Pan-Cancer

Pathways significantly upregulated in cancers

Gene-set enrichment analysis: the GSEA tool

Genes whose upregulation is associated with poor prognosis of cancers

Survival analyses: Kaplan-Meier survival curves and the log-rank test.

Genes whose downregulation is associated with poor prognosis of cancers

Survival analyses: Kaplan-Meier survival curves and the log-rank test.

Genes with increased or decreased expression alterations from normal tissue to low-advanced cancers, and from low-advanced cancers to highly-advanced cancers

A. Genes whose expression follows the pattern: late-stage cancers > early-stage cancers > normal controls;

B. Genes whose expression follows the pattern: high-grade cancers > low-grade cancers > normal controls;

C. Genes whose expression follows the pattern: late-stage cancers < early-stage cancers < normal controls;

D. Genes whose expression follows the pattern: high-grade cancers < low-grade cancers < normal controls.

The cell cycle pathway consistently upregulated in cancers

Genes whose expression is significantly higher in cancer than in normal tissue

The genes with higher expression levels in cancers than in normal tisssue are highlighted in azure, while the genes with lower expression levels in cancers are highlighted in bisque (fold change > 1.5, FDR < 0.05)

Symbol	Name	Chromosome	Cytoband
UBE2C	ubiquitin-conjugating enzyme E2C	20	20q13.12
KIF18B	kinesin family member 18B	17	17q21.31
TROAP	trophinin associated protein	12	12q13.12
UHRF1	ubiquitin-like with PHD and ring finger domains 1	19	19p13.3
KIF20A	kinesin family member 20A	5	5q31
HJURP	Holliday junction recognition protein	2	2q37.1
IQGAP3	IQ motif containing GTPase activating protein 3	1	1q21.3
CDT1	chromatin licensing and DNA replication factor 1	16	16q24.3
GTSE1	G-2 and S-phase expressed 1	22	22q13.2-q13.3
SKA3	spindle and kinetochore associated complex subunit 3	13	13q12.11
TTK	TTK protein kinase	6	6q14.1
ASF1B	anti-silencing function 1B histone chaperone	19	19p13.12
NEK2	NIMA-related kinase 2	1	1q32.3
CDC25C	cell division cycle 25C	5	5q31
AURKB	aurora kinase B	17	17p13.1
NCAPG	non-SMC condensin I complex, subunit G	4	4p15.33
PKMYT1	protein kinase, membrane associated tyrosine/threonine 1	16	16p13.3
CDC45	cell division cycle 45	22	22q11.21
TPX2	TPX2, microtubule-associated	20	20q11.2
BIRC5	baculoviral IAP repeat containing 5	17	17q25
CCNB2	cyclin B2	15	15q22.2
FANCA	Fanconi anemia, complementation group A	16	16q24.3
ORC6	origin recognition complex, subunit 6	16	16q12
MYBL2	v-myb avian myeloblastosis viral oncogene homolog-like 2	20	20q13.1
TOP2A	topoisomerase (DNA) II alpha 170kDa	17	17q21-q22
POLQ	polymerase (DNA directed), theta	3	3q13.33
BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	15	15q15
NCAPH	non-SMC condensin I complex, subunit H	2	2q11.2
MELK	maternal embryonic leucine zipper kinase	9	9p13.2
KIF4A	kinesin family member 4A	X	Xq13.1
MKI67	marker of proliferation Ki-67	10	10q26.2
DLGAP5	discs, large (Drosophila) homolog-associated protein 5	14	14q22.3
CENPA	centromere protein A	2	2p23.3
MTFR2	mitochondrial fission regulator 2	6	6q23.3
CEP55	centrosomal protein 55kDa	10	10q23.33
FOXM1	forkhead box M1	12	12p13
SPC25	SPC25, NDC80 kinetochore complex component	2	2q31.1
