Transcription factor landscape - Cell line - Bone cancer

21 different cell lines are representing bone cancer in the atlas, different ages, collection site and cancer subtypes are represented, find more details about the different cell lines here. For each of the rhabdoid related cell line, up- and downregulated cancer-related pathways can be explored based on the transcriptomics data.

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 53 transcription factors that show elevated expression levels in bone 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

BARHL2

Cancer enriched (Bone 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.
LIPI	Lipase I	0.9032	12
TRAV7	T cell receptor alpha variable 7	0.8963	12
RBM11	RNA binding motif protein 11	0.8905	12

NEUROD6

Cancer enriched (Bone 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.
PRAMEF1	PRAME family member 1	0.8652	12
MBD3L5	Methyl-CpG binding domain protein 3 like 5	0.8628	12
MBD3L3	Methyl-CpG binding domain protein 3 like 3	0.8587	12

RAX

Cancer enriched (Bone 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.
LIPI	Lipase I	0.9089	12
RBM11	RNA binding motif protein 11	0.9051	12
PPP1R1A	Protein phosphatase 1 regulatory inhibitor subunit 1A	0.8965	12

FOXR1

Cancer enriched (Bone 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.
WARS2	Tryptophanyl tRNA synthetase 2, mitochondrial	0.4868	37
TRNT1	TRNA nucleotidyl transferase 1	0.4825	8
TSR1	TSR1 ribosome maturation factor	0.4299	42

PAX7

Cancer enriched (Bone 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.
SYCP1	Synaptonemal complex protein 1	0.9240	12
PPP1R1A	Protein phosphatase 1 regulatory inhibitor subunit 1A	0.9194	12
GOT1L1	Glutamic-oxaloacetic transaminase 1 like 1	0.9111	12

FEZF1

Cancer enriched (Bone 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.
PPP1R1A	Protein phosphatase 1 regulatory inhibitor subunit 1A	0.8197	12
GOT1L1	Glutamic-oxaloacetic transaminase 1 like 1	0.8077	12
ADRB3	Adrenoceptor beta 3	0.8051	12

NKX2-2

Cancer enriched (Bone 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.
RAX	Retina and anterior neural fold homeobox	0.8640	12
LIPI	Lipase I	0.8413	12
RBM11	RNA binding motif protein 11	0.8349	12

TBX5

Cancer enriched (Bone 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.
SGIP1	SH3GL interacting endocytic adaptor 1	0.7041	64
PAMR1	Peptidase domain containing associated with muscle regeneration 1	0.6799	64
MASP1	MBL associated serine protease 1	0.6769	64

VAX1

Cancer enriched (Bone 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.
CYP4F22	Cytochrome P450 family 4 subfamily F member 22	0.8408	12
KCNK18	Potassium two pore domain channel subfamily K member 18	0.8351	12
TMEM114	Transmembrane protein 114	0.8288	12

ARX

Cancer enriched (Bone 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.
DLG2	Discs large MAGUK scaffold protein 2	0.7636	12
MAPT	Microtubule associated protein tau	0.7629	12
TMEM114	Transmembrane protein 114	0.7480	12

HOXD13

Cancer enriched (Bone 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.
RBM11	RNA binding motif protein 11	0.8074	12
LIPI	Lipase I	0.7902	12
BARHL2	BarH like homeobox 2	0.7792	12

NKX2-4

Cancer enriched (Bone 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.
ASIP	Agouti signaling protein	0.6736	12
NEUROD6	Neuronal differentiation 6	0.6518	12
HOOK1	Hook microtubule tethering protein 1	0.6150	12

NKX6-1

Cancer enriched (Bone 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.
PRAMEF1	PRAME family member 1	0.8299	12
MBD3L5	Methyl-CpG binding domain protein 3 like 5	0.8099	12
MBD3L3	Methyl-CpG binding domain protein 3 like 3	0.7962	12

POU3F1

Cancer enriched (Bone 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.
BARHL2	BarH like homeobox 2	0.6007	12
FEZF1	FEZ family zinc finger 1	0.5870	12
UTS2	Urotensin 2	0.5841	12

ALX4

Cancer enriched (Bone 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.
HOXC12	Homeobox C12	0.6922	65
OR14C36	Olfactory receptor family 14 subfamily C member 36	0.6886	65
NPVF	Neuropeptide VF precursor	0.6884	65

