Transcription factor landscape - Cell line - Gallbladder cancer

One cell line is representing gallbladder cancer in the atlas (called SNU-308), find more details about it here. Up- and downregulated cancer-related pathways can be explored based on the transcriptomics data.

Here we provide the expression overview of all 12 transcription factors that show elevated expression levels in gallbladder 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

LHX6

Cancer enriched (Gallbladder 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.
ZFR2	Zinc finger RNA binding protein 2	0.5930	4
CILP2	Cartilage intermediate layer protein 2	0.5463	4
IFNL4	Interferon lambda 4 (gene/pseudogene)	0.5413	4

ZNF644

Cancer enriched (Gallbladder 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.
GLMN	Glomulin, FKBP associated protein	0.5972	37
RPF1	Ribosome production factor 1 homolog	0.5952	37
USP1	Ubiquitin specific peptidase 1	0.5705	37

Enriched transcription factors

Gene

Expression

Expression clustering

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

Enriched transcription factors

Gene

Expression

Expression clustering

GRHL3

Cancer enhanced (Gallbladder 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.
SPRR3	Small proline rich protein 3	0.6783	53
OVOL1	Ovo like transcriptional repressor 1	0.6055	53
GJB6	Gap junction protein beta 6	0.5974	53

HES2

Cancer enhanced (Gallbladder cancer, Head and neck 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.
PGLYRP4	Peptidoglycan recognition protein 4	0.8611	53
RHCG	Rh family C glycoprotein	0.8568	53
PGLYRP3	Peptidoglycan recognition protein 3	0.8527	53

HOXD10

Cancer enhanced (Bone cancer, Gallbladder 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.
HOXD11	Homeobox D11	0.8105	12
HOXD9	Homeobox D9	0.8098	12
NKX2-2	NK2 homeobox 2	0.6363	12

NKX1-2

Cancer enhanced (Gallbladder 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.
NPBWR1	Neuropeptides B and W receptor 1	0.6227	53
DNAH2	Dynein axonemal heavy chain 2	0.5560	53
MUC21	Mucin 21, cell surface associated	0.5429	53

NKX2-8

Cancer enhanced (Gallbladder cancer, Head and neck 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.
PAX9	Paired box 9	0.7510	30
SPINK5	Serine peptidase inhibitor Kazal type 5	0.7226	65
OR2M7	Olfactory receptor family 2 subfamily M member 7	0.7049	65

SOX21

Cancer enhanced (Gallbladder 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.
SOX2	SRY-box transcription factor 2	0.7219	32
LHCGR	Luteinizing hormone/choriogonadotropin receptor	0.5844	72
LRP1B	LDL receptor related protein 1B	0.5798	3

TBX6

Cancer enhanced (Gallbladder 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.
LPAR6	Lysophosphatidic acid receptor 6	0.5632	6
MYLK3	Myosin light chain kinase 3	0.5578	6
DENND3	DENN domain containing 3	0.5414	6

THRB

Cancer enhanced (Gallbladder 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.
BHMT	Betaine--homocysteine S-methyltransferase	0.4717	10
GCGR	Glucagon receptor	0.4663	10
ADH1A	Alcohol dehydrogenase 1A (class I), alpha polypeptide	0.4605	10

TP63

Cancer enhanced (Esophageal cancer, Gallbladder cancer, Head and neck 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.
GBP6	Guanylate binding protein family member 6	0.8877	53
SERPINB13	Serpin family B member 13	0.8377	53
DSC3	Desmocollin 3	0.8369	53