ASPM	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1	1q31
BUB1	BUB1 mitotic checkpoint serine/threonine kinase	2	2q14
MCM10	minichromosome maintenance complex component 10	10	10p13
CENPF	centromere protein F, 350/400kDa	1	1q41
FAM64A	family with sequence similarity 64, member A	17	17p13.2
KIF14	kinesin family member 14	1	1q32.1
EZH2	enhancer of zeste 2 polycomb repressive complex 2 subunit	7	7q35-q36
ERCC6L	excision repair cross-complementation group 6-like	X	Xq13.1
FAM111B	family with sequence similarity 111, member B	11	11q12.1
E2F1	E2F transcription factor 1	20	20q11.2
MND1	meiotic nuclear divisions 1 homolog (S. cerevisiae)	4	4q31.3
CLSPN	claspin	1	1p34.2
GPC2	glypican 2	7	7q22.1
MMP9	matrix metallopeptidase 9	20	20q13.12
C16orf59	chromosome 16 open reading frame 59	16	16p13.3
CDCA8	cell division cycle associated 8	1	1p34.3
KIF2C	kinesin family member 2C	1	1p34.1
CDC20	cell division cycle 20	1	1p34.1
EME1	essential meiotic structure-specific endonuclease 1	17	17q21.33
CDCA3	cell division cycle associated 3	12	12p13
NUF2	NUF2, NDC80 kinetochore complex component	1	1q23.3
SKA1	spindle and kinetochore associated complex subunit 1	18	18q21.1
KIAA0101	KIAA0101	15	15q22.31
AURKA	aurora kinase A	20	20q13
CDC6	cell division cycle 6	17	17q21.3
NUSAP1	nucleolar and spindle associated protein 1	15	15q15.1
FANCI	Fanconi anemia, complementation group I	15	15q26.1
SGOL1	shugoshin-like 1 (S. pombe)	3	3p24.3
HMMR	hyaluronan-mediated motility receptor (RHAMM)	5	5q34
PLK1	polo-like kinase 1	16	16p12.2
UBE2T	ubiquitin-conjugating enzyme E2T	1	1q32.1
CCNA2	cyclin A2	4	4q27
DTL	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	1	1q32
KIFC1	kinesin family member C1	6	6p21.3
CDCA5	cell division cycle associated 5	11	11q12.1
CDCA2	cell division cycle associated 2	8	8p21.2
CKAP2L	cytoskeleton associated protein 2-like	2	2q13
RRM2	ribonucleotide reductase M2	2	2p25-p24
PBK	PDZ binding kinase	8	8p21.2
GINS2	GINS complex subunit 2 (Psf2 homolog)	16	16q24.1
KIF15	kinesin family member 15	3	3p21.31
NDC80	NDC80 kinetochore complex component	18	18p11.32
PAQR4	progestin and adipoQ receptor family member IV	16	16p13.3
TACC3	transforming, acidic coiled-coil containing protein 3	4	4p16.3
CENPU	centromere protein U	4	4q35.1
PTTG1	pituitary tumor-transforming 1	5	5q35.1
PRC1	protein regulator of cytokinesis 1	15	15q26.1
CKS2	CDC28 protein kinase regulatory subunit 2	9	9q22
KNTC1	kinetochore associated 1	12	12q24.31
CENPE	centromere protein E, 312kDa	4	4q24-q25
C19orf48	chromosome 19 open reading frame 48	19	19q13.33
ARHGAP11A	Rho GTPase activating protein 11A	15	15q13.2
PPP1R14B	protein phosphatase 1, regulatory (inhibitor) subunit 14B	11	11q13
EPR1	effector cell peptidase receptor 1 (non-protein coding)	17	17q25
NEIL3	nei endonuclease VIII-like 3 (E. coli)	4	4q34.3
GSG2	germ cell associated 2 (haspin)	17	17p13
DBF4	DBF4 zinc finger	7	7q21.3
CDKN3	cyclin-dependent kinase inhibitor 3	14	14q22
RDM1	RAD52 motif containing 1	17	17q11.2
SPC24	SPC24, NDC80 kinetochore complex component	19	19p13.2
E2F7	E2F transcription factor 7	12	12q21.2
ANLN	anillin, actin binding protein	7	7p15-p14
CCNE2	cyclin E2	8	8q22.1
MMP11	matrix metallopeptidase 11	22	22q11.23
NFE2L3	nuclear factor, erythroid 2-like 3	7	7p15.2
TUBB3	tubulin, beta 3 class III	16	16q24.3
