ovarian cancer (62%, 69%; n = 13), urothelial cancer (71%, 57%; n = 7), and renal cell cancer (58%, 100%; n = 12). Furthermore, soft tissue sarcomas showed methylation of miR-34 gene promoters in FFPE samples (64%, 45%; n = 11), in explanted, cultured cells (53%, 40%; n = 40), and in frozen tissue samples (75%, 75%, n = 8). In the colorectal cancer samples a statistically significant correlation of miR-34a methylation and the absence of p53 mutation was detected. With the exception of sarcoma cell lines, the inactivation of miR-34a and miR-34b/c was concomitant in most cases. These results show that miR-34 inactivation is a common event in tumor formation, and suggest that CpG methylation of miR-34a and miR-34-b/c may have diagnostic value. The mutual exclusiveness of miR-34a methylation and p53 mutation indicates that miR-34a inactivation may substitute for loss of p53 function in cancer.", "publicationTitle": "Virchows Archiv: An International Journal of Pathology", "publisher": "", "place": "", "date": "Mar 2011", "volume": "458", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "313-322", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Virchows Arch", "DOI": "10.1007/s00428-010-1030-5", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21225432", "accessDate": "2011-04-20T19:20:26Z", "PMID": "", "PMCID": "", "ISSN": "1432-2307", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21225432", "tags": [ { "tag": "Breast Neoplasms", "type": 1 }, { "tag": "Cell Line, Tumor", "type": 1 }, { "tag": "Colorectal Neoplasms", "type": 1 }, { "tag": "CpG Islands", "type": 1 }, { "tag": "DNA Methylation", "type": 1 }, { "tag": "DNA, Neoplasm", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Gene Expression Regulation, Neoplastic", "type": 1 }, { "tag": "Gene Silencing", "type": 1 }, { "tag": "Genome", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Immunoenzyme Techniques", "type": 1 }, { "tag": "Kidney Neoplasms", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "MicroRNAs", "type": 1 }, { "tag": "Ovarian Neoplasms", "type": 1 }, { "tag": "Pancreatic Neoplasms", "type": 1 }, { "tag": "Sarcoma", "type": 1 }, { "tag": "Soft Tissue Neoplasms", "type": 1 }, { "tag": "Urologic Neoplasms", "type": 1 }, { "tag": "toread" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T17:36:48Z", "dateModified": "2011-05-26T17:36:48Z" } }, { "key": "64C34HMZ", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/64C34HMZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/64C34HMZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Subramanyam et al.", "parsedDate": "2011-04-13", "numChildren": 2 }, "data": { "key": "64C34HMZ", "version": 1, "itemType": "journalArticle", "title": "Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells", "creators": [ { "creatorType": "author", "firstName": "Deepa", "lastName": "Subramanyam" }, { "creatorType": "author", "firstName": "Samy", "lastName": "Lamouille" }, { "creatorType": "author", "firstName": "Robert L", "lastName": "Judson" }, { "creatorType": "author", "firstName": "Jason Y", "lastName": "Liu" }, { "creatorType": "author", "firstName": "Nathan", "lastName": "Bucay" }, { "creatorType": "author", "firstName": "Rik", "lastName": "Derynck" }, { "creatorType": "author", "firstName": "Robert", "lastName": "Blelloch" } ], "abstractNote": "", "publicationTitle": "Nat Biotech", "publisher": "", "place": "", "date": "online April 13, 2011", "volume": "advance online publication", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Biotech", "DOI": "10.1038/nbt.1862", "citationKey": "", "url": "http://dx.doi.org/10.1038/nbt.1862", "accessDate": "2011-04-20T20:19:02Z", "PMID": "", "PMCID": "", "ISSN": "1546-1696", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Nature", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "toread" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T17:36:35Z", "dateModified": "2011-05-26T17:36:35Z" } }, { "key": "BZMJ899G", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/BZMJ899G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/BZMJ899G", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Munker and Calin", "parsedDate": "2011-08-01", "numChildren": 0 }, "data": { "key": "BZMJ899G", "version": 1, "itemType": "journalArticle", "title": "MicroRNA profiling in cancer", "creators": [ { "creatorType": "author", "firstName": "Reinhold", "lastName": "Munker" }, { "creatorType": "author", "firstName": "George A", "lastName": "Calin" } ], "abstractNote": "The diagnosis of cancer has undergone major changes in the last 40 years. Once based purely on morphology, diagnosis has come to incorporate immunological, cytogenetic and molecular methods. Many cancers, especially leukaemias, are now defined by molecular