Table.

Abrix	Parameter in DCE-MRI which measures the change in tracer concentration within the tissue of interest over time; also known as amplitude
Apparent diffusion coefficient (ADC)	Apparent diffusion coefficient (ADC) measures the magnitude of diffusion (of water molecules) within the tissue during functional MRI.
Basal-like breast carcinoma	Molecular subtype of breast cancer; high grade, ER negative or PR negative or HER2 negative; associated with poor prognosis
CD31	Cluster of differentiation 31 is the protein encoded by the gene platelet endothelial cell molecule (PECAM1); CD31 is a member of the immunoglobulin superfamily and is likely involved in leukocyte migration, angiogenesis, and integrin activation; CD31 is used to demonstrate the presence of endothelial cells in histologic tissue sections.
Chromogranin A	Chromogranin A is the protein encoded by the gene CHGA; It is a member of the granin family of neuroendocrine secretory proteins; Chromogranin A is the precursor to several functional peptides that negatively modulate neuroendocrine function of cells; Chromogranin A can be used to identify neuroendocrine tumors in histologic tissue sections
Claudin-low breast carcinoma	Molecular subtype of breast cancer; claudin-low carcinomas are characterized by low to absent expression of luminal differentiation marks, high epithelial-mesenchymal transition markers, immune response genes, and cancer stem cell like features; clinically, high grade, ER negative or PR negative or HER2 negative; associated with poor prognosis
Deep sequencing	The technology that allows a DNA fragment to be repeatedly sequenced in a very short time and delivers great sensitivity and accuracy; deep sequencing of the transcriptome provides the sequence and frequency of RNA molecules that are present at any particular time in a specific cell type, tissue, or organ; quantifying the RNA encoded by individual genes provides an indicator of protein-coding potential, a major contributor to phenotype
DCE-MRI	Dynamic contrast-enhanced (DCE)-magnetic resonance imaging (MRI); functional imaging technique in which multiphase MRI scans are taken following the intravenous injection of a contrast agent to noninvasively evaluate tumor vascular characteristics
ER; ER alpha and ER beta	Estrogen receptor (ER) is the intracellular protein receptor activated by the hormone estrogen; once activated by estrogen, ER is a DNA-binding transcription factor; ERs are widely expressed in different tissue types; ER alpha is encoded by the gene ESR1 and ER beta is encoded by the gene ESR2
ERBB2	ERBB2 is the gene that encodes the protein HER2; ERBB2 is amplified and overexpressed in approximately 30% of breast cancers and is strongly associated with increased disease recurrence and worse prognosis
18F-FDG-PET	Positron emission tomography (PET) utilizing the radiopharmaceutical fluorodeoxyglucose (FDG) synthesized with the radioactive isotope fluorine-18 (18F); functional imaging technique that images regions of high glucose metabolism via uptake of the glucose analogue 18F-FDG; high–glucose using cells include cancer cells and normal brain and kidney cells
FLT1	FLT1 is the genethat encodes the protein vascular endothelial growth factor receptor 1 (VEGFR-1); VEGFRs are receptors for the signaling protein vascular endothelial growth factor (VEGF), which is produced by cells that stimulate vasculogenesis and angiogenesis; FLT1 is a member of the src gene family and has tyrosine kinase activity, important for the control of cell proliferation and differentiation
Functional imaging	Functional imaging refers to imaging techniques in which a sequence of images follows the distribution of an administered radioactive tracer or contrast agent to delineate one or more physiological processes in the body
Gene expression profiling	The measurement of the expression, or activity, of thousands of genes at one time to create a global picture of cellular function
Histone deacetylase (HDAC)	Class of enzymes that remove acetyl groups from histones, which allows the histones to wrap DNA more tightly; DNA expression is regulated by acetylation and deacetylation
HER2	Human epidermal growth factor receptor 2 (HER2) is a protein encoded by the ERBB2 gene; HER2 is a member of the epidermal growth factor receptor (EGFR) family which are membrane-bound receptor tyrosine kinases; autophosphorylation of the receptors initiates a variety of signaling pathways
HOXC6	HOXC6 is the gene that encodes the homeobox protein Hox-C6; HOXC6 belongs to the homeobox family, members of which encode a family of transcription factors that play an important role in morphogenesis in multicellular organisms.