PLP1	proteolipid protein 1	X	Xq22
SCARA5	scavenger receptor class A, member 5	8	8p21.1
MYOM1	myomesin 1	18	18p11.31
HMGCLL1	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	6	6p12.1
ADH1B	alcohol dehydrogenase 1B (class I), beta polypeptide	4	4q23
NKAPL	NFKB activating protein-like	6	6p22.1
SYNE1	spectrin repeat containing, nuclear envelope 1	6	6q25
PEG3	paternally expressed 3	19	19q13.4
USP2	ubiquitin specific peptidase 2	11	11q23.3
PCDH9	protocadherin 9	13	13q21.32
SLC5A7	solute carrier family 5 (sodium/choline cotransporter), member 7	2	2q12
SORCS1	sortilin-related VPS10 domain containing receptor 1	10	10q23-q25
NRXN1	neurexin 1	2	2p16.3
HLF	hepatic leukemia factor	17	17q22
SCN7A	sodium channel, voltage gated, type VII alpha subunit	2	2q21-q23
TMEM132C	transmembrane protein 132C	12	12q24.32
CD300LG	CD300 molecule-like family member g	17	17q21.31
FXYD1	FXYD domain containing ion transport regulator 1	19	19q13.1
SYNPO2	synaptopodin 2	4	4q26
ADAMTSL3	ADAMTS-like 3	15	15q25.2
ADGRB3	adhesion G protein-coupled receptor B3	6	6q12
EPM2A	epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)	6	6q24
ASPA	aspartoacylase	17	17p13.3
GPRASP1	G protein-coupled receptor associated sorting protein 1	X	Xq22.1
PID1	phosphotyrosine interaction domain containing 1	2	2q36.3
PGM5	phosphoglucomutase 5	9	9q13
NEGR1	neuronal growth regulator 1	1	1p31.1
ADGRD1	adhesion G protein-coupled receptor D1	12	12q24.33
TCEAL2	transcription elongation factor A (SII)-like 2	X	Xq22.1-q22.3
ACACB	acetyl-CoA carboxylase beta	12	12q24.11
FAXDC2	fatty acid hydroxylase domain containing 2	5	5q31-q32
AOX1	aldehyde oxidase 1	2	2q33
TCEAL7	transcription elongation factor A (SII)-like 7	X	Xq22.1
IGSF10	immunoglobulin superfamily, member 10	3	3q25.1
GPM6A	glycoprotein M6A	4	4q34
RANBP3L	RAN binding protein 3-like	5	5p13.2
FOSB	FBJ murine osteosarcoma viral oncogene homolog B	19	19q13.32
CRHBP	corticotropin releasing hormone binding protein	5	5q13.3
PTH1R	parathyroid hormone 1 receptor	3	3p22-p21.1
ARHGAP20	Rho GTPase activating protein 20	11	11q23.1
FGL2	fibrinogen-like 2	7	7q11.23
C7	complement component 7	5	5p13
GFRA2	GDNF family receptor alpha 2	8	8p21.3
NR3C2	nuclear receptor subfamily 3, group C, member 2	4	4q31.1
KCND3	potassium channel, voltage gated Shal related subfamily D, member 3	1	1p13.3
ANK2	ankyrin 2, neuronal	4	4q25-q27
LEPR	leptin receptor	1	1p31
DPT	dermatopontin	1	1q12-q23
CADM2	cell adhesion molecule 2	3	3p12.1
ASXL3	additional sex combs like transcriptional regulator 3	18	18q11
SCUBE1	signal peptide, CUB domain, EGF-like 1	22	22q13
SCN11A	sodium channel, voltage gated, type XI alpha subunit	3	3p22.2
CXCL12	chemokine (C-X-C motif) ligand 12	10	10q11.1
TGFBR3	transforming growth factor, beta receptor III	1	1p33-p32
SYT15	synaptotagmin XV	10	10q11.1
ANO5	anoctamin 5	11	11p14.3
PTGDS	prostaglandin D2 synthase 21kDa (brain)	9	9q34.2-q34.3
ABCA9	ATP-binding cassette, sub-family A (ABC1), member 9	17	17q24.2
SLITRK3	SLIT and NTRK-like family, member 3	3	3q26.1
CNTFR	ciliary neurotrophic factor receptor	9	9p13
DLGAP2	discs, large (Drosophila) homolog-associated protein 2	8	8p23
ABCA6	ATP-binding cassette, sub-family A (ABC1), member 6	17	17q24.3
NPY5R	neuropeptide Y receptor Y5	4	4q31-q32
PDE8B	phosphodiesterase 8B	5	5q13.3