markers. Gene expression profiling based on mRNA has led to further refinement of the classification and diagnosis of cancer. More recently, miRNAs (microRNAs), among other small non-coding RNA molecules, have been discovered and found to be major players in cell biology. miRNAs, having both oncogenic and tumour-suppressive functions, are dysregulated in many types of cancer. miRNAs also interfere with metastasis, apoptosis and invasiveness of cancer cells. In the present review, we discuss recent advances in miRNA profiling in human cancer. We discuss both frequent and rare tumour types and give an outlook on future developments.", "publicationTitle": "Clinical Science (London, England: 1979)", "publisher": "", "place": "", "date": "Aug 1, 2011", "volume": "121", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "141-158", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Clin. Sci", "DOI": "10.1042/CS20110005", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21526983", "accessDate": "2011-05-01T19:47:28Z", "PMID": "", "PMCID": "", "ISSN": "1470-8736", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21526983", "tags": [ { "tag": "toget" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T17:36:17Z", "dateModified": "2011-05-26T17:36:17Z" } }, { "key": "6982URHS", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/6982URHS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/6982URHS", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Kim et al.", "parsedDate": "2011-04-25", "numChildren": 0 }, "data": { "key": "6982URHS", "version": 1, "itemType": "journalArticle", "title": "p53 regulates epithelial-mesenchymal transition through microRNAs targeting ZEB1 and ZEB2", "creators": [ { "creatorType": "author", "firstName": "Taewan", "lastName": "Kim" }, { "creatorType": "author", "firstName": "Angelo", "lastName": "Veronese" }, { "creatorType": "author", "firstName": "Flavia", "lastName": "Pichiorri" }, { "creatorType": "author", "firstName": "Tae Jin", "lastName": "Lee" }, { "creatorType": "author", "firstName": "Young-Jun", "lastName": "Jeon" }, { "creatorType": "author", "firstName": "Stefano", "lastName": "Volinia" }, { "creatorType": "author", "firstName": "Pascal", "lastName": "Pineau" }, { "creatorType": "author", "firstName": "Agnès", "lastName": "Marchio" }, { "creatorType": "author", "firstName": "Jeff", "lastName": "Palatini" }, { "creatorType": "author", "firstName": "Sung-Suk", "lastName": "Suh" }, { "creatorType": "author", "firstName": "Hansjuerg", "lastName": "Alder" }, { "creatorType": "author", "firstName": "Chang-Gong", "lastName": "Liu" }, { "creatorType": "author", "firstName": "Anne", "lastName": "Dejean" }, { "creatorType": "author", "firstName": "Carlo M", "lastName": "Croce" } ], "abstractNote": "p53 suppresses tumor progression and metastasis. Epithelial-mesenchymal transition (EMT) is a key process in tumor progression and metastasis. The transcription factors ZEB1 and ZEB2 promote EMT. Here, we show that p53 suppresses EMT by repressing expression of ZEB1 and ZEB2. By profiling 92 primary hepatocellular carcinomas (HCCs) and 9 HCC cell lines, we found that p53 up-regulates microRNAs (miRNAs), including miR-200 and miR-192 family members. The miR-200 family members transactivated by p53 then repress ZEB1/2 expression. p53-regulated miR-192 family members also repress ZEB2 expression. Inhibition or overexpression of the miRNAs affects p53-regulated EMT by altering ZEB1 and ZEB2 expression. Our findings indicate that p53 can regulate EMT, and that p53-regulated miRNAs are critical mediators of p53-regulated EMT.", "publicationTitle": "The Journal of Experimental Medicine", "publisher": "", "place": "", "date": "Apr 25, 2011", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Exp Med", "DOI": "10.1084/jem.20110235", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21518799", "accessDate": "2011-05-01T19:54:38Z", "PMID": "", "PMCID": "", "ISSN": "1540-9538", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21518799", "tags": [ { "tag": "toget" }, { "tag": "toread-soon" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T17:36:10Z", "dateModified": "2011-05-26T17:36:10Z" } }, { "key": "53NEBDFI", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/53NEBDFI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/53NEBDFI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Bonnet et al.", "parsedDate": "2010-04-14", "numChildren": 2 }, "data": { "key": "53NEBDFI", "version": 1, "itemType": "journalArticle", "title": "Module Network Inference from a Cancer Gene Expression Data Set Identifies MicroRNA Regulated Modules", "creators": [ { "creatorType": "author", "firstName": "Eric", "lastName": "Bonnet" }, { "creatorType": "author", "firstName": "Marianthi", "lastName": "Tatari" }, { "creatorType": "author", "firstName": "Anagha", "lastName": "Joshi" }, { "creatorType": "author", "firstName": "Tom", "lastName": "Michoel" }, { "creatorType": "author", "firstName": "Kathleen", "lastName": "Marchal" }, { "creatorType": "author", "firstName": "Geert", "lastName": "Berx" }, { "creatorType": "author", "firstName": "Yves", "lastName": "Van de Peer" } ], "abstractNote": "MicroRNAs (miRNAs) are small RNAs that recognize and regulate mRNA target genes. Multiple lines of evidence indicate that they are key regulators of numerous critical functions in development and disease, including cancer. However, defining the place and function of miRNAs in complex regulatory networks is not straightforward. Systems approaches, like the inference of a module network from expression data, can help to achieve this goal.\n\nDuring the last decade, much progress has been made in the development of robust and powerful module network inference algorithms. In this study, we analyze and assess experimentally a module network inferred from both miRNA and mRNA expression data, using our recently developed module network inference algorithm based on probabilistic optimization techniques. We show that several miRNAs are predicted as statistically significant regulators for various modules of tightly co-expressed genes. A detailed analysis of three of those modules demonstrates that the specific assignment of miRNAs is functionally coherent and supported by literature. We further designed a set of experiments to test the assignment of miR-200a as the top regulator of a small module of nine genes. The results strongly suggest that miR-200a is regulating the module genes via the transcription factor ZEB1. Interestingly, this module is most likely involved in epithelial homeostasis and its dysregulation might contribute to the malignant process in cancer cells.\n\nOur results show that a robust module network analysis of expression data can provide novel insights of miRNA function in important cellular processes. Such a computational approach, starting from expression data alone, can be helpful in the process of identifying the function of miRNAs by suggesting modules of co-expressed genes in which they play a regulatory role. As shown in this study, those modules can then be tested experimentally to further investigate and refine the function of the miRNA in the regulatory network.", "publicationTitle": "PLoS ONE", "publisher": "", "place": "", "date": "April 14, 2010", "volume": "5", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "e10162", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS ONE", "DOI": "10.1371/journal.pone.0010162", "citationKey": "", "url": "http://dx.doi.org/10.1371/journal.pone.0010162", "accessDate": "2011-05-02T19:36:09Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PLoS ONE", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "toread" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T17:35:47Z", "dateModified": "2011-05-26T17:35:47Z" } }, { "key": "IXD4Q3CZ", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/IXD4Q3CZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/IXD4Q3CZ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/46360/items/IDTDHTZX", "type": "application/json" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } } }, "data": { "key": "IXD4Q3CZ", "version": 1, "parentItem": "IDTDHTZX", "itemType": "attachment", "linkMode": "imported_url", "title": "ScienceDirect Snapshot", "accessDate": "2011-05-23T23:00:44Z", "url": "http://www.sciencedirect.com/science/article/pii/S0090825811003349", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "S0090825811003349.html", "md5": null, "mtime": 1306191644853, "tags": [], "relations": {}, "dateAdded": "2011-05-26T16:00:36Z", "dateModified": "2011-05-26T16:01:34Z" } }, { "key": "VJBETTHU", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/VJBETTHU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/VJBETTHU", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/46360/items/SKNUQZFK", "type": "application/json" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } } }, "data": { "key": "VJBETTHU", "version": 1, "parentItem": "SKNUQZFK", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2011-05-24T21:10:20Z", "url": "http://bioinformatics.oxfordjournals.org/content/27/10/1346.short?rss=1", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "1346.html", "md5": null, "mtime": 1306271421149, "tags": [], "relations": {}, "dateAdded": "2011-05-26T16:00:20Z", "dateModified": "2011-05-26T16:01:34Z" } }, { "key": "NZK2T5AN", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/NZK2T5AN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/NZK2T5AN", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/46360/items/SKNUQZFK", "type": "application/json" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "NZK2T5AN", "version": 1, "parentItem": "SKNUQZFK", "itemType": "attachment", "linkMode": "imported_url", "title": "Ellwanger et al. - 2011 - The sufficient minimal set of miRNA seed types.pdf", "accessDate": "2011-05-24T21:10:21Z", "url": "http://bioinformatics.oxfordjournals.org/content/27/10/1346.full.