Hsp90	Heat shock protein 90 (Hsp90) is a chaperone protein that assists other proteins in proper folding, stabilizes proteins against heat stress, facilitates intracellular transport, cell signaling, and maintenance and degradation of proteins; 5 functional genes encode Hsp90
Inositol trisphosphate receptor 3	Inositol trisphosphate receptor 3 is a membrane glycoprotein complex in the endoplasmic reticulum acting as a Ca2+ channel activated by inositol trisphosphate; InsP3R3 is encoded by the gene ITPR3
KDR	Kinase insert domain receptor (KDR); also known as vascular endothelial growth factor receptor-2 (VEGFR-2) is a VEGF receptor protein encoded by the gene KDR; KDR is a receptor tyrosine kinase and functions as the main mediator of VEGF-induced endothelial proliferation, survival, migration, tubular morphogenesis, and sprouting
Luminal type A breast carcinoma	Molecular subtype of breast cancer; ER positive, low grade
Luminal type B breast carcinoma	Molecular subtype of breast cancer; ER positive, but often high grade
Metagene, signature, and multigene predictors	A list of genes that is associated with certain biological processes or predictive of biological phenotypes, such as different response to radiotherapy
Next generation, massively parallel or deep sequencing, and sequencing	Post-Sanger sequencing methods that generate large amount of data (orders of magnitude more) at incredibly low cost (again, orders of magnitude). This can be accomplished by several platforms, including Illumina, SOLID, Ion Torrent, and those by other companies. This has created amazing opportunities in the biological sciences and enabled amazing new experiments, including the genetic characterization of human cancers.
Normal breast-like carcinoma	Molecular subtype of breast cancer; similar expression pattern to normal breast tissue
p53	P53 is a tumor suppressor protein that is encoded by the TP53 gene; regulates the cell cycle and activates DNA repair or initiates apoptosis or both
PDGF-B	Platelet-derived growth factor subunit B is a protein encoded by the PDGFB gene; a member of the platelet-derived growth factor family, which are mitogenic factors for cells of mesenchymal orgin and play a significant role in angiogenesis
PDK2	Pyruvate dehydrogenase kinase isoform 2 (PDK2) is a protein that is encoded by the PDK2 gene; acts to inactivate the enzyme pyruvate dehydrogenase, located within the mitochondria, and contributes to the regulation of glucose metabolism
PR	Progesterone receptor (PR) is an intracellular protein activated by the hormone progesterone; encoded by the PGR gene; once activated by progesterone, PR is a DNA-binding transcription factor
RAD23A	RAD23 homolog A (RAD23)is a protein encoded by the RAD23 geneand is involved in nucleotide excision repair
Ras	Ras includes a family of related proteins belonging to a class of protein called small GTPase, and are involved in transmitting signals within cells; the name ras refers to the family of genes encoding these proteins; activates genes involved in cell growth, differentiation, and survival
SAM	Significance analysis of microarrays (SAM) is a statistical technique for determining what genes are statistically significant among different samples from microarrays
STAT1	STAT1 protein is a member of the Signal Transducers and Activators of Transcription family of transcription factors; encoded by STAT1 gene; involved in upregulating genes because of signal by interferons; regulates many aspects of growth, survival, and differentiation in cells; involved in the function of the immune system and maintaining immune tolerance
Sialyltransferase-1	Sialyltransferase-1 is an enzyme that transfers sialic acid to oligosaccharide; membrane protein localized to the Golgi network; expression and activity are associated with tumor metastasis in breast and colon cancers
Standard uptake value (SUV)	A ratio of tissue radioactivity concentration at time T and injected dose at the time of injection divided by body weight.
TCGA	The Cancer Genome Atlas (TCGA) Project is a large-scale collaborative effort to characterize the genomic changes that occur in cancer. The overarching goal is to comprehensively define the important genomic changes involved in cancer. This knowledge will advance our molecular understanding of the disease and improve our ability to diagnose, treat, and prevent it.
TERT	Telomerase reverse transcriptase (TERT) is a catalytic subunit of the enzyme telomerase; telomerase lengthens telomeres in DNA strands, allowing cells that would otherwise become postmitotic and undergo apoptosis to become potentially immortal; TERT is responsible for catalyzing the addition of nucleotides to the ends of a chromosome's telomeres
VCAM-1	Vascular cell adhesion molecule-1 (VCAM-1) is a protein that is encoded by the VCAM1 gene; functions as a cell adhesion molecule, expressed on both large and small blood vessels after the endothelial cells are stimulated by cytokines
Vinexin beta	Vinexin is a protein encoded by the SORBS3 gene; the vinexin beta isoform plays a role in cell spreading and enhances the activation of cell growth, differentiation, and survival pathways in response to epidermal growth factor stimulation
vWF	Von Willebrand factor (vWF) is a blood glycoprotein crucial to the hemostasis process; encoded by the gene VWF; produced in endothelium, megakaryocytes, and subendothelial connective tissue
Zinc finger proteins	A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions to stabilize the fold; their functions are extraordinarily diverse and include DNA recognition, RNA packaging, transcriptional activation, regulation of apoptosis, protein folding and assembly, and lipid binding