Genes whose expression is significantly higher or lower in high-grade cancers than in low-grade cancers

The genes with higher expression levels in high-grade cancers than in low-grade cancers are highlighted in azure, while the genes with lower expression levels in high-grade cancers are highlighted in bisque (fold change > 1.5, FDR < 0.05).

Symbol	Name	Chromosome	Cytoband
FLNC	filamin C, gamma	7	7q32-q35
MYBL2	v-myb avian myeloblastosis viral oncogene homolog-like 2	20	20q13.1
CENPA	centromere protein A	2	2p23.3
TPX2	TPX2, microtubule-associated	20	20q11.2
FOXM1	forkhead box M1	12	12p13
RAB42	RAB42, member RAS oncogene family	1	1p35.3
CEP55	centrosomal protein 55kDa	10	10q23.33
KIF15	kinesin family member 15	3	3p21.31
BUB1	BUB1 mitotic checkpoint serine/threonine kinase	2	2q14
BIRC5	baculoviral IAP repeat containing 5	17	17q25
PLK1	polo-like kinase 1	16	16p12.2
ASPM	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1	1q31
RRM2	ribonucleotide reductase M2	2	2p25-p24
CDC20	cell division cycle 20	1	1p34.1
NEIL3	nei endonuclease VIII-like 3 (E. coli)	4	4q34.3
NUF2	NUF2, NDC80 kinetochore complex component	1	1q23.3
KIF18B	kinesin family member 18B	17	17q21.31
KIF14	kinesin family member 14	1	1q32.1
TROAP	trophinin associated protein	12	12q13.12
CDCA3	In multiple Geneids
UBE2C	ubiquitin-conjugating enzyme E2C	20	20q13.12
IGF2BP3	insulin-like growth factor 2 mRNA binding protein 3	7	7p11
MFI2	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	3	3q28-q29
REEP2	receptor accessory protein 2	5	5q31
GTSE1	G-2 and S-phase expressed 1	22	22q13.2-q13.3
LAG3	lymphocyte-activation gene 3	12	12p13.32
IGF2BP2	insulin-like growth factor 2 mRNA binding protein 2	3	3q27.2
HMMR	hyaluronan-mediated motility receptor (RHAMM)	5	5q34
CDC25C	cell division cycle 25C	5	5q31
KIF20A	kinesin family member 20A	5	5q31
FAM64A	family with sequence similarity 64, member A	17	17p13.2
AURKB	aurora kinase B	17	17p13.1
PDCD1	programmed cell death 1	2	2q37.3
IQGAP3	IQ motif containing GTPase activating protein 3	1	1q21.3
ZIC2	Zic family member 2	13	13q32
PTPN7	protein tyrosine phosphatase, non-receptor type 7	1	1q32.1
MIR155HG	MIR155 host gene	21
HJURP	Holliday junction recognition protein	2	2q37.1
RDM1	RAD52 motif containing 1	17	17q11.2
MAP4K1	mitogen-activated protein kinase kinase kinase kinase 1	19	19q13.1-q13.4
C5orf34	chromosome 5 open reading frame 34	5	5p12
SIT1	signaling threshold regulating transmembrane adaptor 1	9	9p13-p12
EPHA6	In multiple Geneids
PTTG1	pituitary tumor-transforming 1	5	5q35.1
CXCR3	In multiple Geneids
GZMK	granzyme K (granzyme 3; tryptase II)	5	5q11.2
FAM26F	family with sequence similarity 26, member F	6	6q22.1
CCDC8	coiled-coil domain containing 8	19	19q13.32
SIX2	SIX homeobox 2	2	2p21
CDCA5	In multiple Geneids
MCM10	minichromosome maintenance complex component 10	10	10p13
KIF4A	kinesin family member 4A	X	Xq13.1
SHOX2	short stature homeobox 2	3	3q25.32
MELK	maternal embryonic leucine zipper kinase	9	9p13.2
MCM2	minichromosome maintenance complex component 2	3	3q21
ECT2	epithelial cell transforming 2	3	3q26.1-q26.2
CHEK1	checkpoint kinase 1	11	11q24.2
APOE	apolipoprotein E	19	19q13.2
ORC1	origin recognition complex, subunit 1	1	1p32
BEND6	BEN domain containing 6	6	6p12.1
GFPT2	glutamine-fructose-6-phosphate transaminase 2	5	5q34-q35
NCAPH	non-SMC condensin I complex, subunit H	2	2q11.2
CENPI	centromere protein I	X	Xq22.1
