Integration of multiomics data shows down regulation of mismatch repair and tubulin pathways in triple-negative chemotherapy-resistant breast tumors

Table 2 List of the 17 gene signature

Gene	Beauty logFC	Beauty p-value	ISPY logFC	ISPY p-value	logrank test p-value	logrank test (LN +) p-value	Location	Type(s)	Cytoband
RSPO3	− 2.32	0.00114	− 0.692	0.152	0.0422	0.05	Extracellular space	Kinase	6q22.33
FHL2	− 1.06	0.0014	− 0.345	0.518	0.0008	0.0004	Nucleus	Transcription regulator	2q12.2
COL4A6	− 3.27	0.00197	− 0.2	0.722	0.0009	0.019	Extracellular space	Other	Xq22.3
LCP2	1.82	0.00225	0.091	0.742	0.0407	0.22	Cytoplasm	Other	5q35.1
MCCC2	− 0.942	0.00356	− 0.118	0.73	0.0083	0.039	Cytoplasm	Enzyme	5q13.2
TANK	− 1.04	0.00396	− 0.275	0.622	0.028	0.17	Cytoplasm	Other	2q24.2
THRA (AR7)	− 1.32	0.00635	− 0.11	0.819	0.0266	0.19	Nucleus	Nuclear hormone receptor	17q21.1
MCM3	0.907	0.0111	0.478	0.343	0.0139	0.0017	Nucleus	Enzyme	6p12.2
TBXA2R	1.24	0.0119	0.088	0.812	0.0162	0.017	Plasma membrane	G-protein coupled receptor	19p13.3
MED1	− 0.676	0.0181	− 0.14	0.569	0.0333	0.077	Nucleus	Transcription regulator	17q12
CD3G	− 1.4	0.0211	− 0.506	0.133	0.0079	0.13	Plasma membrane	Transmembrane receptor	11q23.3
PDE2A	− 1.38	0.0313	− 0.301	0.435	0.0498	0.053	Cytoplasm	Enzyme	11q13.4
CITED2	− 1.11	0.032	− 1.403	0.046	0.0032	0.13	Nucleus	Transcription regulator	6q24.1
NR1D2	− 0.818	0.0358	− 0.591	0.236	0.022	0.014	Nucleus	Ligand-dependent nuclear receptor	3p24.2
AGGF1	− 0.606	0.039	− 0.626	0.099	0.0278	0.48	Cytoplasm	Other	5q13.3
RPS6KA4	0.744	0.0391	0.633	0.135	0.0147	0.017	Cytoplasm	Kinase	11q13.1
SNRPF	0.609	0.0492	0.743	0.072	0.0493	0.13	Nucleus	Other	12q23.1

Here we report the log fold change (logFC) and p-values observed in the BEAUTY and I-SPY1 cohorts. We also report the p-values obtained from the Kaplan–Meier plotter tool (https://kmplot.com) and annotations including genomic location, cellular location and functional type

ISSN: 1465-542X