High-throughput identification of reference genes for research and clinical RT-qPCR analysis of breast cancer samples

Maltseva, Diana V; Khaustova, Nadezda A; Fedotov, Nikita N; Matveeva, Elona O; Lebedev, Alexey E; Shkurnikov, Maxim U; Galatenko, Vladimir V; Schumacher, Udo; Tonevitsky, Alexander G

doi:10.1186/2043-9113-3-13

Table 1 Description of selected candidate reference genes

From: High-throughput identification of reference genes for research and clinical RT-qPCR analysis of breast cancer samples

Gene symbol	Gene name	GeneBank number	Gene function	Pseudo-genes	Source***
ACTB	Beta actin	NM_001101.3	Cytoskeletal structural protein involved in are involved in cell motility, structure, and integrity.	No	Oncotype DX, [23, 27, 48]
EEF1A1	Elongation factor 1-alpha 1	NM_001402.5	Involved in protein biosynthesis.	No	Microarray search
GAPDH	Glyceraldehyde-3-phosphate dehydrogenase	NM_002046.4	Catalyzes the reversible oxidative phosphorylation of glyceraldehyde-3-phosphate.	Yes*	Oncotype DX, [23, 48]
GUSB	Beta-D-glucuronidase	NM_000181.3	A hydrolase that degrades glycosaminoglycans.	Yes*	Oncotype DX, [48]
HCFC1	Host cell factor C1	NM_005334.2	Involved in control of the cell cycle.	No	Microarray search
HUWE1	E3 ubiquitin-protein ligase HUWE1	NM_031407.5	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	No	Microarray search
MRPL19	Mitochondrial ribosomal protein L19	NM_014763.3	Protein synthesis within the mitochondrion.	No	[23]
PSMC4	26S protease regulatory subunit 6B	NM_153001.2	Encodes a member of the triple-A family of ATPases that play a role in 26S proteasome assembly.	No	[23]
PSMC4	26S protease regulatory subunit 6B	NM_006503.3		No	[23]
PTMA	Prothymosin alpha	NM_001099285.1 NM_002823.4	Prothymosin alpha may mediate immune function	No	Microarray search
RPLP0	Ribosomal protein P0	NM_001002.3	Encodes a ribosomal protein that is a component of the 60S subunit.	Yes*	Oncotype DX, [47]
RPLP0	Ribosomal protein P0	NM_053275.3		Yes*	Oncotype DX, [47]
RPL23A	Ribosomal protein L23a	NM_000984.5	Encodes a ribosomal protein that is a component of the 60S subunit.	Yes*	Microarray search
RPL37A	Ribosomal protein L37a	NM_000998.4	Encodes a ribosomal protein that is a component of the 60S subunit.	Yes*	Microarray search
RPL39	Ribosomal protein L39	NM_001000.3	Encodes a ribosomal protein that is a component of the 60S subunit.	No	Microarray search
RPS23	40S ribosomal protein S23	NM_001025.4	Encodes a ribosomal protein that is a component of the 40S subunit.	No	Microarray search
SF3A1	Splicing factor 3 subunit 1	NM_005877.4	Encodes subunit 1 of the splicing factor 3a protein complex. It is necessary for a formation of an active 17S particle that performs pre-mRNA splicing.	No	[23]
SF3A1	Splicing factor 3 subunit 1	NM_001005409.1		No	[23]
TBP	TATA box binding protein	NM_001172085.1	General transcription factor playing a role in the activation of eukaryotic gene transcription.	No	[23, 47]
TBP	TATA box binding protein	NM_003194.4		No	[23, 47]
TFRC	Transferrin receptor protein 1	NM_003234.2	Required for iron delivery from transferrin to cells.	No	Oncotype DX, [48]
TFRC	Transferrin receptor protein 1	NM_001128148.1	Required for iron delivery from transferrin to cells.	No	Oncotype DX, [48]
TPT1	Translationally-controlled tumor protein	NM_003295.2	Involved in calcium binding and microtubule stabilization.	No**	Microarray search, [23]

*Presented set of primer pair and probe do not anneal on these pseudogenes.
**The primers can anneal on TPT1-like protein gene with two mismatches, but the whole set has a unique specific probe.
***Oncotype DX - a commercial Oncotype DX Breast Cancer diagnostic test [2].

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Journal of Clinical Bioinformatics