Enriched transcription factors

Gene

Expression

Expression clustering

TCF21

Group enriched (Bone cancer, Liver 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.
INMT	Indolethylamine N-methyltransferase	0.8776	64
CHRM2	Cholinergic receptor muscarinic 2	0.8632	64
PF4V1	Platelet factor 4 variant 1	0.8626	64

SOX1

Group enriched (Bone 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.
GAD2	Glutamate decarboxylase 2	0.8273	10
SPHKAP	SPHK1 interactor, AKAP domain containing	0.8099	10
GHRH	Growth hormone releasing hormone	0.7871	10

TFAP2B

Group enriched (Bone cancer, Breast cancer, Neuroblastoma)

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.
CHRM1	Cholinergic receptor muscarinic 1	0.6244	17
TMEM229A	Transmembrane protein 229A	0.5835	12
CRABP1	Cellular retinoic acid binding protein 1	0.5670	17

BCL11B

Group enriched (Bone 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.
TRAV6	T cell receptor alpha variable 6	0.6663	12
OR4E1	Olfactory receptor family 4 subfamily E member 1	0.6515	12
C22orf15	Chromosome 22 open reading frame 15	0.6357	12

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

BHLHE22

Group enriched (Bone cancer, Myeloma)

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.
TENM1	Teneurin transmembrane protein 1	0.6642	12
KRTAP10-10	Keratin associated protein 10-10	0.6621	10
KRTAP10-11	Keratin associated protein 10-11	0.6373	10

CTCFL

Group enriched (Bone cancer, Cervical 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.
MEIOB	Meiosis specific with OB-fold	0.5867	4
PRSS50	Serine protease 50	0.5864	4
ENSG00000230707	Novel protein (LOC389895)	0.5064	15

FOXD3

Group enriched (Bone cancer, 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.
MRGPRX4	MAS related GPR family member X4	0.8279	69
EXTL1	Exostosin like glycosyltransferase 1	0.8279	69
ITIH6	Inter-alpha-trypsin inhibitor heavy chain family member 6	0.8196	69

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

SOX11

Group enriched (Bone cancer, Neuroblastoma)

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.
GPC2	Glypican 2	0.6849	17
DPYSL5	Dihydropyrimidinase like 5	0.6664	17
TMEFF1	Transmembrane protein with EGF like and two follistatin like domains 1	0.6645	17

Enriched transcription factors

Gene

Expression

Expression clustering

CUX2

Cancer enhanced (Bone cancer, Lymphoma, Neuroblastoma)

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.
MYO9A	Myosin IXA	0.5380	46
C8orf89	Chromosome 8 open reading frame 89	0.5321	46
MAPK10	Mitogen-activated protein kinase 10	0.5315	46

DLX4

Cancer enhanced (Bone 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.
PRSS56	Serine protease 56	0.7916	65
DLX3	Distal-less homeobox 3	0.7326	34
PRR35	Proline rich 35	0.6881	65

EBF3

Cancer enhanced (Bone cancer, Neuroblastoma)

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.
TAFA5	TAFA chemokine like family member 5	0.5732	12
INKA2	Inka box actin regulator 2	0.5330	64
EGFLAM	EGF like, fibronectin type III and laminin G domains	0.5132	12

ESRRB

Cancer enhanced (Bone 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.
ENSG00000272297	Novel protein	0.7366	12
WDR64	WD repeat domain 64	0.7096	12
TMEM114	Transmembrane protein 114	0.7018	12

HOXC11

Cancer enhanced (Bone 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.
HOXC12	Homeobox C12	0.7768	65
HOXC10	Homeobox C10	0.6885	27
ALX4	ALX homeobox 4	0.5976	65

HOXC12

Cancer enhanced (Bone 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.
HOXC11	Homeobox C11	0.7768	65
ALX4	ALX homeobox 4	0.6922	65
TBX1	T-box transcription factor 1	0.6719	65

HOXD10

Cancer enhanced (Bone cancer, Gallbladder 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.
HOXD11	Homeobox D11	0.8105	12
HOXD9	Homeobox D9	0.8098	12
NKX2-2	NK2 homeobox 2	0.6363	12

