Transcription factor landscape - Cell line - thyroid cancer

11 different cell lines are representing thyroid 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 Thyroid Carcinoma (THCA), 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 10 transcription factors that show elevated expression levels in thyroid 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

NOTO

Cancer enriched (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.
GFRA4	GDNF family receptor alpha 4	0.9935	16
SSTR4	Somatostatin receptor 4	0.9907	16
OTOS	Otospiralin	0.9901	16

Enriched transcription factors

Gene

Expression

Expression clustering

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

PAX8

Group enriched (Kidney cancer, Ovarian cancer, Sarcoma, Thyroid cancer, 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.
CLDN16	Claudin 16	0.8523	15
NYX	Nyctalopin	0.7808	15
RXFP1	Relaxin family peptide receptor 1	0.7757	15

Enriched transcription factors

Gene

Expression

Expression clustering

DMRT3

Cancer enhanced (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.
FAM181A	Family with sequence similarity 181 member A	0.5531	15
LHCGR	Luteinizing hormone/choriogonadotropin receptor	0.4980	72
AQP4	Aquaporin 4	0.4887	72

IRX6

Cancer enhanced (Neuroblastoma, Skin 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.
GFRA4	GDNF family receptor alpha 4	0.7410	16
SSTR4	Somatostatin receptor 4	0.7360	16
OTOS	Otospiralin	0.7350	16

LHX1

Cancer enhanced (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.
ADRA1B	Adrenoceptor alpha 1B	0.6275	15
OPRPN	Opiorphin prepropeptide	0.5450	15
HTN3	Histatin 3	0.4822	5

NFKBIL1

Cancer enhanced (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.
PRRC2A	Proline rich coiled-coil 2A	0.7641	28
C6orf47	Chromosome 6 open reading frame 47	0.5956	28
DDX39B	DExD-box helicase 39B	0.5242	28

PRDM9

Cancer enhanced (Myeloma, 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.
OR4C6	Olfactory receptor family 4 subfamily C member 6	0.5503	51
IGKV1-16	Immunoglobulin kappa variable 1-16	0.5163	51
FAM237B	Family with sequence similarity 237 member B	0.4625	53

RFX8

Cancer enhanced (Leukemia, Sarcoma, 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.
ARL5C	ADP ribosylation factor like GTPase 5C	0.6939	14
SIRPD	Signal regulatory protein delta	0.6746	14
RXFP2	Relaxin family peptide receptor 2	0.6445	14

ZNF541

Cancer enhanced (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.
IFNL4	Interferon lambda 4 (gene/pseudogene)	0.6018	4
PFN3	Profilin 3	0.5180	53
CBY3	Chibby family member 3	0.5104	4