Transcription factor landscape - Cell line - Gastric cancer

42 different cell lines are representing gastric 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 Stomach Adenocarcinoma (STAD), 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 21 transcription factors that show elevated expression levels in gastric 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

DMRTB1

Cancer enriched (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.
REC114	REC114 meiotic recombination protein	0.7939	57
NPSR1	Neuropeptide S receptor 1	0.7325	57
TMEM213	Transmembrane protein 213	0.7039	57

NKX6-3

Cancer enriched (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.
CYP2C18	Cytochrome P450 family 2 subfamily C member 18	0.6860	57
ONECUT3	One cut homeobox 3	0.6582	57
SULT1C2	Sulfotransferase family 1C member 2	0.6410	57

TBX4

Cancer enriched (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.
LCE4A	Late cornified envelope 4A	0.6177	64
LCE2A	Late cornified envelope 2A	0.6113	64
PDE5A	Phosphodiesterase 5A	0.5875	64

Enriched transcription factors

Gene

Expression

Expression clustering

ATOH1

Group enriched (Colorectal cancer, Gastric cancer, Lung 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	0.9465	11
CLEC18A	C-type lectin domain family 18 member A	0.9364	11
POU4F3	POU class 4 homeobox 3	0.9226	11

ASCL2

Group enriched (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.
CCL24	C-C motif chemokine ligand 24	0.8604	57
DPEP1	Dipeptidase 1	0.8557	57
WFDC9	WAP four-disulfide core domain 9	0.8358	57

EVX1

Group enriched (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.
R3HDML	R3H domain containing like	0.8515	57
NOX1	NADPH oxidase 1	0.8488	57
CDX1	Caudal type homeobox 1	0.8455	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

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

RHOXF2B

Group enriched (Gastric cancer, Leukemia, 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.
RHOXF2	Rhox homeobox family member 2	0.9077	51
EPX	Eosinophil peroxidase	0.6403	51
NAA11	N-alpha-acetyltransferase 11, NatA catalytic subunit	0.5515	51

Enriched transcription factors

Gene

Expression

Expression clustering

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

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

GATA4

Cancer enhanced (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.
MTTP	Microsomal triglyceride transfer protein	0.6465	18
A1CF	APOBEC1 complementation factor	0.6331	18
C2orf72	Chromosome 2 open reading frame 72	0.6068	18

GATA5

Cancer enhanced (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.
SPRR2F	Small proline rich protein 2F	0.4751	72
CARNS1	Carnosine synthase 1	0.4725	72
ZFPM1	Zinc finger protein, FOG family member 1	0.4701	47

LMX1A

Cancer enhanced (Bone 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.
F9	Coagulation factor IX	0.8799	10
GRIN3A	Glutamate ionotropic receptor NMDA type subunit 3A	0.8749	10
BHMT	Betaine--homocysteine S-methyltransferase	0.8743	10

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

NR1I2

Cancer enhanced (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.
MYO1A	Myosin IA	0.9130	57
CDH17	Cadherin 17	0.8465	57
ANKRD40CL	ANKRD40 C-terminal like	0.8443	57

ONECUT3

Cancer enhanced (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.
C1QTNF8	C1q and TNF related 8	0.8013	57
SULT1C2	Sulfotransferase family 1C member 2	0.7781	57
CYP2C18	Cytochrome P450 family 2 subfamily C member 18	0.7337	57

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

PDX1

Cancer enhanced (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.
GBA3	Glucosylceramidase beta 3 (gene/pseudogene)	0.5550	59
TRBV4-1	T cell receptor beta variable 4-1	0.5490	59
TRAV16	T cell receptor alpha variable 16	0.5266	59

POU4F2

Cancer enhanced (Bone 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.
GRIN3A	Glutamate ionotropic receptor NMDA type subunit 3A	0.9246	10
F9	Coagulation factor IX	0.8942	10
VWA5B2	Von Willebrand factor A domain containing 5B2	0.8890	10

RFX6

Cancer enhanced (Gastric cancer, Lung 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.
VWA5B2	Von Willebrand factor A domain containing 5B2	0.9370	10
GRIN3A	Glutamate ionotropic receptor NMDA type subunit 3A	0.9317	10
PPP3R2	Protein phosphatase 3 regulatory subunit B, beta	0.9124	10