DEPDC1	DEP domain containing 1	1	1p31.2
KIF2C	kinesin family member 2C	1	1p34.1
CDKN3	cyclin-dependent kinase inhibitor 3	14	14q22
FAM72B	In multiple Geneids
GINS1	GINS complex subunit 1 (Psf1 homolog)	20	20p11.21
RAD51AP1	RAD51 associated protein 1	12	12p13.2-p13.1
CKAP2L	cytoskeleton associated protein 2-like	2	2q13
FAM72D	family with sequence similarity 72, member D	1	1q21.1
CDCA8	In multiple Geneids
SPHK1	sphingosine kinase 1	17	17q25.2
EXO1	exonuclease 1	1	1q43
DLGAP5	discs, large (Drosophila) homolog-associated protein 5	14	14q22.3
KIF23	kinesin family member 23	15	15q23
DEPDC1B	DEP domain containing 1B	5	5q12.1
SUSD3	sushi domain containing 3	9	9q22.31
NEK2	NIMA-related kinase 2	1	1q32.3
DTL	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	1	1q32
FANCB	Fanconi anemia, complementation group B	X	Xp22.2
NDC80	NDC80 kinetochore complex component	18	18p11.32
CCNA2	cyclin A2	4	4q27
PRC1	protein regulator of cytokinesis 1	15	15q26.1
KIF11	kinesin family member 11	10	10q24.1
CENPF	centromere protein F, 350/400kDa	1	1q41
CCNB2	cyclin B2	15	15q22.2
PRR11	proline rich 11	17	17q22
ALPK2	alpha-kinase 2	18	18q21.31
CLSPN	claspin	1	1p34.2
GAS1	growth arrest-specific 1	9	9q21.3-q22
KIF18A	kinesin family member 18A	11	11p14.1
GSG2	germ cell associated 2 (haspin)	17	17p13
TCF19	transcription factor 19	6	6p21.3
OIP5	Opa interacting protein 5	15	15q15.1
SPC25	SPC25, NDC80 kinetochore complex component	2	2q31.1
FAM20A	family with sequence similarity 20, member A	17	17q24.2
MKI67	marker of proliferation Ki-67	10	10q26.2
SGOL2	shugoshin-like 2 (S. pombe)	2	2q33.1
NCAPG	non-SMC condensin I complex, subunit G	4	4p15.33
SGOL1	shugoshin-like 1 (S. pombe)	3	3p24.3
RAD54L	RAD54-like (S. cerevisiae)	1	1p32
WDR62	WD repeat domain 62	19	19q13.12
RAD51	RAD51 recombinase	15	15q15.1
E2F1	E2F transcription factor 1	20	20q11.2
TENM3	teneurin transmembrane protein 3	4	4q35.1
C1R	complement component 1, r subcomponent	12	12p13
SLAMF8	SLAM family member 8	1	1q23.2
EPR1	effector cell peptidase receptor 1 (non-protein coding)	17	17q25
FAM72A	In multiple Geneids
NUSAP1	nucleolar and spindle associated protein 1	15	15q15.1
SKA3	spindle and kinetochore associated complex subunit 3	13	13q12.11
ESCO2	establishment of sister chromatid cohesion N-acetyltransferase 2	8	8p21.1
TRIP13	thyroid hormone receptor interactor 13	5	5p15.33
XRCC2	X-ray repair complementing defective repair in Chinese hamster cells 2	7	7q36.1
KIFC1	kinesin family member C1	6	6p21.3
UCHL1	ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)	4	4p14
CDC45	cell division cycle 45	22	22q11.21
PKMYT1	protein kinase, membrane associated tyrosine/threonine 1	16	16p13.3
SIGLEC1	sialic acid binding Ig-like lectin 1, sialoadhesin	20	20p13
POLQ	polymerase (DNA directed), theta	3	3q13.33
TYMS	thymidylate synthetase	18	18p11.32
BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	15	15q15
TOP2A	topoisomerase (DNA) II alpha 170kDa	17	17q21-q22
SKA1	spindle and kinetochore associated complex subunit 1	18	18q21.1
CENPE	centromere protein E, 312kDa	4	4q24-q25
ARHGAP11A	Rho GTPase activating protein 11A	15	15q13.2
ERCC6L	excision repair cross-complementation group 6-like	X	Xq13.1
PDGFRL	platelet-derived growth factor receptor-like	8	8p22-p21.3
CCNB1	cyclin B1	5	5q12
ARHGAP29	Rho GTPase activating protein 29	1	1p22.1
PIF1	In multiple Geneids
CDCA2	In multiple Geneids
3-Sep	Data not found