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Ellwanger et al. - 2011 - The sufficient minimal set of miRNA seed types.pdf", "md5": "3366f5a2e068bb4f00c9d33d373ca88e", "mtime": 1306271422870, "tags": [], "relations": {}, "dateAdded": "2011-05-26T16:00:20Z", "dateModified": "2011-05-26T16:01:34Z" } }, { "key": "H54PT2PH", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/H54PT2PH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/H54PT2PH", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/46360/items/HVU99ZJU", "type": "application/json" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "H54PT2PH", "version": 1, "parentItem": "HVU99ZJU", "itemType": "attachment", "linkMode": "imported_file", "title": "Plaisier et al. - 2011 - miRvestigator web application to identify miRNAs .pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Plaisier et al. - 2011 - miRvestigator web application to identify miRNAs .pdf", "md5": "cae78a0e280ba8d425978387cdedd0f3", "mtime": 1306273312442, "tags": [], "relations": {}, "dateAdded": "2011-05-26T16:00:06Z", "dateModified": "2011-05-26T16:01:34Z" } }, { "key": "IDTDHTZX", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/IDTDHTZX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/IDTDHTZX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Lu et al.", "numChildren": 1 }, "data": { "key": "IDTDHTZX", "version": 1, "itemType": "journalArticle", "title": "MicroRNA let-7a: A potential marker for selection of paclitaxel in ovarian cancer management", "creators": [ { "creatorType": "author", "firstName": "Lingeng", "lastName": "Lu" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Schwartz" }, { "creatorType": "author", "firstName": "Luca", "lastName": "Scarampi" }, { "creatorType": "author", "firstName": "Thomas", "lastName": "Rutherford" }, { "creatorType": "author", "firstName": "Emilie Marion", "lastName": "Canuto" }, { "creatorType": "author", "firstName": "Herbert", "lastName": "Yu" }, { "creatorType": "author", "firstName": "Dionyssios", "lastName": "Katsaros" } ], "abstractNote": "

Objectives
Let-7 is a family of small non-coding RNAs regulating the expression of many genes that control important cellular activities. Let-7 is shown in vitro to sensitize cancer cells to platinum, but induce ovarian cancer resistance to paclitaxel. This study aims to investigate the effect of let-7a expression on survival outcomes of epithelial ovarian cancer (EOC) patients treated with different chemotherapy.Methods
Let-7a expression was measured with qRT-PCR in ovarian tumors of 178 EOC patients who received platinum-based chemotherapy with and without paclitaxel after surgery. Survival analysis was performed to assess the effects of let-7a and chemotherapy on disease outcomes.Results
Let-7a expression was detectable in the EOC samples, but the expression was not associated with disease stage, tumor grade, histology and debulking results. Patients who responded to platinum with paclitaxel had significantly lower let-7a than those who did not. Survival analyses showed that patients with high let-7a had better survival compared to those with low let-7a when they were treated with platinum without paclitaxel. The hazards ratios (HRs) for death and disease progression were 0.52 (95% CI: 0.29-0.96) and 0.48 (0.26-0.89) for high let-7a when compared to low let-7a, respectively. However, when patients were treated with platinum and paclitaxel, high let-7a was associated with worse progression-free and overall survival. The HRs for death and disease progression were 3.87 (95% CI: 1.28-11.66) and 3.48 (95% CI: 1.25-9.67) for high let-7a when compared to low let-7a, respectively. Further studies showed that among patients with low let-7a, those treated with paclitaxel in addition to platinum survived better than those treated without paclitaxel [adjusted-HRs were 0.31 (95% CI: 0.15-0.66) for death and 0.40 (95% CI: 0.22-0.75) for disease], while among those with high let-7a, the two types of treatment made no difference in patient survival.Conclusions
The study suggests that the beneficial impact of the addition of paclitaxel on EOC survival was significantly linked to let-7a levels, and that miRNAs such as let-7a may be a useful marker for selection of chemotherapeutic agents in EOC management.

