Transcription factor landscape - Cell line - breast cancer

62 different cell lines are representing breast cancer in the atlas, different ages, collection site and cancer subtypes are represented, find more details about the different cell lines here. The expression profile of the different cell lines can be explored in comparison to the bulk RNAseq transcriptomics data from TCGA's Breast Invasive Carcinoma (BRCA), defining the cell lines most similar to the tumour expression profile.

The mean value of the different cell lines are used as representation, when classifying gene expression based on specificity in the different cancer types represented by cell lines. To explore the expression profile in the indivudial cell lines- click the bar in the bar chart and you will reach the overivew of the different cell lines.

Here we provide the expression overview of all 22 transcription factors that show elevated expression levels in breast cancer compared to other cancer cell lines. The gene expression overview, across different cancer types, is accopanied by the top 3 nearest neighbours based on RNA expression and correlation in the clustering analysis.

Enriched transcription factors

Gene

Expression

Expression clustering

PGR

Cancer enriched (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
PRLR	Prolactin receptor	0.8768	27
PGLYRP2	Peptidoglycan recognition protein 2	0.7468	27
SPTSSB	Serine palmitoyltransferase small subunit B	0.7394	27

IRX5

Cancer enriched (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
IL20	Interleukin 20	0.7139	27
PRLR	Prolactin receptor	0.6918	27
PRLH	Prolactin releasing hormone	0.6891	27

TRPS1

Cancer enriched (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
EFHD1	EF-hand domain family member D1	0.6392	27
CLPSL1	Colipase like 1	0.6190	27
CLPS	Colipase	0.6167	27

Enriched transcription factors

Gene

Expression

Expression clustering

SPDEF

Group enriched (Breast cancer, Prostate cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
NCBP2L	Nuclear cap binding protein subunit 2 like	0.8148	27
SRARP	Steroid receptor associated and regulated protein	0.8060	27
CREB3L4	CAMP responsive element binding protein 3 like 4	0.7814	27

TFAP2B

Group enriched (Bone cancer, Breast cancer, Neuroblastoma)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CHRM1	Cholinergic receptor muscarinic 1	0.6244	17
TMEM229A	Transmembrane protein 229A	0.5835	12
CRABP1	Cellular retinoic acid binding protein 1	0.5670	17

ELF5

Group enriched (Bile duct cancer, Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
OR13C7	Olfactory receptor family 13 subfamily C member 7 (gene/pseudogene)	0.9373	27
DCD	Dermcidin	0.8599	27
AARD	Alanine and arginine rich domain containing protein	0.8526	27

FOXA1

Group enriched (Breast cancer, Gallbladder cancer, Prostate cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TTC6	Tetratricopeptide repeat domain 6	0.7987	60
SPDEF	SAM pointed domain containing ETS transcription factor	0.7338	27
NCBP2L	Nuclear cap binding protein subunit 2 like	0.6538	27

GATA3

Group enriched (Bladder cancer, Breast cancer, Neuroblastoma)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
GPR139	G protein-coupled receptor 139	0.7347	27
CACNG4	Calcium voltage-gated channel auxiliary subunit gamma 4	0.7152	27
ESR1	Estrogen receptor 1	0.7151	27

Enriched transcription factors

Gene

Expression

Expression clustering

CREB3L4

Cancer enhanced (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
SPDEF	SAM pointed domain containing ETS transcription factor	0.7814	27
PIP	Prolactin induced protein	0.7579	27
TMEM210	Transmembrane protein 210	0.7213	60

EN1

Cancer enhanced (Brain cancer, Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
BOC	BOC cell adhesion associated, oncogene regulated	0.7290	44
AARD	Alanine and arginine rich domain containing protein	0.7197	27
STAC2	SH3 and cysteine rich domain 2	0.6953	27

ESR1

Cancer enhanced (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
SCUBE2	Signal peptide, CUB domain and EGF like domain containing 2	0.9434	27
SLC5A8	Solute carrier family 5 member 8	0.9195	27
GPR139	G protein-coupled receptor 139	0.8487	27

FOXI1

Cancer enhanced (Breast cancer, Testis cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
RGS21	Regulator of G protein signaling 21	0.5790	24
AMY2A	Amylase alpha 2A	0.5628	24
POU2F3	POU class 2 homeobox 3	0.5562	24

HOXC11

Cancer enhanced (Bone cancer, Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
HOXC12	Homeobox C12	0.7768	65
HOXC10	Homeobox C10	0.6885	27
ALX4	ALX homeobox 4	0.5976	65

HOXC12

Cancer enhanced (Bone cancer, Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
HOXC11	Homeobox C11	0.7768	65
ALX4	ALX homeobox 4	0.6922	65
TBX1	T-box transcription factor 1	0.6719	65

IRX2

Cancer enhanced (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CLEC18B	C-type lectin domain family 18 member B	0.5592	11
CLEC18A	C-type lectin domain family 18 member A	0.5583	11
GPR156	G protein-coupled receptor 156	0.5582	11

IRX3

Cancer enhanced (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
IRX5	Iroquois homeobox 5	0.6574	27
LPAR4	Lysophosphatidic acid receptor 4	0.5215	14
FAM205C	Family with sequence similarity 205 member C	0.4913	14

LMX1B

Cancer enhanced (Breast cancer, Rhabdoid)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
PRLR	Prolactin receptor	0.6615	27
P2RX2	Purinergic receptor P2X 2	0.6526	27
ETNK2	Ethanolamine kinase 2	0.6477	27

RORC

Cancer enhanced (Breast cancer, Prostate cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
LINGO4	Leucine rich repeat and Ig domain containing 4	0.8230	71
CLDN24	Claudin 24	0.7500	71
CLEC4F	C-type lectin domain family 4 member F	0.7237	71

SOHLH1

Cancer enhanced (Breast cancer, Myeloma)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
KIR2DL1	Killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1	0.8055	70
GABRA1	Gamma-aminobutyric acid type A receptor subunit alpha1	0.7982	70
CACNA1S	Calcium voltage-gated channel subunit alpha1 S	0.7958	70

TFAP2C

Cancer enhanced (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CLPSL1	Colipase like 1	0.6004	27
TINCR	TINCR ubiquitin domain containing	0.5926	53
SERTAD4	SERTA domain containing 4	0.5759	69

XBP1

Cancer enhanced (Breast cancer, Myeloma)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
SRARP	Steroid receptor associated and regulated protein	0.6794	27
SLC9A3R1	SLC9A3 regulator 1	0.6732	27
NCBP2L	Nuclear cap binding protein subunit 2 like	0.6723	27

YBX2

Cancer enhanced (Breast cancer)

3 nearest neighbours based on cell line RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
SYCP2	Synaptonemal complex protein 2	0.5327	27
LAGE3	L antigen family member 3	0.4942	36
EFHD1	EF-hand domain family member D1	0.4688	27