ESPL1	extra spindle pole bodies homolog 1 (S. cerevisiae)	12	12q
CHRDL2	chordin-like 2	11	11q14
SALL4	spalt-like transcription factor 4	20	20q13.2
GINS4	GINS complex subunit 4 (Sld5 homolog)	8	8p11.21
CXCL13	chemokine (C-X-C motif) ligand 13	4	4q21
STAC	SH3 and cysteine rich domain	3	3p22.3
CDCA7	cell division cycle associated 7	2	2q31
GBP5	guanylate binding protein 5	1	1p22.2
C17orf53	chromosome 17 open reading frame 53	17	17q21.31
TTK	TTK protein kinase	6	6q14.1
ADAMDEC1	ADAM-like, decysin 1	8	8p21.2
ASF1B	anti-silencing function 1B histone chaperone	19	19p13.12
C2orf48	chromosome 2 open reading frame 48	2	2p25.1
FXYD6	FXYD domain containing ion transport regulator 6	11	11q23.3
E2F2	E2F transcription factor 2	1	1p36
NECAB1	N-terminal EF-hand calcium binding protein 1	8	8q21.3
HLA-DQA1	major histocompatibility complex, class II, DQ alpha 1	6	6p21.3
RAB39B	RAB39B, member RAS oncogene family	X	Xq28
COL8A1	collagen, type VIII, alpha 1	3	3q12.3
ARHGAP11B	In multiple Geneids
PBK	PDZ binding kinase	8	8p21.2
CDC25A	cell division cycle 25A	3	3p21
CPVL	carboxypeptidase, vitellogenic-like	7	7p15.1
CLGN	calmegin	4	4q28.3-q31.1
IGF2BP1	insulin-like growth factor 2 mRNA binding protein 1	17	17q21.32
HLA-DQA2	major histocompatibility complex, class II, DQ alpha 2	6	6p21.3
KREMEN2	kringle containing transmembrane protein 2	16	16p13.3
CD19	CD19 molecule	16	16p11.2
CXCR6	chemokine (C-X-C motif) receptor 6	3	3p21
CXCL9	chemokine (C-X-C motif) ligand 9	4	4q21
LTA	lymphotoxin alpha	6	6p21.3
CD72	CD72 molecule	9	9p13.3
CDKN2C	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	1	1p32
CXCL10	chemokine (C-X-C motif) ligand 10	4	4q21
FNDC5	fibronectin type III domain containing 5	1	1p35.1
MEI1	meiosis inhibitor 1	22	22q13.2
LOC90768	uncharacterized LOC90768	4	4q34.3
MTFR2	mitochondrial fission regulator 2	6	6q23.3
GBP1	guanylate binding protein 1, interferon-inducible	1	1p22.2
CR2	complement component (3d/Epstein Barr virus) receptor 2	1	1q32
ELOVL2	ELOVL fatty acid elongase 2	6	6p24.2
CD2	CD2 molecule	1	1p13.1
HMGA2	high mobility group AT-hook 2	12	12q15
CHRDL1	chordin-like 1	X	Xq23
CCL5	chemokine (C-C motif) ligand 5	17	17q12
RMI2	RecQ mediated genome instability 2	16	16p13.13
DES	desmin	2	2q35
FDCSP	follicular dendritic cell secreted protein	4	4q13
HOXB13	homeobox B13	17	17q21.2
HAMP	hepcidin antimicrobial peptide	19	19q13.1
CCL19	chemokine (C-C motif) ligand 19	9	9p13
SPIB	Spi-B transcription factor (Spi-1/PU.1 related)	19	19q13.3-q13.4
CD3E	CD3e molecule, epsilon (CD3-TCR complex)	11	11q23
FOXD3	forkhead box D3	1	1p31.3
C3	complement component 3	19	19p13.3-p13.2
LRP8	In multiple Geneids
SMC1B	structural maintenance of chromosomes 1B	22	22q13.31
CXCR2P1	chemokine (C-X-C motif) receptor 2 pseudogene 1	2	2q35
PLA2G2D	phospholipase A2, group IID	1	1p36.12
UBASH3A	ubiquitin associated and SH3 domain containing A	21	21q22.3
MAP1LC3C	microtubule-associated protein 1 light chain 3 gamma	1	1q43
ADAM6	ADAM metallopeptidase domain 6 (pseudogene)	14	14q32.33
SLC2A4	solute carrier family 2 (facilitated glucose transporter), member 4	17	17p13
CHI3L2	chitinase 3-like 2	1	1p13.3
GBP1P1	guanylate binding protein 1, interferon-inducible pseudogene 1	1	1p22.2
IL2RG	interleukin 2 receptor, gamma	X	Xq13.1
LTB	lymphotoxin beta (TNF superfamily, member 3)	6	6p21.3
GDF1	growth differentiation factor 1	19	19p12
LOC399815	chromosome 10 open reading frame 88 pseudogene	10	10q26.13
