Transcription factor landscape - Cell line - Brain cancer

80 different cell lines are representing brain 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 Glioblastoma Multiforme (GBM) and Brain Lower Grade Glioma (LGG), 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 16 transcription factors that show elevated expression levels in brain 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

NEUROG1

Cancer enriched (Brain 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.
PDE6H	Phosphodiesterase 6H	0.9928	1
TULP1	TUB like protein 1	0.9891	1
WFIKKN2	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	0.9746	1

Enriched transcription factors

Gene

Expression

Expression clustering

SOX3

Group enriched (Brain cancer, Testis 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.
C7orf57	Chromosome 7 open reading frame 57	0.7825	72
DIRAS3	DIRAS family GTPase 3	0.6841	72
LHCGR	Luteinizing hormone/choriogonadotropin receptor	0.6743	72

GLI1

Group enriched (Bone cancer, Brain cancer, Rhabdoid, Sarcoma)

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.
BSPH1	Binder of sperm protein homolog 1	0.7406	38
SOX18	SRY-box transcription factor 18	0.7312	38
IL17B	Interleukin 17B	0.7254	38

Enriched transcription factors

Gene

Expression

Expression clustering

CRX

Cancer enhanced (Brain 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.
AIPL1	Aryl hydrocarbon receptor interacting protein like 1	0.9792	1
OTX2	Orthodenticle homeobox 2	0.9549	1
PCARE	Photoreceptor cilium actin regulator	0.9441	1

DMRTA2

Cancer enhanced (Brain cancer, Sarcoma)

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.
C1QTNF2	C1q and TNF related 2	0.6435	33
PRDM12	PR/SET domain 12	0.5925	33
PIPOX	Pipecolic acid and sarcosine oxidase	0.5733	72

EN1

Cancer enhanced (Brain cancer, Breast 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.
BOC	BOC cell adhesion associated, oncogene regulated	0.7290	44
AARD	Alanine and arginine rich domain containing protein	0.7197	27
STAC2	SH3 and cysteine rich domain 2	0.6953	27

FOXF1

Cancer enhanced (Brain 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.
PDE5A	Phosphodiesterase 5A	0.7922	64
ITGA8	Integrin subunit alpha 8	0.7573	64
TRPA1	Transient receptor potential cation channel subfamily A member 1	0.7487	64

FOXG1

Cancer enhanced (Brain 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.
AMPH	Amphiphysin	0.5538	72
NDP	Norrin cystine knot growth factor NDP	0.5483	72
GPM6A	Glycoprotein M6A	0.5381	72

GLIS1

Cancer enhanced (Brain 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.
RTL3	Retrotransposon Gag like 3	0.6400	72
BEND6	BEN domain containing 6	0.6236	72
KCNA7	Potassium voltage-gated channel subfamily A member 7	0.6100	72

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

IRX1

Cancer enhanced (Brain cancer, Leukemia)

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.
HPSE2	Heparanase 2 (inactive)	0.7099	47
ICAM4	Intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)	0.6971	47
DHH	Desert hedgehog signaling molecule	0.6406	47

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

NR2E1

Cancer enhanced (Brain 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.
LHCGR	Luteinizing hormone/choriogonadotropin receptor	0.7201	72
AQP4	Aquaporin 4	0.7032	72
GSX2	GS homeobox 2	0.6838	72

OTX2

Cancer enhanced (Bone cancer, Brain 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.
CRX	Cone-rod homeobox	0.9549	1
IMPG2	Interphotoreceptor matrix proteoglycan 2	0.9527	1
NPS	Neuropeptide S	0.9337	1

PRRX1

Cancer enhanced (Brain cancer, Rhabdoid)

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.
COL6A1	Collagen type VI alpha 1 chain	0.7162	64
PLPP3	Phospholipid phosphatase 3	0.6999	64
OMD	Osteomodulin	0.6988	44

TBR1

Cancer enhanced (Brain cancer, Rhabdoid)

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.
PDE6H	Phosphodiesterase 6H	0.8384	1
EFCAB10	EF-hand calcium binding domain 10	0.8316	1
PCARE	Photoreceptor cilium actin regulator	0.8313	1