", "publicationTitle": "Gynecologic Oncology", "publisher": "", "place": "", "date": "", "volume": "In Press, Corrected Proof", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "16/j.ygyno.2011.04.033", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0090825811003349", "accessDate": "2011-05-23T23:00:38Z", "PMID": "", "PMCID": "", "ISSN": "0090-8258", "archive": "", "archiveLocation": "", "shortTitle": "MicroRNA let-7a", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Chemotherapy", "type": 1 }, { "tag": "Let-7a", "type": 1 }, { "tag": "Ovarian cancer", "type": 1 }, { "tag": "Prognosis", "type": 1 }, { "tag": "miRNA", "type": 1 }, { "tag": "toget" }, { "tag": "toread" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T16:00:36Z", "dateModified": "2011-05-26T16:00:36Z" } }, { "key": "F4DKTNTX", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/F4DKTNTX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/F4DKTNTX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Chan et al.", "parsedDate": "2011-06-01", "numChildren": 0 }, "data": { "key": "F4DKTNTX", "version": 1, "itemType": "journalArticle", "title": "MicroRNA signatures differentiate melanoma subtypes", "creators": [ { "creatorType": "author", "firstName": "Elcie", "lastName": "Chan" }, { "creatorType": "author", "firstName": "Rajeshvari", "lastName": "Patel" }, { "creatorType": "author", "firstName": "Sunitha", "lastName": "Nallur" }, { "creatorType": "author", "firstName": "Elena", "lastName": "Ratner" }, { "creatorType": "author", "firstName": "Antonella", "lastName": "Bacchiocchi" }, { "creatorType": "author", "firstName": "Kathleen", "lastName": "Hoyt" }, { "creatorType": "author", "firstName": "Sebastian", "lastName": "Szpakowski" }, { "creatorType": "author", "firstName": "Sirie", "lastName": "Godshalk" }, { "creatorType": "author", "firstName": "Stephan", "lastName": "Ariyan" }, { "creatorType": "author", "firstName": "Mario", "lastName": "Sznol" }, { "creatorType": "author", "firstName": "Ruth", "lastName": "Halaban" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Krauthammer" }, { "creatorType": "author", "firstName": "David", "lastName": "Tuck" }, { "creatorType": "author", "firstName": "Frank J", "lastName": "Slack" }, { "creatorType": "author", "firstName": "Joanne Barnes", "lastName": "Weidhaas" } ], "abstractNote": "Melanoma is an aggressive cancer that is highly resistance to therapies once metastasized. We studied microRNA (miRNA) expression in clinical melanoma subtypes and evaluated different miRNA signatures in the background of gain of function somatic and inherited mutations associated with melanoma. Total RNA from 42 patient derived primary melanoma cell lines and three independent normal primary melanocyte cell cultures was evaluated by miRNA array. MiRNA expression was then analyzed comparing subtypes and additional clinicopathologic criteria including somatic mutations. The prevalence and association of an inherited variant in a miRNA binding site in the 3'UTR of the KRAS oncogene, referred to as the KRAS-variant, was also evaluated. We show that seven miRNAs, miR-142-3p, miR-486, miR-214, miR-218, miR-362, miR-650 and miR-31, were significantly correlated with acral as compared to non-acral melanomas (p < 0.04). In addition, we discovered that the KRAS-variant was enriched in non-acral melanoma (25%), and that miR-137 under expression was significantly associated with melanomas with the KRAS-variant. Our findings indicate that miRNAs are differentially expressed in melanoma subtypes and that their misregulation can be impacted by inherited gene variants, supporting the hypothesis that miRNA misregulation reflects biological differences in melanoma.", "publicationTitle": "Cell Cycle (Georgetown, Tex.)", "publisher": "", "place": "", "date": "Jun 1, 2011", "volume": "10", "issue": "11", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cell Cycle", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21543894", "accessDate": "2011-05-24T04:13:46Z", "PMID": "", "PMCID": "", "ISSN": "1551-4005", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21543894", "tags": [ { "tag": "classification" }, { "tag": "melanoma" }, { "tag": "mirna" }, { "tag": "toget" }, { "tag": "toread" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T16:00:25Z", "dateModified": "2011-05-26T16:00:25Z" } }, { "key": "SKNUQZFK", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/SKNUQZFK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/SKNUQZFK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Ellwanger et al.", "parsedDate": "2011-05-15", "numChildren": 2 }, "data": { "key": "SKNUQZFK", "version": 1, "itemType": "journalArticle", "title": "The sufficient minimal set of miRNA seed types", "creators": [ { "creatorType": "author", "firstName": "Daniel C.", "lastName": "Ellwanger" }, { "creatorType": "author", "firstName": "Florian A.", "lastName": "Büttner" }, { "creatorType": "author", "firstName": "Hans-Werner", "lastName": "Mewes" }, { "creatorType": "author", "firstName": "Volker", "lastName": "Stümpflen" } ], "abstractNote": "Motivation: Pairing between the target sequence and the 6–8 nt long seed sequence of the miRNA presents the most important feature for miRNA target site prediction. Novel high-throughput technologies such as Argonaute HITS-CLIP afford meanwhile a detailed study of miRNA:mRNA duplices. These interaction maps enable a first discrimination between functional and non-functional target sites in a bulky fashion. Prediction algorithms apply different seed paradigms to identify miRNA target sites. Therefore, a quantitative assessment of miRNA target site prediction is of major interest.Results: We identified a set of canonical seed types based on a transcriptome wide analysis of experimentally verified functional target sites. We confirmed the specificity of long seeds but we found that the majority of functional target sites are formed by less specific seeds of only 6 nt indicating a crucial role of this type. A substantial fraction of genuine target sites arenon-conserved. Moreover, the majority of functional sites remain uncovered by common prediction methods.Contact: florian.buettner@helmholtz-muenchen.de v.stuempflen@helmholtz-muenchen.deSupplementary Information: Supplementary data are available at Bioinformatics online.", "publicationTitle": "Bioinformatics", "publisher": "", "place": "", "date": "May 15 , 2011", "volume": "27", "issue": "10", "section": "", "partNumber": "", "partTitle": "", "pages": "1346 -1350", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/bioinformatics/btr149", "citationKey": "", "url": "http://bioinformatics.oxfordjournals.org/content/27/10/1346.abstract", "accessDate": "2011-05-24T21:10:19Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Highwire 2.0", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "mirna" }, { "tag": "target-prediction" }, { "tag": "toread" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T16:00:20Z", "dateModified": "2011-05-26T16:00:20Z" } }, { "key": "HVU99ZJU", "version": 1, "library": { "type": "group", "id": 46360, "name": "cancer miRNA", "links": { "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/46360/items/HVU99ZJU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cancer_mirna/items/HVU99ZJU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 18598, "username": "eleanorahowe", "name": "Eleanor Howe", "links": { "alternate": { "href": "https://www.zotero.org/eleanorahowe", "type": "text/html" } } }, "creatorSummary": "Plaisier et al.", "parsedDate": "2011-05-20", "numChildren": 1 }, "data": { "key": "HVU99ZJU", "version": 1, "itemType": "journalArticle", "title": "miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling", "creators": [ { "creatorType": "author", "firstName": "Christopher L", "lastName": "Plaisier" }, { "creatorType": "author", "firstName": "J Christopher", "lastName": "Bare" }, { "creatorType": "author", "firstName": "Nitin S", "lastName": "Baliga" } ], "abstractNote": "Transcriptome profiling studies have produced staggering numbers of gene co-expression signatures for a variety of biological systems. A significant fraction of these signatures will be partially or fully explained by miRNA-mediated targeted transcript degradation. miRvestigator takes as input lists of co-expressed genes from Caenorhabditis elegans, Drosophila melanogaster, G. gallus, Homo sapiens, Mus musculus or Rattus norvegicus and identifies the specific miRNAs that are likely to bind to 3' un-translated region (UTR) sequences to mediate the observed co-regulation. The novelty of our approach is the miRvestigator hidden Markov model (HMM) algorithm which systematically computes a similarity P-value for each unique miRNA seed sequence from the miRNA database miRBase to an overrepresented sequence motif identified within the 3'-UTR of the query genes. We have made this miRNA discovery tool accessible to the community by integrating our HMM algorithm with a proven algorithm for de novo discovery of miRNA seed sequences and wrapping these algorithms into a user-friendly interface. Additionally, the miRvestigator web server also produces a list of putative miRNA binding sites within 3'-UTRs of the query transcripts to facilitate the design of validation experiments. The miRvestigator is freely available at http://mirvestigator.systemsbiology.net.", "publicationTitle": "Nucleic Acids Research", "publisher": "", "place": "", "date": "May 20, 2011", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nucleic Acids Res", "DOI": "10.1093/nar/gkr374", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21602264", "accessDate": "2011-05-24T21:38:28Z", "PMID": "", "PMCID": "", "ISSN": "1362-4962", "archive": "", "archiveLocation": "", "shortTitle": "miRvestigator", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21602264", "tags": [ { "tag": "mirna" }, { "tag": "toget" }, { "tag": "toread" } ], "collections": [], "relations": {}, "dateAdded": "2011-05-26T16:00:06Z", "dateModified": "2011-05-26T16:00:06Z" } } ]