Transcription factor landscape - Cell line - head and neck cancer

38 different cell lines are representing head and neck cancer in the atlas, all but one based on squamoise cell carcinoma, different ages and collection site 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 Head and Neck Squamous Cell Carcinoma (HNSC), 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 head and neck 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

FOXN1

Group enriched (Cervical cancer, Esophageal 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.
GJB6	Gap junction protein beta 6	0.8621	53
KRT84	Keratin 84	0.8558	53
USH1G	USH1 protein network component sans	0.8493	53

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

BNC1

Cancer enhanced (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.
KRT17	Keratin 17	0.6460	53
CFAP251	Cilia and flagella associated protein 251	0.6295	53
ANXA8	Annexin A8	0.6210	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

IRF6

Cancer enhanced (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.
ENSG00000289700	Novel protein	0.8379	53
GJB5	Gap junction protein beta 5	0.8256	53
DSG3	Desmoglein 3	0.7909	53

IRX4

Cancer enhanced (Cervical cancer, Esophageal 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.
KHDC1L	KH domain containing 1 like	0.7072	53
IL1F10	Interleukin 1 family member 10	0.6364	53
SOX15	SRY-box transcription factor 15	0.6229	53

LHX5

Cancer enhanced (Cervical 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.
LYPD5	LY6/PLAUR domain containing 5	0.5559	4
NEU2	Neuraminidase 2	0.5371	53
PROSER2	Proline and serine rich 2	0.4680	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

PAX9

Cancer enhanced (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.
NKX2-8	NK2 homeobox 8	0.7510	65
MIPOL1	Mirror-image polydactyly 1	0.7254	30
SLC25A21	Solute carrier family 25 member 21	0.5829	65

SOX15

Cancer enhanced (Cervical cancer, Esophageal 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.
CFAP251	Cilia and flagella associated protein 251	0.7942	53
SFN	Stratifin	0.7574	53
ENSG00000289700	Novel protein	0.7498	53

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