Name
Title | ||
|---|---|---|
Analyzing M-CSF dependent monocyte/macrophage differentiation: expression modes and meta-modes derived from an independent component analysis. |
Abstract | ||
|---|---|---|
The analysis of high-throughput gene expression data sets derived from microarray experiments still is a field of extensive investigation. Although new approaches and algorithms are published continuously, mostly conventional methods like hierarchical clustering algorithms or variance analysis tools are used. Here we take a closer look at independent component analysis (ICA) which is already discussed widely as a new analysis approach. However, deep exploration of its applicability and relevance to concrete biological problems is still missing. In this study, we investigate the relevance of ICA in gaining new insights into well characterized regulatory mechanisms of M-CSF dependent macrophage differentiation.Statistically independent gene expression modes (GEM) were extracted from observed gene expression signatures (GES) through ICA of different microarray experiments. From each GEM we deduced a group of genes, henceforth called sub-mode. These sub-modes were further analyzed with different database query and literature mining tools and then combined to form so called meta-modes. With them we performed a knowledge-based pathway analysis and reconstructed a well known signal cascade.We show that ICA is an appropriate tool to uncover underlying biological mechanisms from microarray data. Most of the well known pathways of M-CSF dependent monocyte to macrophage differentiation can be identified by this unsupervised microarray data analysis. Moreover, recent research results like the involvement of proliferation associated cellular mechanisms during macrophage differentiation can be corroborated. |
Year | DOI | Venue |
|---|---|---|
2008 | 10.1186/1471-2105-9-100 | BMC Bioinformatics |
Keywords | Field | DocType |
statistical independence,macrophage colony stimulating factor,cell differentiation,algorithms,gene expression profiling,signal transduction,knowledge base,gene expression,bioinformatics,microarrays,principal component analysis,microarray data,high throughput,hierarchical clustering,microarray data analysis,independent component analysis | Hierarchical clustering,Data mining,Monocyte,Data set,Biology,Independent component analysis,Bioinformatics,Principal component analysis,Gene expression profiling,DNA microarray,Macrophage differentiation | Journal |
Volume | Issue | ISSN |
9 | 1 | 1471-2105 |
Citations | PageRank | References |
34 | 0.59 | 7 |
Authors | ||
7 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Dominik Lutter | 1 | 158 | 9.67 |
| Peter Ugocsai | 2 | 34 | 0.59 |
| Margot Grandl | 3 | 34 | 0.59 |
| Evelyn Orso | 4 | 34 | 0.59 |
| Fabian J. Theis | 5 | 931 | 85.37 |
| Elmar Wolfgang Lang | 6 | 260 | 36.10 |
| Gerd Schmitz | 7 | 40 | 2.30 |