HOXD11

Cancer enhanced (Bone 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.
HOXD10	Homeobox D10	0.8105	12
HOXD9	Homeobox D9	0.7485	12
NKX2-2	NK2 homeobox 2	0.6824	12

HOXD12

Cancer enhanced (Bone 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.
HOXD13	Homeobox D13	0.6713	12
LIPM	Lipase family member M	0.6285	12
HOXD11	Homeobox D11	0.5824	12

HOXD9

Cancer enhanced (Bone cancer, Neuroblastoma)

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.
HOXD10	Homeobox D10	0.8098	12
HOXD11	Homeobox D11	0.7485	12
HOXD8	Homeobox D8	0.6726	17

LBX1

Cancer enhanced (Bone 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.
PDYN	Prodynorphin	0.9224	12
CACNG3	Calcium voltage-gated channel auxiliary subunit gamma 3	0.9209	12
GDF10	Growth differentiation factor 10	0.9208	12

LMX1A

Cancer enhanced (Bone cancer, Gastric 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.
F9	Coagulation factor IX	0.8799	10
GRIN3A	Glutamate ionotropic receptor NMDA type subunit 3A	0.8749	10
BHMT	Betaine--homocysteine S-methyltransferase	0.8743	10

MAFB

Cancer enhanced (Bone 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.
TMEM132B	Transmembrane protein 132B	0.6162	12
HAP1	Huntingtin associated protein 1	0.5431	12
TCHHL1	Trichohyalin like 1	0.5430	53

NKX3-2

Cancer enhanced (Bone 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.
CSPG5	Chondroitin sulfate proteoglycan 5	0.4922	12
PKNOX2	PBX/knotted 1 homeobox 2	0.4343	33
ADRA1D	Adrenoceptor alpha 1D	0.4343	12

NR0B1

Cancer enhanced (Bone 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.
SRXN1	Sulfiredoxin 1	0.6818	7
CES1	Carboxylesterase 1	0.6720	7
AKR1C3	Aldo-keto reductase family 1 member C3	0.6584	7

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

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

POU1F1

Cancer enhanced (Bone 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.
TRAV1-2	T cell receptor alpha variable 1-2	0.6946	12
LIPI	Lipase I	0.6863	12
OR4E2	Olfactory receptor family 4 subfamily E member 2	0.6671	12

POU3F2

Cancer enhanced (Bone cancer, 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.
PRSS35	Serine protease 35	0.7068	12
DNAH9	Dynein axonemal heavy chain 9	0.6880	69
FEZF1	FEZ family zinc finger 1	0.6622	12

POU4F2

Cancer enhanced (Bone cancer, Gastric 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.
GRIN3A	Glutamate ionotropic receptor NMDA type subunit 3A	0.9246	10
F9	Coagulation factor IX	0.8942	10
VWA5B2	Von Willebrand factor A domain containing 5B2	0.8890	10

PRRX2

Cancer enhanced (Bone 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.
GREM2	Gremlin 2, DAN family BMP antagonist	0.7177	64
CD248	CD248 molecule	0.6614	64
KRTAP1-5	Keratin associated protein 1-5	0.6505	64

SOX18

Cancer enhanced (Bone 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.
BSPH1	Binder of sperm protein homolog 1	0.7665	38
IL17B	Interleukin 17B	0.7457	38
ELSPBP1	Epididymal sperm binding protein 1	0.7408	38

SOX6

Cancer enhanced (Bone cancer, 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.
GLUD2	Glutamate dehydrogenase 2	0.5992	47
PHOSPHO1	Phosphoethanolamine/phosphocholine phosphatase 1	0.5937	12
FAXDC2	Fatty acid hydroxylase domain containing 2	0.5379	47

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

TLX1

Cancer enhanced (Bone 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.
GDF10	Growth differentiation factor 10	0.6273	12
TPTE2	Transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	0.6049	12
XKR4	XK related 4	0.5946	12

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

UNCX

Cancer enhanced (Bone 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.
PDZD7	PDZ domain containing 7	0.6834	11
C1orf232	Chromosome 1 open reading frame 230	0.6646	11
USH2A	Usherin	0.6426	11

ZFPM2

Cancer enhanced (Bone 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.
ENSG00000289766	Novel protein	0.5705	1
KIAA1614	KIAA1614	0.5617	1
MRLN	Myoregulin	0.5467	1