HLA-DOA	major histocompatibility complex, class II, DO alpha	6	6p21.3
JAK3	Janus kinase 3	19	19p13.1
ZAP70	zeta-chain (TCR) associated protein kinase 70kDa	2	2q12
CD8B	CD8b molecule	2	2p12
ZNF683	zinc finger protein 683	1	1p36.11
NTNG1	In multiple Geneids
IDO1	indoleamine 2,3-dioxygenase 1	8	8p12-p11
TNNT1	troponin T type 1 (skeletal, slow)	19	19q13.4
LGALS17A	Charcot-Leyden crystal protein pseudogene	19	19q13.2
FABP4	fatty acid binding protein 4, adipocyte	8	8q21
VIPR1	vasoactive intestinal peptide receptor 1	3	3p22
GPX2	glutathione peroxidase 2	14	14q24.1
DUOX1	dual oxidase 1	15	15q15.3
LAD1	ladinin 1	1	1q25.1-q32.3
TMEM184A	transmembrane protein 184A	7	7p22.3
OVOL1	ovo-like zinc finger 1	11	11q13
FUT3	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	19	19p13.3
FAM3D	family with sequence similarity 3, member D	3	3p14.2
RAPGEFL1	Rap guanine nucleotide exchange factor (GEF)-like 1	17	17q21.1
AZGP1	alpha-2-glycoprotein 1, zinc-binding	7	7q22.1
DEGS2	delta(4)-desaturase, sphingolipid 2	14	14q32.2
ALDH1L1	aldehyde dehydrogenase 1 family, member L1	3	3q21.3
C10orf99	chromosome 10 open reading frame 99	10	10q23.1
TCN1	transcobalamin I (vitamin B12 binding protein, R binder family)	11	11q11-q12
TMPRSS4	transmembrane protease, serine 4	11	11q23.3
ZBTB7C	In multiple Geneids
SLC44A4	solute carrier family 44, member 4	6	6p21.3
BCAS1	breast carcinoma amplified sequence 1	20	20q13.2
FSTL4	follistatin-like 4	5	5q31.1
ATP2C2	ATPase, Ca++ transporting, type 2C, member 2	16	16q24.1
CA12	carbonic anhydrase XII	15	15q22
TMEM154	transmembrane protein 154	4	4q31.3
CYP2J2	cytochrome P450, family 2, subfamily J, polypeptide 2	1	1p31.3-p31.2
CNGA1	cyclic nucleotide gated channel alpha 1	4	4p12
DUOXA1	dual oxidase maturation factor 1	15	15q21.1
CCDC64B	coiled-coil domain containing 64B	16	16p13.3
IYD	iodotyrosine deiodinase	6	6q25.1
CNTN3	contactin 3 (plasmacytoma associated)	3	3p12.3
GOLGA7B	golgin A7 family, member B	10	10q24.2
PTPRR	protein tyrosine phosphatase, receptor type, R	12	12q15
MSX2	msh homeobox 2	5	5q35.2
REEP6	receptor accessory protein 6	19	19p13.3
SMIM5	small integral membrane protein 5	17	17q25.1
EVPL	envoplakin	17	17q25
WIF1	WNT inhibitory factor 1	12	12q14.3
GJB5	gap junction protein, beta 5, 31.1kDa	1	1p35.1
SULT2B1	sulfotransferase family, cytosolic, 2B, member 1	19	19q13.3
CEACAM5	carcinoembryonic antigen-related cell adhesion molecule 5	19	19q13.1-q13.2
TGM3	transglutaminase 3	20	20q11.2
TMPRSS2	transmembrane protease, serine 2	21	21q22.3
DSC2	desmocollin 2	18	18q12.1
CYP4F3	cytochrome P450, family 4, subfamily F, polypeptide 3	19	19p13.2
SPINK5	serine peptidase inhibitor, Kazal type 5	5	5q32
PVRL4	poliovirus receptor-related 4	1	1q23.3
CEACAM6	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	19	19q13.2
UNC93A	unc-93 homolog A (C. elegans)	6	6q27
CALML3	calmodulin-like 3	10	10p15.1
FGFBP1	fibroblast growth factor binding protein 1	4	4p15.32
KRT31	keratin 31, type I	17	17q21.2
SLC5A1	solute carrier family 5 (sodium/glucose cotransporter), member 1	22	22q12.3
HOMER2	homer scaffolding protein 2	15	15q24.3
CYP39A1	cytochrome P450, family 39, subfamily A, polypeptide 1	6	6p12.3
TMEM125	transmembrane protein 125	1	1p34.2
HKDC1	In multiple Geneids
SOWAHB	sosondowah ankyrin repeat domain family member B	4	4q21.1
FMO2	flavin containing monooxygenase 2 (non-functional)	1	1q24.3
CRYM	crystallin, mu	16	16p12.2

