Transcription factor landscape - Cell line - liver cancer

24 different cell lines are representing liver cancer in the atlas, from hepatocellular cardinomas, different ages 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 Liver Hepatocellular Carcinoma (LIHC), 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 15 transcription factors that show elevated expression levels in liver 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

ZSCAN5B

Cancer enriched (Liver 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.
SLC6A12	Solute carrier family 6 member 12	0.6808	15
S100G	S100 calcium binding protein G	0.6786	15
RXFP1	Relaxin family peptide receptor 1	0.6673	15

Enriched transcription factors

Gene

Expression

Expression clustering

TCF21

Group enriched (Bone cancer, Liver 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.
INMT	Indolethylamine N-methyltransferase	0.8776	64
CHRM2	Cholinergic receptor muscarinic 2	0.8632	64
PF4V1	Platelet factor 4 variant 1	0.8626	64

SOX17

Group enriched (Liver cancer, Ovarian cancer, Rhabdoid, Uterine 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.
LIX1	Limb and CNS expressed 1	0.8005	15
SPON1	Spondin 1	0.7934	15
COL26A1	Collagen type XXVI alpha 1 chain	0.7854	15

HNF4A

Group enriched (Bile duct cancer, Colorectal cancer, Gastric cancer, Liver 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.
MOGAT3	Monoacylglycerol O-acyltransferase 3	0.8299	57
MEP1A	Meprin A subunit alpha	0.8162	57
SLC39A5	Solute carrier family 39 member 5	0.7932	57

NR1H4

Group enriched (Gastric cancer, Kidney cancer, Liver 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.
SLC17A2	Solute carrier family 17 member 2	0.6967	18
ACSM2A	Acyl-CoA synthetase medium chain family member 2A	0.6937	18
CFAP221	Cilia and flagella associated protein 221	0.6934	15

NR5A1

Group enriched (Head and neck cancer, Leukemia, Liver 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.
OR4N5	Olfactory receptor family 4 subfamily N member 5	0.8024	47
CATSPERD	Cation channel sperm associated auxiliary subunit delta	0.7981	47
PSKH2	Protein serine kinase H2	0.7857	47

Enriched transcription factors

Gene

Expression

Expression clustering

CEBPA

Cancer enhanced (Leukemia, Liver 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.
LINC02218	Long intergenic non-protein coding RNA 2218	0.6823	14
CD300LF	CD300 molecule like family member f	0.6739	14
CLEC12A	C-type lectin domain family 12 member A	0.6667	14

CREB3L3

Cancer enhanced (Gastric cancer, Liver cancer, Pancreatic 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.
CDHR2	Cadherin related family member 2	0.7288	53
LIPC	Lipase C, hepatic type	0.7262	18
LGALS2	Galectin 2	0.7106	53

FOXA2

Cancer enhanced (Liver 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.
SCGN	Secretagogin, EF-hand calcium binding protein	0.6481	10
RFX6	Regulatory factor X6	0.6380	10
CACNA1H	Calcium voltage-gated channel subunit alpha1 H	0.6369	10

HLF

Cancer enhanced (Liver 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.
G6PC1	Glucose-6-phosphatase catalytic subunit 1	0.8936	18
SERPINA7	Serpin family A member 7	0.8808	18
SMLR1	Small leucine rich protein 1	0.8748	18

MYRF

Cancer enhanced (Liver 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.
MUCL3	Mucin like 3	0.6970	66
TMEM37	Transmembrane protein 37	0.6595	18
CARNS1	Carnosine synthase 1	0.6541	72

NR0B2

Cancer enhanced (Gastric cancer, Liver 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.
KRTAP5-5	Keratin associated protein 5-5	0.7782	10
OR51E2	Olfactory receptor family 51 subfamily E member 2	0.7690	10
C2CD4B	C2 calcium dependent domain containing 4B	0.7377	10

ONECUT1

Cancer enhanced (Liver 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.
NAT8	N-acetyltransferase 8 (putative)	0.7048	18
ANGPTL3	Angiopoietin like 3	0.6736	18
MTTP	Microsomal triglyceride transfer protein	0.6692	18

PROX1

Cancer enhanced (Liver 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.
CA6	Carbonic anhydrase 6	0.7050	70
TBX10	T-box transcription factor 10	0.6979	70
FAM3B	FAM3 metabolism regulating signaling molecule B	0.6953	10

SP5

Cancer enhanced (Cervical cancer, Colorectal cancer, Liver 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.
NOTUM	Notum, palmitoleoyl-protein carboxylesterase	0.8076	32
NKD1	NKD inhibitor of WNT signaling pathway 1	0.7102	32
ASPSCR1	ASPSCR1 tether for SLC2A4, UBX domain containing	0.6731	70