Transcription factor landscape - Cell line - skin cancer

62 different cell lines are representing skin 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 Skin Cutaneous Melanoma (SKCM), 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 27 transcription factors that show elevated expression levels in skin 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

SOX10

Cancer enriched (Skin 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.
PLP1	Proteolipid protein 1	0.8276	69
MIA	MIA SH3 domain containing	0.8190	69
ROPN1	Rhophilin associated tail protein 1	0.7963	69

MITF

Cancer enriched (Skin 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.
MLANA	Melan-A	0.9512	9
SLC24A5	Solute carrier family 24 member 5	0.9414	9
SLC45A2	Solute carrier family 45 member 2	0.9399	9

RXRG

Cancer enriched (Skin 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.
KCNG4	Potassium voltage-gated channel modifier subfamily G member 4	0.7495	1
CABP5	Calcium binding protein 5	0.6958	1
RS1	Retinoschisin 1	0.6953	1

Enriched transcription factors

Gene

Expression

Expression clustering

TBX2

Group enriched (Neuroblastoma, Rhabdoid, Skin 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.
ARMC9	Armadillo repeat containing 9	0.6941	5
MCHR1	Melanin concentrating hormone receptor 1	0.5550	5
TCF21	Transcription factor 21	0.5515	64

FOXD3

Group enriched (Bone cancer, Skin 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.
MRGPRX4	MAS related GPR family member X4	0.8279	69
EXTL1	Exostosin like glycosyltransferase 1	0.8279	69
ITIH6	Inter-alpha-trypsin inhibitor heavy chain family member 6	0.8196	69

NR4A3

Group enriched (Cervical cancer, Skin 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.
TYRP1	Tyrosinase related protein 1	0.9013	9
SLC45A2	Solute carrier family 45 member 2	0.8926	9
PMEL	Premelanosome protein	0.8879	9

SOX8

Group enriched (Rhabdoid, Sarcoma, Skin 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.
MEGF10	Multiple EGF like domains 10	0.8973	33
ENSG00000284779	Novel protein	0.8809	33
MYMK	Myomaker, myoblast fusion factor	0.8793	33

PKNOX2

Group enriched (Bone cancer, Sarcoma, Skin 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.
COL9A1	Collagen type IX alpha 1 chain	0.6955	54
MEGF10	Multiple EGF like domains 10	0.6647	33
SOX8	SRY-box transcription factor 8	0.6575	33

Enriched transcription factors

Gene

Expression

Expression clustering

ALX1

Cancer enhanced (Skin 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.
C8orf48	Chromosome 8 open reading frame 48	0.5325	69
EPHA3	EPH receptor A3	0.5176	72
HMCN1	Hemicentin 1	0.5127	12

ARNT2

Cancer enhanced (Skin 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.
BACE2	Beta-secretase 2	0.5240	7
MGAT5B	Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B	0.5021	72
ARMH4	Armadillo like helical domain containing 4	0.4923	24

EGR3

Cancer enhanced (Skin 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.
OR5AK3P	Olfactory receptor family 5 subfamily AK member 3 pseudogene	0.7437	65
OR5AK2	Olfactory receptor family 5 subfamily AK member 2	0.7221	65
DNASE2B	Deoxyribonuclease 2 beta	0.6946	65

EN2

Cancer enhanced (Skin 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.
OCA2	OCA2 melanosomal transmembrane protein	0.6392	9
UBAP1L	Ubiquitin associated protein 1 like	0.6245	9
OR7A5	Olfactory receptor family 7 subfamily A member 5	0.6111	9

ETV5

Cancer enhanced (Skin 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.
ETV4	ETS variant transcription factor 4	0.6918	54
IDI2	Isopentenyl-diphosphate delta isomerase 2	0.5891	69
MMP17	Matrix metallopeptidase 17	0.5628	69

HEY1

Cancer enhanced (Skin 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.
SEMA3D	Semaphorin 3D	0.6262	5
EPHA7	EPH receptor A7	0.6079	5
VGLL2	Vestigial like family member 2	0.5993	5

IRX6

Cancer enhanced (Neuroblastoma, Skin cancer, Thyroid 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.
GFRA4	GDNF family receptor alpha 4	0.7410	16
SSTR4	Somatostatin receptor 4	0.7360	16
OTOS	Otospiralin	0.7350	16

KLF9

Cancer enhanced (Skin 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.
LAMA4	Laminin subunit alpha 4	0.6185	69
PLN	Phospholamban	0.5662	69
SERPINA3	Serpin family A member 3	0.5563	69

MAFF

Cancer enhanced (Skin 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.
BEST1	Bestrophin 1	0.5661	9
SLC5A4	Solute carrier family 5 member 4	0.5575	9
CAPN3	Calpain 3	0.5444	9

NFATC2

Cancer enhanced (Skin 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.
MIA	MIA SH3 domain containing	0.8100	69
LOXL4	Lysyl oxidase like 4	0.7961	69
S100B	S100 calcium binding protein B	0.7931	69

NPAS1

Cancer enhanced (Skin 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.
FMN2	Formin 2	0.5462	64
RXRG	Retinoid X receptor gamma	0.5461	1
SGCD	Sarcoglycan delta	0.5078	64

OLIG2

Cancer enhanced (Leukemia, Sarcoma, Skin 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.
C3AR1	Complement C3a receptor 1	0.6799	49
C3orf80	Chromosome 3 open reading frame 80	0.6536	49
LTC4S	Leukotriene C4 synthase	0.6306	49

PAX3

Cancer enhanced (Bone cancer, Sarcoma, Skin 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.
DAAM2	Dishevelled associated activator of morphogenesis 2	0.6277	69
ENSG00000251569	Novel protein	0.5999	33
PKNOX2	PBX/knotted 1 homeobox 2	0.5974	33

POU3F2

Cancer enhanced (Bone cancer, Skin 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.
PRSS35	Serine protease 35	0.7068	12
DNAH9	Dynein axonemal heavy chain 9	0.6880	69
FEZF1	FEZ family zinc finger 1	0.6622	12

SOX5

Cancer enhanced (Skin 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.
ABCB4	ATP binding cassette subfamily B member 4	0.5508	69
PLN	Phospholamban	0.5255	69
CDH19	Cadherin 19	0.5183	69

SOX6

Cancer enhanced (Bone cancer, Skin 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.
GLUD2	Glutamate dehydrogenase 2	0.5992	47
PHOSPHO1	Phosphoethanolamine/phosphocholine phosphatase 1	0.5937	12
FAXDC2	Fatty acid hydroxylase domain containing 2	0.5379	47

ZEB2

Cancer enhanced (Leukemia, Skin 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.
MS4A6A	Membrane spanning 4-domains A6A	0.5472	14
CCL23	C-C motif chemokine ligand 23	0.5157	14
SERPINI2	Serpin family I member 2	0.4901	14

ZNF280A

Cancer enhanced (Skin 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.
PRAME	PRAME nuclear receptor transcriptional regulator	0.6726	5
TP53TG3D	TP53 target 3D	0.4817	9
AKR1E2	Aldo-keto reductase family 1 member E2	0.4806	5

ZNF697

Cancer enhanced (Skin 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.
ZC3H11B	Zinc finger CCCH-type containing 11B	0.6332	9
PRDM7	PR/SET domain 7	0.6227	9
FMN1	Formin 1	0.6160	9