Genes whose expression is significantly higher or lower in late-stage cancers than in early-stage cancers

The genes with higher expression levels in late-stage cancers than in early-stage cancers are highlighted in azure, while the genes with lower expression levels in late-stage cancers are highlighted in bisque (fold change > 1.5, FDR < 0.05)

Symbol	Name	Chromosome	Cytoband
SOX11	SRY (sex determining region Y)-box 11	2	2p25
PODNL1	podocan-like 1	19	19p13.12
COMP	cartilage oligomeric matrix protein	19	19p13.1
PTPRN	protein tyrosine phosphatase, receptor type, N	2	2q35-q36.1
PYCR1	pyrroline-5-carboxylate reductase 1	17	17q25.3
COL5A1	collagen, type V, alpha 1	9	9q34.2-q34.3
CTHRC1	collagen triple helix repeat containing 1	8	8q22.3
FAP	fibroblast activation protein, alpha	2	2q23
APCDD1L	adenomatosis polyposis coli down-regulated 1-like	20	20q13.32
THBS2	thrombospondin 2	6	6q27
LAMP5	lysosomal-associated membrane protein family, member 5	20	20p12
SHOX2	short stature homeobox 2	3	3q25.32
TICRR	TOPBP1-interacting checkpoint and replication regulator	15	15q26.1
CEP55	centrosomal protein 55kDa	10	10q23.33
NXPH4	neurexophilin 4	12	12q13.3
RAD54L	RAD54-like (S. cerevisiae)	1	1p32
DUSP5P1	dual specificity phosphatase 5 pseudogene 1	1	1q42.13
TMEM59L	transmembrane protein 59-like	19	19p12
FOXD1	forkhead box D1	5	5q13.2
CDH11	cadherin 11, type 2, OB-cadherin (osteoblast)	16	16q21
SFRP2	secreted frizzled-related protein 2	4	4q31.3
SFRP4	secreted frizzled-related protein 4	7	7p14.1
COL10A1	collagen, type X, alpha 1	6	6q21-q22
COL1A1	collagen, type I, alpha 1	17	17q21.33
GREM1	gremlin 1, DAN family BMP antagonist	15	15q13.3
FN1	fibronectin 1	2	2q34
POSTN	periostin, osteoblast specific factor	13	13q13.3
LRRC15	leucine rich repeat containing 15	3	3q29
OMD	osteomodulin	9	9q22.31
ITGA11	integrin, alpha 11	15	15q23
MFAP5	microfibrillar associated protein 5	12	12p13.1-p12.3
PPAPDC1A	phosphatidic acid phosphatase type 2 domain containing 1A	10	10q26.12
COL11A1	collagen, type XI, alpha 1	1	1p21
ASPN	asporin	9	9q22
ADAM12	ADAM metallopeptidase domain 12	10	10q26
COL8A2	collagen, type VIII, alpha 2	1	1p34.2
ARSI	arylsulfatase family, member I	5	5q32
CERCAM	cerebral endothelial cell adhesion molecule	9	9q34.11
COL16A1	collagen, type XVI, alpha 1	1	1p35-p34
COL8A1	collagen, type VIII, alpha 1	3	3q12.3
PRRX2	paired related homeobox 2	9	9q34.1
C5orf46	chromosome 5 open reading frame 46	5	5q32
BEND6	BEN domain containing 6	6	6p12.1
RPLP0P2	ribosomal protein, large, P0 pseudogene 2	11	11cen-q12
C1S	complement component 1, s subcomponent	12	12p13
ZFHX4	zinc finger homeobox 4	8	8q21.11
DCHS2	dachsous cadherin-related 2	4	4q31.3
AHNAK2	AHNAK nucleoprotein 2	14	14q32.33
WT1	Wilms tumor 1	11	11p13
CST2	cystatin SA	20	20p11.21
SLC6A17	solute carrier family 6 (neutral amino acid transporter), member 17	1	1p13.3
WISP2	WNT1 inducible signaling pathway protein 2	20	20q13.12
SLITRK2	SLIT and NTRK-like family, member 2	X	Xq27.3
GAP43	growth associated protein 43	3	3q13.31
NPTX1	neuronal pentraxin I	17	17q25.3
PCBP3	poly(rC) binding protein 3	21	21q22.3
L1CAM	L1 cell adhesion molecule	X	Xq28
FXYD1	FXYD domain containing ion transport regulator 1	19	19q13.1
IGLON5	IgLON family member 5	19	19q13.41
CILP2	cartilage intermediate layer protein 2	19	19p13.11
STRA6	stimulated by retinoic acid 6	15	15q24.1
POPDC3	popeye domain containing 3	6	6q21
H19	In multiple Geneids
PNCK	pregnancy up-regulated nonubiquitous CaM kinase	X	Xq28
TINCR	tissue differentiation-inducing non-protein coding RNA	19	19p13.3
CRABP2	cellular retinoic acid binding protein 2	1	1q21.3
COL22A1	collagen, type XXII, alpha 1	8	8q24.3
NKAIN1	Na+/K+ transporting ATPase interacting 1	1	1p35.2
HMGA2	high mobility group AT-hook 2	12	12q15
TEX15	testis expressed 15	8	8p12
MMP1	matrix metallopeptidase 1	11	11q22.3
DNASE1L3	deoxyribonuclease I-like 3	3	3p14.3
CD1E	CD1e molecule	1	1q23.1
SLC44A4	solute carrier family 44, member 4	6	6p21.3
PLIN5	perilipin 5	19	19p13.3
IYD	iodotyrosine deiodinase	6	6q25.1
RORC	RAR-related orphan receptor C	1	1q21
GGT6	gamma-glutamyltransferase 6	17	17p13.2
FBP1	fructose-1,6-bisphosphatase 1	9	9q22.3
ALDH1L1	aldehyde dehydrogenase 1 family, member L1	3	3q21.3
PIGR	polymeric immunoglobulin receptor	1	1q31-q41
SPATA18	In multiple Geneids
ARPP21	cAMP-regulated phosphoprotein, 21kDa	3	3p22.3
CWH43	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	4	4p11

Median mutational burden (defined here as the total number of substitutions, regardless of type) for each cancer type