Search: onr:"swepub:oai:DiVA.org:kth-9744" >
A web-based tool fo...
A web-based tool for in silico biomarker discovery based on tissue-specific protein profiles in normal and cancer tissues
-
- Björling, Erik (author)
- KTH,Proteomik
-
- Lindskog, Cecilia (author)
- Uppsala universitet,Institutionen för genetik och patologi
-
- Oksvold, Per (author)
- KTH,Proteomik
-
show more...
-
- Linné, Jerker (author)
- Uppsala universitet,Institutionen för genetik och patologi
-
- Kampf, Caroline (author)
- Uppsala universitet,Institutionen för genetik och patologi
-
- Hober, Sophia (author)
- KTH,Proteomik
-
- Uhlén, Mathias (author)
- KTH,Skolan för bioteknologi (BIO)
-
- Pontén, Fredrik (author)
- Uppsala universitet,Institutionen för genetik och patologi
-
show less...
-
(creator_code:org_t)
- 2008
- 2008
- English.
-
In: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 7:5, s. 825-844
- Related links:
-
https://urn.kb.se/re...
-
show more...
-
https://doi.org/10.1...
-
https://urn.kb.se/re...
-
show less...
Abstract
Subject headings
Close
- Here we report the development of a publicly available Web-based analysis tool for exploring proteins expressed in a tissue- or cancer-specific manner. The search queries are based on the human tissue profiles in normal and cancer cells in the Human Protein Atlas portal and rely on the individual annotation performed by pathologists of images representing immunohistochemically stained tissue sections. Approximately 1.8 million images representing more than 3000 antibodies directed toward human proteins were used in the study. The search tool allows for the systematic exploration of the protein atlas to discover potential protein biomarkers. Such biomarkers include tissue-specific markers, cell type-specific markers, tumor type-specific markers, markers of malignancy, and prognostic or predictive markers of cancers. Here we show examples of database queries to generate sets of candidate biomarker proteins for several of these different categories. Expression profiles of candidate proteins can then subsequently be validated by examination of the underlying high resolution images. The present study shows examples of search strategies revealing several potential protein biomarkers, including proteins specifically expressed in normal cells and in cancer cells from specified tumor types. The lists of candidate proteins can be used as a starting point for further validation in larger patient cohorts using both immunological approaches and technologies utilizing more classical proteomics tools.
Subject headings
- TEKNIK OCH TEKNOLOGIER -- Industriell bioteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Industrial Biotechnology (hsv//eng)
Keyword
- ANTIBODY-BASED PROTEOMICS; HUMAN BREAST-CANCER; PROSTATE-CANCER; GENE-EXPRESSION; IMMUNOHISTOCHEMICAL MARKERS; CELL MICROARRAYS; METASTASIS; RESOURCE; ANTIGEN; GROWTH
- Bioengineering
- Bioteknik
- MEDICINE
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database