Transcription factor landscape - Cell line - Kidney cancer

35 different cell lines are representing kidney cancer in the atlas, the origine is renal cell carcinoma and different ages 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 Kidney Chromophobe (KICH), Kidney Renal Clear Cell Carcinoma (KIRC) and Kidney Renal Papillary Cell Carcinoma (KIRP), defining the cell lines most similar to the different 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 kidney 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

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

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

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

Enriched transcription factors

Gene

Expression

Expression clustering

GSX2

Cancer enhanced (Brain cancer, Kidney 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.
GRIA1	Glutamate ionotropic receptor AMPA type subunit 1	0.7262	5
NR2E1	Nuclear receptor subfamily 2 group E member 1	0.6838	72
LHCGR	Luteinizing hormone/choriogonadotropin receptor	0.5552	72

HNF1B

Cancer enhanced (Kidney 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.
CCDC198	Coiled-coil domain containing 198	0.8503	15
SLC3A1	Solute carrier family 3 member 1	0.7663	15
PCSK5	Proprotein convertase subtilisin/kexin type 5	0.7615	15

HOXA4

Cancer enhanced (Kidney 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.
HOXA5	Homeobox A5	0.6963	15
HOXA1	Homeobox A1	0.5366	10
HOXA2	Homeobox A2	0.5347	24

HOXA9

Cancer enhanced (Colorectal cancer, Kidney 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.
HOXA10	Homeobox A10	0.8144	15
HOXA6	Homeobox A6	0.7602	14
HOXA7	Homeobox A7	0.7350	32

NFKBIZ

Cancer enhanced (Kidney 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.
PDZK1IP1	PDZK1 interacting protein 1	0.6014	15
ZC3H12A	Zinc finger CCCH-type containing 12A	0.5296	53
CXCL10	C-X-C motif chemokine ligand 10	0.5284	55

POU3F3

Cancer enhanced (Kidney 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.
SALL1	Spalt like transcription factor 1	0.5860	72
RFX4	Regulatory factor X4	0.5842	72
CDH16	Cadherin 16	0.5746	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