title: CoD: inferring immune-cell quantities related to disease states.
abstract: BACKGROUND
  The immune system comprises a complex network of genes, cells and tissues, coordinated through signaling pathways and cell-cell communications. However, the orchestrated role of the multiple immunological components in disease is still poorly understood. Classifications based on gene-expression data have revealed immune-related signaling pathways in various diseases, but how such pathways describe the immune cellular physiology remains largely unknown.
  
  
  RESULTS
  We identify alterations in cell quantities discriminating between disease states using ' Cell type of Disease' (CoD), a classification-based approach that relies on computational immune-cell decomposition in gene-expression datasets. CoD attains significantly higher accuracy than alternative state-of-the-art methods. Our approach is shown to recapitulate and extend previous knowledge acquired with experimental cell-quantification technologies.
  
  
  CONCLUSIONS
  The results suggest that CoD can reveal disease-relevant cell types in an unbiased manner, potentially heralding improved diagnostics and treatment.
  
  
  METHODS
  The software described in this article is available at http://www.csgi.tau.ac.il/CoD/.
authors: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
authors: Amit
authors: A
authors: Frishberg
authors: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
authors: Yael
authors: Y
authors: Steuerman
authors: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
authors: Irit
authors: I
authors: Gat-Viks
mesh_terms: D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D007107:Immune System / Q000166:cytology / Q000378:metabolism*; D007109:Immunity / Q000235:genetics; D008325:Mammary Neoplasms, Experimental / Q000235:genetics / Q000276:immunology; D051379:Mice; D012984:Software