Outlier Analysis and Top Scoring Pairfor Integrated Data Analysisand Biomarker Discovery
Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug development. Deregulation can be driven by a number of molecular events, including gene mutation, epigenetic changes in gene promoters, overexpression,...
Uloženo v:
| Vydáno v: | IEEE/ACM transactions on computational biology and bioinformatics Ročník 11; číslo 3; s. 520 - 532 |
|---|---|
| Hlavní autoři: | , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
New York
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
01.05.2014
|
| Témata: | |
| ISSN: | 1545-5963, 1557-9964 |
| On-line přístup: | Získat plný text |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug development. Deregulation can be driven by a number of molecular events, including gene mutation, epigenetic changes in gene promoters, overexpression, and gene amplifications or deletions. We demonstrate a novel approach that identifies pathways of interest by integrating outlier analysis within and across molecular data types with gene set analysis. We use the results to seed the top-scoring pair algorithm to identify robust biomarkers associated with pathway deregulation. We demonstrate this methodology on pediatric acute myeloid leukemia (AML) data. We develop a biomarker in primary AML tumors, demonstrate robustness with an independent primary tumor data set, and show that the identified biomarkers also function well in relapsed pediatric AML tumors. |
|---|---|
| AbstractList | Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug development. Deregulation can be driven by a number of molecular events, including gene mutation, epigenetic changes in gene promoters, overexpression, and gene amplifications or deletions. We demonstrate a novel approach that identifies pathways of interest by integrating outlier analysis within and across molecular data types with gene set analysis. We use the results to seed the top-scoring pair algorithm to identify robust biomarkers associated with pathway deregulation. We demonstrate this methodology on pediatric acute myeloid leukemia (AML) data. We develop a biomarker in primary AML tumors, demonstrate robustness with an independent primary tumor data set, and show that the identified biomarkers also function well in relapsed pediatric AML tumors. |
| Author | Considine, Michael Wei, Yingying Ochs, Michael F Farrar, Jason E Meshinchi, Soheil Arceci, Robert J |
| Author_xml | – sequence: 1 givenname: Michael surname: Ochs middlename: F fullname: Ochs, Michael F – sequence: 2 givenname: Jason surname: Farrar middlename: E fullname: Farrar, Jason E – sequence: 3 givenname: Michael surname: Considine fullname: Considine, Michael – sequence: 4 givenname: Yingying surname: Wei fullname: Wei, Yingying – sequence: 5 givenname: Soheil surname: Meshinchi fullname: Meshinchi, Soheil – sequence: 6 givenname: Robert surname: Arceci middlename: J fullname: Arceci, Robert J |
| BookMark | eNqNj0tLw0AUhQepYFtduh9w4yZx3sks-_BRKFSwgrtyk9yU1DRTZxKh_94UxYUrV_dw-c7hnBEZNK5BQq45izln9m49m05jwbiMuZZnZMi1TiJrjRqctNKRtkZekFEIO8aEskwNyduqa-sKPZ00UB9DFSg0BV27A33Jna-aLX2GypfO00XT4tZDiwWdQwu_hhM_rdwe_HsfM69C7j7RHy_JeQl1wKufOyavD_fr2VO0XD0uZpNldOBGtZESmIG0IE0C3EBfM9WlTQ1ykKIQgLxMdJ6DKFiRMcUZQoanb8lFZrGUY3L7nXvw7qPD0G72fQWsa2jQdWHDTZJYppnh_0BNKgzTadKjN3_Qnet8v7intNFa2jSV8gsXSHHX |
| ContentType | Journal Article |
| Copyright | Copyright The Institute of Electrical and Electronics Engineers, Inc. (IEEE) May 2014 |
| Copyright_xml | – notice: Copyright The Institute of Electrical and Electronics Engineers, Inc. (IEEE) May 2014 |
| DBID | 7QF 7QO 7QQ 7SC 7SE 7SP 7SR 7TA 7TB 7U5 8BQ 8FD F28 FR3 H8D JG9 JQ2 KR7 L7M L~C L~D P64 |
| DOI | 10.1109/TCBB.2013.153 |
| DatabaseName | Aluminium Industry Abstracts Biotechnology Research Abstracts Ceramic Abstracts Computer and Information Systems Abstracts Corrosion Abstracts Electronics & Communications Abstracts Engineered Materials Abstracts Materials Business File Mechanical & Transportation Engineering Abstracts Solid State and Superconductivity Abstracts METADEX Technology Research Database ANTE: Abstracts in New Technology & Engineering Engineering Research Database Aerospace Database Materials Research Database ProQuest Computer Science Collection Civil Engineering Abstracts Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional Biotechnology and BioEngineering Abstracts |
