Method
Identification of novel stem cell markers using gap analysis of gene expression data
1 Molecular Medicine, Ottawa Health Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
2 Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
Genome Biology 2007, 8:R193 doi:10.1186/gb-2007-8-9-r193
Published: 17 September 2007Additional files
Additional data file 1:
Columns indicate Affymetrix probe set identifier (1 Affy id), chip set (2 chip), gene symbol (3 gene), and (4 patterns). A marker might be associated to multiple patterns, and those are encoded in column 4 using the marker server pattern identifier followed by the score for the pattern between brackets, with information for different patterns separated by a colon. Patterns can be retrieved at the marker server [21] using the marker server identifier or they can be queried with the Affymetrix probe set identifier.
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Additional data file 2:
The meaning of the columns is identical to that given for Additional data file 1.
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Additional data file 3:
Columns indicate Affymetrix probe set identifier (1 Affy id), chip set (2 chip), gene symbol (3 gene), and marker server pattern identifier chosen (4 pattern). Columns five and six are related to the clustering analysis (see Materials and methods): National Center for Biotechnology Information NCBI identifier for the protein sequence used (5 protein) and label for the protein cluster (6 cluster). Columns seven to 18 indicate segregation (value of 1) in pairs of stem cell samples and their differentiated derivatives, respectively: J1 mESC (7 J1-U and 8 J1-D), V6.5 mESC (9 V6.5-U and 10 V6.5-D), mast cell precursors (11 Mast-U and 12 Mast-D), mammospheres (13 MaSC-U and 14 MaSC-D), osteoblasts (15 Osteo-U and 16 Osteo-D), and hematopoietic cells (17 HSC-U and 18 HSC-D). Column 19 (multi) indicates (value 0/1) 17 genes differentially expressed along multiple stem cell lineages (one at least being non-mESC). Samples used were S255 versus S256 for mammary stem cells (undifferentiated and differentiated, respectively), S294 versus five samples (S291, S292, S293, S295, and S296) for hematopoietic stem cells (HSC), S128 versus S127 for J1 ESCs, S153 versus S175 for V6.5 ESCs, S185 versus S196 for osteoblasts, and S236 versus S237 for mast cells.
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Additional data file 4:
Protein identifiers (GenBank) of the sequences used for the phylogenetic analysis depicted in Figure 5. Occasionally, the label used (for example, Ebf) differs from the gene name in the database. Labels used are derived from the phylogenetic analysis.
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