Transcription factor landscape - Cell line - Bile duct cancer

7 different cell lines are representing bile duct cancer in the atlas, all cholangiocarcinomas, different ages and collection sites 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 Cholangiocarcinoma (CHOL), 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 11 transcription factors that show elevated expression levels in bile duct 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

CDX1

Group enriched (Bile duct cancer, Colorectal 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.
SLC6A7	Solute carrier family 6 member 7	0.9569	57
GPA33	Glycoprotein A33	0.9563	57
LRRC19	Leucine rich repeat containing 19	0.9485	57

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

ISX

Group enriched (Bile duct cancer, Colorectal 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.
HNF4A	Hepatocyte nuclear factor 4 alpha	0.5820	57
POF1B	POF1B actin binding protein	0.5665	57
MEP1A	Meprin A subunit alpha	0.5663	57

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

Enriched transcription factors

Gene

Expression

Expression clustering

FOXA3

Cancer enhanced (Bile duct cancer, Colorectal cancer, Gastric 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.
TM4SF5	Transmembrane 4 L six family member 5	0.7606	2
ANKS4B	Ankyrin repeat and sterile alpha motif domain containing 4B	0.7570	10
HNF1A	HNF1 homeobox A	0.7365	10

FOXJ1

Cancer enhanced (Bile duct 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.
ARMC3	Armadillo repeat containing 3	0.7471	10
DRC1	Dynein regulatory complex subunit 1	0.6964	10
CEACAM16	CEA cell adhesion molecule 16, tectorial membrane component	0.6453	10

FOXQ1

Cancer enhanced (Bile duct 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.
EDAR	Ectodysplasin A receptor	0.7746	53
SHH	Sonic hedgehog signaling molecule	0.6547	32
FGF3	Fibroblast growth factor 3	0.6320	32

FOXS1

Cancer enhanced (Bile duct 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.
MYLK2	Myosin light chain kinase 2	0.6411	38
CPZ	Carboxypeptidase Z	0.6279	38
IL17B	Interleukin 17B	0.6029	38

LHX8

Cancer enhanced (Bile duct 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.
TRIM51G	Tripartite motif-containing 51G	0.8743	1
ENSG00000290147	Novel protein	0.8680	1
GALP	Galanin like peptide	0.8572	1

OSR1

Cancer enhanced (Bile duct cancer, Gastric cancer, Sarcoma)

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.
ELN	Elastin	0.7965	64
HSPB7	Heat shock protein family B (small) member 7	0.7687	64
SCUBE3	Signal peptide, CUB domain and EGF like domain containing 3	0.7546	64

PRDM16

Cancer enhanced (Bile duct 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.
PRICKLE4	Prickle planar cell polarity protein 4	0.4913	57
PGC	Progastricsin	0.4617	57
ONECUT3	One cut homeobox 3	0.4274	57