Transcription factor landscape - Cell line - Sarcoma

15 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 Sarcoma (SARC), 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 27 transcription factors that show elevated expression levels in sarcoma 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

MYOD1

Cancer enriched (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.
CAV3	Caveolin 3	0.9905	33
RAPSN	Receptor associated protein of the synapse	0.9869	33
MYOG	Myogenin	0.9862	33

MYOG

Cancer enriched (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.
KLHL40	Kelch like family member 40	0.9957	33
CAV3	Caveolin 3	0.9907	33
MYOD1	Myogenic differentiation 1	0.9862	33

EBF2

Cancer enriched (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.
OR2T5	Olfactory receptor family 2 subfamily T member 5	0.7979	54
LIM2	Lens intrinsic membrane protein 2	0.7948	54
TACR3	Tachykinin receptor 3	0.7820	54

PITX3

Cancer enriched (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.
RAPSN	Receptor associated protein of the synapse	0.9681	33
MYOD1	Myogenic differentiation 1	0.9670	33
CHRND	Cholinergic receptor nicotinic delta subunit	0.9619	33

MYF5

Cancer enriched (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.
ASB5	Ankyrin repeat and SOCS box containing 5	0.9271	33
ACTC1	Actin alpha cardiac muscle 1	0.7972	33
MYF6	Myogenic factor 6	0.6173	5

Enriched transcription factors

Gene

Expression

Expression clustering

DBX1

Group enriched (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.
STATH	Statherin	0.8622	33
FGF8	Fibroblast growth factor 8	0.8419	33
MUSTN1	Musculoskeletal, embryonic nuclear protein 1	0.8158	33

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

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

DRGX

Group enriched (Neuroblastoma, 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.
DCLK3	Doublecortin like kinase 3	0.9176	11
CLEC18B	C-type lectin domain family 18 member B	0.8881	11
CLEC18A	C-type lectin domain family 18 member A	0.8838	11

NKX2-6

Group enriched (Neuroblastoma, 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.
RBMY1B	RNA binding motif protein Y-linked family 1 member B	0.7427	17
PIRT	Phosphoinositide interacting regulator of transient receptor potential channels	0.7373	17
HTR3B	5-hydroxytryptamine receptor 3B	0.7175	17

SOX8

Group enriched (Rhabdoid, Sarcoma, Skin 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.
MEGF10	Multiple EGF like domains 10	0.8973	33
ENSG00000284779	Novel protein	0.8809	33
MYMK	Myomaker, myoblast fusion factor	0.8793	33

PKNOX2

Group enriched (Bone cancer, Sarcoma, Skin 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.
COL9A1	Collagen type IX alpha 1 chain	0.6955	54
MEGF10	Multiple EGF like domains 10	0.6647	33
SOX8	SRY-box transcription factor 8	0.6575	33

Enriched transcription factors

Gene

Expression

Expression clustering

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

FOXC2

Cancer enhanced (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.
LDB2	LIM domain binding 2	0.6223	12
EBF2	EBF transcription factor 2	0.5882	54
SBSPON	Somatomedin B and thrombospondin type 1 domain containing	0.5624	12

HEYL

Cancer enhanced (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.
MYOD1	Myogenic differentiation 1	0.8334	33
PITX3	Paired like homeodomain 3	0.8320	33
DES	Desmin	0.8304	33

MYF6

Cancer enhanced (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.
MYF5	Myogenic factor 5	0.6173	33
ZSWIM2	Zinc finger SWIM-type containing 2	0.6004	5
CALHM4	Calcium homeostasis modulator family member 4	0.5675	5

NKX2-5

Cancer enhanced (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.
TRBV4-2	T cell receptor beta variable 4-2	0.5206	59
TRDV1	T cell receptor delta variable 1	0.5197	59
SEMA3D	Semaphorin 3D	0.5167	5

OLIG2

Cancer enhanced (Leukemia, Sarcoma, Skin 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.
C3AR1	Complement C3a receptor 1	0.6799	49
C3orf80	Chromosome 3 open reading frame 80	0.6536	49
LTC4S	Leukotriene C4 synthase	0.6306	49

OSR1

Cancer enhanced (Bile duct cancer, Gastric 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.
ELN	Elastin	0.7965	64
HSPB7	Heat shock protein family B (small) member 7	0.7687	64
SCUBE3	Signal peptide, CUB domain and EGF like domain containing 3	0.7546	64

PAX3

Cancer enhanced (Bone cancer, Sarcoma, Skin 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.
DAAM2	Dishevelled associated activator of morphogenesis 2	0.6277	69
ENSG00000251569	Novel protein	0.5999	33
PKNOX2	PBX/knotted 1 homeobox 2	0.5974	33

POU4F1

Cancer enhanced (Leukemia, 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.
FOXO6	Forkhead box O6	0.6768	11
SEMA6C	Semaphorin 6C	0.5913	6
LRRC30	Leucine rich repeat containing 30	0.5561	33

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

SIX2

Cancer enhanced (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.
KLHL41	Kelch like family member 41	0.5783	33
IL1RAPL2	Interleukin 1 receptor accessory protein like 2	0.5651	33
ALPK3	Alpha kinase 3	0.5326	33

TBX15

Cancer enhanced (Bone 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.
CXCL12	C-X-C motif chemokine ligand 12	0.5563	44
MYMK	Myomaker, myoblast fusion factor	0.5519	33
MYH3	Myosin heavy chain 3	0.5496	33

TSHZ3

Cancer enhanced (Bone 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.
ADRA1D	Adrenoceptor alpha 1D	0.5644	12
TMEM233	Transmembrane protein 233	0.5469	33
TMEM114	Transmembrane protein 114	0.5423	12

TWIST2

Cancer enhanced (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.
ADAM33	ADAM metallopeptidase domain 33	0.7750	44
MMP3	Matrix metallopeptidase 3	0.7180	64
LPAR1	Lysophosphatidic acid receptor 1	0.7123	44