Transcription factor landscape - Cell line - lung cancer

232 different cell lines are representing lung cancer in the atlas, different ages, collection site and cancer type 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 Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC), defining the cell lines most similar to the two cancer types.

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 17 transcription factors that show elevated expression levels in lung 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

POU4F3

Cancer enriched (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.
AKNAD1	AKNA domain containing 1	0.9778	11
MYO15A	Myosin XVA	0.9757	11
ACTL7B	Actin like 7B	0.9731	11

Enriched transcription factors

Gene

Expression

Expression clustering

SOX1

Group enriched (Bone 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.
GAD2	Glutamate decarboxylase 2	0.8273	10
SPHKAP	SPHK1 interactor, AKAP domain containing	0.8099	10
GHRH	Growth hormone releasing hormone	0.7871	10

NKX2-1

Group enriched (Lung cancer, Prostate 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.
MBIP	MAP3K12 binding inhibitory protein 1	0.8413	30
SFTPA1	Surfactant protein A1	0.7135	53
MFSD4A	Major facilitator superfamily domain containing 4A	0.6778	53

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

TBXT

Group enriched (Leukemia, Lung cancer, Lymphoma)

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.
LCN1	Lipocalin 1	0.6990	7
IL4I1	Interleukin 4 induced 1	0.4915	50
UGT2B17	UDP glucuronosyltransferase family 2 member B17	0.4796	55

ASCL1

Group enriched (Lung cancer, Neuroblastoma, 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.
SCGN	Secretagogin, EF-hand calcium binding protein	0.8816	10
OR51G2	Olfactory receptor family 51 subfamily G member 2	0.8777	10
OR51C1P	Olfactory receptor family 51 subfamily C member 1 pseudogene	0.8528	10

INSM1

Group enriched (Lung 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.
PAX4	Paired box 4	0.8800	10
VWA5B2	Von Willebrand factor A domain containing 5B2	0.8546	10
HEPACAM2	HEPACAM family member 2	0.8441	10

NEUROD4

Group enriched (Lung cancer, Neuroblastoma, 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.
NEUROD1	Neuronal differentiation 1	0.7520	1
CABP7	Calcium binding protein 7	0.7493	10
ELAVL2	ELAV like RNA binding protein 2	0.7287	17

Enriched transcription factors

Gene

Expression

Expression clustering

ATOH7

Cancer enhanced (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.
MYH6	Myosin heavy chain 6	0.9854	1
NXNL1	Nucleoredoxin like 1	0.9769	1
RBP3	Retinol binding protein 3	0.9730	1

LHX3

Cancer enhanced (Brain 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.
KIAA2012	KIAA2012	0.7879	11
LMOD2	Leiomodin 2	0.7361	1
GRM6	Glutamate metabotropic receptor 6	0.7338	1

MYCL

Cancer enhanced (Lung cancer, 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.
TRIT1	TRNA isopentenyltransferase 1	0.8868	10
RLF	RLF zinc finger	0.7524	37
PPIE	Peptidylprolyl isomerase E	0.7440	10

NEUROD1

Cancer enhanced (Lung 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.
NTN3	Netrin 3	0.8153	1
CERKL	Ceramide kinase like	0.7887	17
NEUROD4	Neuronal differentiation 4	0.7520	10

NEUROD2

Cancer enhanced (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.
HPCA	Hippocalcin	0.8554	1
NHLH1	Nescient helix-loop-helix 1	0.7780	11
ZDHHC22	Zinc finger DHHC-type palmitoyltransferase 22	0.7362	1

NHLH1

Cancer enhanced (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.
NEUROD2	Neuronal differentiation 2	0.7780	1
CDCP2	CUB domain containing protein 2	0.7728	11
HPCA	Hippocalcin	0.7177	1

POU2F3

Cancer enhanced (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.
POU2AF2	POU class 2 homeobox associating factor 2	0.9774	24
AVIL	Advillin	0.9737	24
PSD2	Pleckstrin and Sec7 domain containing 2	0.9667	24

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

ST18

Cancer enhanced (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.
MS4A8	Membrane spanning 4-domains A8	0.7511	10
SCN3A	Sodium voltage-gated channel alpha subunit 3	0.7504	10
LRRIQ4	Leucine rich repeats and IQ motif containing 4	0.7275	10