The Macrophage Colony Stimulating Factor-1 Response Signature in Breast Carcinoma | Andrew H Beck, Inigo Espinosa, Badreddin Edris, Rui Li, Kelli Montgomery, Shirley Zhu, Sushama Varma, Robert J Marinelli, Matt van de Rijn, Robert B West <body bgcolor=white link="#000080" alink=red vlink="#000080"> <table width=800 cellspacing=6> <tr> <td width=200 valign=top> <center> <img src="topleft.gif"><p> <table width=150 cellpadding=4> <tr> <td bgcolor="#E0E0E0"> <font face="verdana, tahoma, arial"><font color="#000080"><center><a href="index.html" style="text-decoration: none; ">Home</a></font></font> </td> </tr> </table> <p> <table width=150 cellpadding=4> <tr> <td bgcolor="#E0E0E0"> <font face="verdana, tahoma, arial"><font color="#000080"><center><a href="figures.html" style="text-decoration: none;">Figures</a></font></font> </td> </tr> </table> <p> <table width=150 cellpadding=4> <tr> <td bgcolor="#E0E0E0"> <font face="verdana, tahoma, arial"><font color="#000080"><center><a href="images.html" style="text-decoration: none;">Histological Images</a></font> </font> </td> </tr> </table> <p> <table width=150 cellpadding=4> <tr> <td bgcolor="#E0E0E0"> <font face="verdana, tahoma, arial"><font color="#000080"><center><a href="data.html" style="text-decoration: none;">Supplementary Data</a></font></font> </td> </tr> </table> <p> <table width=150 cellpadding=4> <tr> <td bgcolor="#E0E0E0"> <font face="verdana, tahoma, arial"><font color="#000080"><center><A HREF="/tma_portal/" style="text-decoration: none;">WebPortal</A></font> </font> </td> </tr> </table> <p> <table width=150 cellpadding=4> <tr> <td bgcolor="#E0E0E0"> <font face="verdana, tahoma, arial"><font color="#000080"><center><a href="authors.html" style="text-decoration: none;">Authors</a></font></font> </td> </tr> </table> </td> <td valign=top> <center> <font face="verdana, tahoma, arial"> <font size=+2>The Macrophage Colony Stimulating Factor-1 Response Signature in Breast Carcinoma</font><p> Andrew H Beck*<sup>1</sup>, Inigo Espinosa*<sup>1</sup>, Badreddin Edris<sup>1</sup>, Rui Li<sup>1</sup>, Kelli Montgomery<sup>1</sup>, Shirley Zhu<sup>1</sup>, Sushama Varma<sup>1</sup>, Robert J Marinelli<sup>1</sup>, Matt van de Rijn<sup>1</sup>, Robert B West<sup>1,2</sup><p> <table width=100% cellpadding=4> <tr> <td bgcolor="#E0E0E0"> <font face="verdana, tahoma, arial"><font size=+1 color="#000080">Supplementary Data</font></font> </td> </tr> <tr> <td> <font face="verdana, tahoma, arial"> <font size=-1> <p> <b><a href="SupFig1_CSF_CCR.gif" style="text-decoration: none;">Supplemental Figure 1.</a></b> A, CSF1 Response Signature Core Protein-Protein Interaction Network. B, CSF1 Response Signature Non-Core Protein-Protein Interaction Network. The figures depict the PPI networks created from the CSF1 response signature core proteins (A) and the CSF1 response signature non-core proteins (B). The PPI networks are created and visualized using the STRING database. The nodes represent proteins and the links between nodes represent predicted protein-protein interactions. The thickness of the links corresponds to the confidence of the predicted interaction. The network created using the 80 core proteins (A) is a more centralized and tightly connected network than the network created using the 285 non-core proteins (B) (See Supplemental Table 1). <p> <center><a href="SupFig1_CSF_CCR.gif" style="text-decoration: none;"><img src="SupFig1_CSF_CCR.gif" width=500 border=0></a></center><p><br> <b><a href="SupFig2.gif" style="text-decoration: none;">Supplemental Figure 2.</a></b> Unsupervised Hierarchical Clustering of Breast Carcinomas with CSF1 Response Genes in Three Laser Capture Microdissection Breast Cancer Datasets. A, GSE5847 (n=46 cases with 1 stromal and 1 epithelial sample per case). B, GSE9014 (n=28 cases with 1 stromal and 1 epithelial sample per case). C, GSE10797 (n=52 cases, with 1 stromal sample per case). Within the heatmap, red represents high expression, black represents median expression, and green represents low expression. The red highlighted region of the dendrograms above the heatmaps indicates the cluster of samples with the CSF1 response signature in each dataset. The colorbar on the left of each heatmap indicates whether the CSF1 response gene belongs to the core CSF1 response gene set. The core CSF1 response genes are indicated in red and the non-core CSF1 response genes are green.<p> <center><a href="SupFig2.gif" style="text-decoration: none;"><img src="SupFig2.gif" width=500 border=0></center><p><br></a> <a href="suppTable1.gif"><img src="suppTable1.gif" width=490 border=0></a><P><br> <a href="suppTable2.gif"><img src="suppTable2.gif" width=490 border=0></a><P><br> <a href="suppTable3.gif"><img src="suppTable3.gif" width=490 border=0></a><P><br> <b><a href="CSF1 Breast Supp Methods_CCR.doc" style="text-decoration: none;">Supplemental Methods.</a></b> The supplemental methods describes the eight breast cancer datasets and associated gene microarray platforms utilized in this paper, as well as the antibodies, staining procedures, and scoring procedures used for the immunohistochemical and in situ hybridization studies. <a href="CSF1 Breast Supp Methods_CCR.doc" style="text-decoration: none;">[Click here to view (.doc)]</a><p><br> <b><a href="Sep27_CSF1 SupplementalWorkbook.xls" style="text-decoration: none;">Supplemental Workbook.</a></b> The supplemental workbook contains a total of four spreadsheets. The first spreadsheet (“CSF1ResponseCoreGenes”) lists the 207 CSF1 response genes that were present in the CSF1 response core gene cluster in at least one dataset with columns listing information as follows: the first column of the spreadsheet lists the gene symbol; the second column lists the number of times the gene was present in the CSF1 response core gene cluster; the third column lists the number of times the gene was present on the array platform; and the fourth column lists the percent of times the gene was present in the CSF1 response core cluster when it was also present on the array platform. The top 112 genes present on this list fulfilled criteria for inclusion in the CSF1 response core gene set. The second spreadsheet (“CSF1ResposneCoreGeneFunctAnnot”) lists the CSF1 response core genes with functional annotation data associated with each gene. The annotation data listed for each gene includes: Gene Ontology terms, KEGG pathways, and BioCarta pathways associated with each gene. The third spreadsheet (“CSF1ResponseFunctAnnotGroups”) lists the annotation terms that show significant enrichment in the CSF1 response core gene set (Fisher exact p value <0.05). The annotation data were obtained using the DAVID: Database for Annotation, Visualization, and Integrated Discovery. The fourth spreadsheet lists the 603 unique genes that constitute the CSF1 response signature. The genes are displayed in rank order from the Significance Analysis of Microarrays output, which was performed to identify genes with significantly increased expression in TGCT/PVNS as compared with desmoid type fibromatosis and solitary fibrous tumor with false discovery rate of 0.02%. <a href="Sep27_CSF1 SupplementalWorkbook.xls" style="text-decoration: none;">[Click here to view (.xls)]</a><p> </td> </tr> </table> </td> </tr> </table> </body> </html>