Transcription factor landscape - Cell line - ovarian cancer

59 different cell lines are representing ovarian 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 Ovarian Serous Cystadenocarcinoma (OV), 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 9 transcription factors that show elevated expression levels in ovarian 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

SOX17

Group enriched (Liver cancer, Ovarian cancer, Rhabdoid, 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.
LIX1	Limb and CNS expressed 1	0.8005	15
SPON1	Spondin 1	0.7934	15
COL26A1	Collagen type XXVI alpha 1 chain	0.7854	15

PAX2

Group enriched (Kidney cancer, Ovarian cancer, Rhabdoid, 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.
C10orf62	Chromosome 10 open reading frame 62	0.7155	15
BIVM-ERCC5	BIVM-ERCC5 readthrough	0.7139	15
FAM149A	Family with sequence similarity 149 member A	0.7038	15

MEOX1

Group enriched (Ovarian cancer, Rhabdoid, Sarcoma, 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.
EMX2	Empty spiracles homeobox 2	0.8123	15
SPON1	Spondin 1	0.7829	15
OPRPN	Opiorphin prepropeptide	0.7747	15

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

EMX2

Group enriched (Kidney cancer, Ovarian 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.
SPON1	Spondin 1	0.8397	15
OPRPN	Opiorphin prepropeptide	0.8320	15
MEOX1	Mesenchyme homeobox 1	0.8123	15

Enriched transcription factors

Gene

Expression

Expression clustering

BCL6B

Cancer enhanced (Leukemia, Ovarian 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.
ECSCR	Endothelial cell surface expressed chemotaxis and apoptosis regulator	0.8276	48
ROBO4	Roundabout guidance receptor 4	0.8042	48
CDH5	Cadherin 5	0.7916	48

HOXD1

Cancer enhanced (Ovarian 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.
ENSG00000283809	Novel protein	0.8054	15
SLC6A12	Solute carrier family 6 member 12	0.7639	15
TAAR9	Trace amine associated receptor 9	0.7268	15

SIM1

Cancer enhanced (Kidney cancer, Ovarian 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.
CDH6	Cadherin 6	0.5379	15
ANKRD34B	Ankyrin repeat domain 34B	0.5224	15
IL15	Interleukin 15	0.5014	59

WT1

Cancer enhanced (Leukemia, Ovarian 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.
EMX2	Empty spiracles homeobox 2	0.6743	15
OPRPN	Opiorphin prepropeptide	0.6140	15
MEOX1	Mesenchyme homeobox 1	0.6090	15