Open Access Highly Accessed Research article

Human breast cancer associated fibroblasts exhibit subtype specific gene expression profiles

Julia Tchou1*, Andrew V Kossenkov2, Lisa Chang2, Celine Satija1, Meenhard Herlyn2, Louise C Showe2 and Ellen Puré2

Author Affiliations

1 Department of Surgery, Division of Endocrine and Oncologic Surgery, Rena Rowan Breast Center, Abramson Cancer Center, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, 19104, USA

2 The Wistar Institute, Philadelphia, PA, 19104, PA

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BMC Medical Genomics 2012, 5:39  doi:10.1186/1755-8794-5-39

Published: 6 September 2012

Additional files

Additional file 1: Table S1:

Clinical Characteristics of Study Cohort.

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Additional file 2: Table S2:

Annotation categories enriched in the list of genes significantly differentially expressed in Her2+ compared to ER+ samples as determined by DAVID software. Cat=category, Term=enriched annotation term, Enr=enrichment, TN=enrichment of the Term in Her2+ vs. TNBC comparison, Sens=sensitivity in a form K/N(P%), where K=number of genes in the list, N=total known number of genes, P=K/N in percentage. P=Fisher exact p-value for enrichment, FDR=false discovery rate, ↑ = number of genes upregulated in Her2+, ↓ = number of genes downregulated in Her2+, SP.KW = SwissProt keyword, KEGG=KEGG pathway, GO=gene ontology, BP=biological process, FM=molecular function, CC=cellular component.

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Additional file 3: Table S3:

Annotation categories enriched in the list of genes significantly differentially expressed in Her2+ compared to TNBC samples as determined by DAVID software. Cat=category, Term=enriched annotation term, Enr=enrichment, ER+=enrichment of the Term in Her2+ vs. ER+ comparison, Sens=sensitivity in a form K/N(P%), where K=number of genes in the list, N=total known number of genes, P=K/N in percentage. P=Fisher exact p-value for enrichment, FDR=false discovery rate, ↑ = number of genes upregulated in Her2+, ↓ = number of genes downregulated in Her2+, SP.KW = SwissProt keyword, GO=gene ontology, BP=biological process, FM=molecular function, CC=cellular component.

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Additional file 4: Table S4:

Fold changes and p-values obtained by qRT-PCR validation experiment for 6 genes found to be significantly different in either Her2+ vs ER+, Her2+ vs TNBC or ER+ vs TNBC comparison in microarrays data. FC=fold change, P=significance by t-test. Visual comparison of expression values between microarrays and qRT-PCR are presented in Figure 6.

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