| DatabaseTitle | Materials Research Database Civil Engineering Abstracts Aluminium Industry Abstracts Technology Research Database Computer and Information Systems Abstracts – Academic Mechanical & Transportation Engineering Abstracts Electronics & Communications Abstracts ProQuest Computer Science Collection Computer and Information Systems Abstracts Ceramic Abstracts Materials Business File METADEX Biotechnology and BioEngineering Abstracts Computer and Information Systems Abstracts Professional Aerospace Database Engineered Materials Abstracts Biotechnology Research Abstracts Solid State and Superconductivity Abstracts Engineering Research Database Corrosion Abstracts Advanced Technologies Database with Aerospace ANTE: Abstracts in New Technology & Engineering |
| DatabaseTitleList | Technology Research Database Materials Research Database Engineering Research Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1557-9964 |
| EndPage | 532 |
| ExternalDocumentID | 3443611781 |
| GroupedDBID | 0R~ 29I 4.4 53G 5GY 5VS 6IK 7QF 7QO 7QQ 7SC 7SE 7SP 7SR 7TA 7TB 7U5 8BQ 8FD 8US 97E AAJGR AAKMM AALFJ AASAJ AAWTH AAWTV ABAZT ABQJQ ABVLG ACGFO ACGFS ACIWK ACM ACPRK ADBCU ADL AEBYY AEFXT AEJOY AENEX AENSD AFRAH AFWIH AFWXC AGQYO AGSQL AHBIQ AIKLT AKQYR AKRVB ALMA_UNASSIGNED_HOLDINGS ASPBG ATWAV AVWKF BDXCO BEFXN BFFAM BGNUA BKEBE BPEOZ CCLIF CS3 DU5 EBS EJD F28 FEDTE FR3 GUFHI H8D HGAVV HZ~ I07 IEDLZ IFIPE IPLJI JAVBF JG9 JQ2 KR7 L7M LAI LHSKQ L~C L~D M43 O9- OCL P1C P2P P64 PQQKQ RIA RIE RNS ROL TN5 |
| ID | FETCH-LOGICAL-p164t-42eba39a367a16a15485f986e1a32d2ae1f75cca2d0db0410eabeae1ff12b9ef3 |
| ISSN | 1545-5963 |
| IngestDate | Wed Oct 01 14:20:51 EDT 2025 Tue Oct 07 09:39:10 EDT 2025 Sun Nov 09 08:15:41 EST 2025 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 3 |
| Language | English |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-p164t-42eba39a367a16a15485f986e1a32d2ae1f75cca2d0db0410eabeae1ff12b9ef3 |
| Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-1 ObjectType-Feature-2 content type line 23 |
| PQID | 1565539883 |
| PQPubID | 85499 |
| PageCount | 13 |
| ParticipantIDs | proquest_miscellaneous_1677905061 proquest_miscellaneous_1668260587 proquest_journals_1565539883 |
| PublicationCentury | 2000 |
| PublicationDate | 20140501 |
| PublicationDateYYYYMMDD | 2014-05-01 |
| PublicationDate_xml | – month: 05 year: 2014 text: 20140501 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | New York |
| PublicationPlace_xml | – name: New York |
| PublicationTitle | IEEE/ACM transactions on computational biology and bioinformatics |
| PublicationYear | 2014 |
| Publisher | The Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher_xml | – name: The Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| SSID | ssj0024904 |
| Score | 2.0796602 |
| Snippet | Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug... |
| SourceID | proquest |
| SourceType | Aggregation Database |
| StartPage | 520 |
| SubjectTerms | Algorithms Biomarkers Carcinogens Deregulation Drugs Genes Medical treatment Pathways Pediatrics Tumors |
| Title | Outlier Analysis and Top Scoring Pairfor Integrated Data Analysisand Biomarker Discovery |
| URI | https://www.proquest.com/docview/1565539883 https://www.proquest.com/docview/1668260587 https://www.proquest.com/docview/1677905061 |
| Volume | 11 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVIEE databaseName: IEEE Electronic Library (IEL) customDbUrl: eissn: 1557-9964 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0024904 issn: 1545-5963 databaseCode: RIE dateStart: 20040101 isFulltext: true titleUrlDefault: https://ieeexplore.ieee.org/ providerName: IEEE |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3Pb9MwFLbKAIkLggHaYCAjTdwy4jhO7COtNqFptDtkUjlVTuKISlvatem0_UP8nbznOD-qSdM47BJFrpO0fZ_tvPc-f4-QQ2XSXGqVezrL0UFhhSejNPR0pJldTzkvbLGJeDyW06k6Hwz-Nnthbi7jspS3t2r5pKaGNjA2bp39D3O3N4UGOAejwxHMDsdHGX6yqS5xC0krN4Kh8WSxhGFck-3O9Rwp7TYYaJUicrB9pdsLsP9wvrhC4s4K5TkzpHlupX_RRUQlhtEvrDHRFBy3mYfMloloQox9jSc4dzKtVY9iP8n-rHv8_Y5pjPKQNfv7VGOZxG7LhK0xOq9DsX3av00wWXbCb_idd82i7GIaLOwYhM00HApPKDf1NfM06-GR9yZdEfi99VvU8dL7S4NVVk1GwyES-vgRq0WKtyW4x5PZycXZ2Sw5nibfltceVifDLL4r1fKMPA9ioVi9T7DTdFS2TGX7rTst1-9bz7u33tuXmOQNee28D_qjRs1bMjDlLnlZ1yO9e0emDju0gQIFu1HADnXYoQ47tMMORezQHnZoix3aYuc9uTg5TkY_PVd6w1uC_1x5YWBSzZXmUawZDFvwa0WhZGSY5kEeaMOKWMDgD3I_T_2Q-UanBlsLFqTKFPwD2SkXpdkjNITZwPgRJuwleAdG61Ry6YdwNfRX6T45aP6UmRtG6xkDP0NwJSXfJ1_bj2Hmw3SWLs1iA30iuClm9eOH-qCepoCX1o-PuM8n8qpD4wHZqVYb85m8yG6q-Xr1xdr8HzGAjFs |
| linkProvider | IEEE |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Outlier+Analysis+and+Top+Scoring+Pairfor+Integrated+Data+Analysisand+Biomarker+Discovery&rft.jtitle=IEEE%2FACM+transactions+on+computational+biology+and+bioinformatics&rft.au=Ochs%2C+Michael+F&rft.au=Farrar%2C+Jason+E&rft.au=Considine%2C+Michael&rft.au=Wei%2C+Yingying&rft.date=2014-05-01&rft.issn=1545-5963&rft.volume=11&rft.issue=3&rft.spage=520&rft.epage=532&rft_id=info:doi/10.1109%2FTCBB.2013.153&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1545-5963&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1545-5963&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1545-5963&client=summon |