supplementary materials for...2 fig. s1 fig. s1. schematic drawing, indicating the anatomical...

science.sciencemag.org/content/367/6482/eaay5947/suppl/DC1

Supplementary Materials for

An atlas of the protein-coding genes in the human, pig, and mouse brain

Evelina Sjöstedt, Wen Zhong, Linn Fagerberg, Max Karlsson, Nicholas Mitsios,

Csaba Adori, Per Oksvold, Fredrik Edfors, Agnieszka Limiszewska, Feria Hikmet,

Jinrong Huang, Yutao Du, Lin Lin, Zhanying Dong, Ling Yang, Xin Liu, Hui Jiang,

Xun Xu, Jian Wang, Huanming Yang, Lars Bolund, Adil Mardinoglu, Cheng Zhang,

Kalle von Feilitzen, Cecilia Lindskog, Fredrik Pontén, Yonglun Luo, Tomas Hökfelt,

Mathias Uhlén*†, Jan Mulder*†

*These authors contributed equally to this work.

†Corresponding author. Email: [email protected] (M.U.); [email protected] (J.M.)

Published 6 March 2020, Science 367, eaay5947 (2020)

DOI: 10.1126/science.aay5947

This PDF file includes:

Materials and Methods

Figs. S1 to S35

Tables S4, S7, S8, S10, and S13

Captions for Tables S1 to S3, S5, S6, S9, S11, and S12

Caption for Movie S1

Other Supplementary Material for this manuscript includes the following:

(available at science.sciencemag.org/content/367/6482/eaay5947/suppl/DC1)

Tables S1 to S3, S5, S6, S9, S11, and S12 (as a single .xlsx file)

Movie S1 (.mp4)

2

Fig. S1

Fig. S1. Schematic drawing, indicating the anatomical regions of the human brain, with a focus on the regions included in this study. Midsagittal image is marked with approximate locations of the coronal drawings of the half hemispheres (1-3).

3

Fig. S2

Fig. S2. Schematic drawing, indicating the anatomical regions of the pig brain, with a focus on the regions included in this study. Sagittal image is marked with approximate locations of the coronal drawings of the half hemispheres (1-5).

4

Fig. S3

Fig. S3. Schematic drawing, indicating the anatomical regions of the mouse brain, with a focus on the regions included in this study. Sagittal image is marked with approximate locations of the coronal drawings of the half hemispheres (1-5).

5

Fig. S4

Fig S4. Schematic overview of the normalization strategy. Flowchart demonstrating the pipeline used for normalizing the transcriptomics data in the Human Protein Atlas.

6

Fig. S5

Fig. S5. Gene overview for the normalization strategy and orthologue translation. Gray circles indicate genes represented by one, two, or three different datasets. Only 309 genes are missing mapped expression data in the brain based on GTEx, FANTOM5, pig, or mouse datasets. The HPA-human, FANTOM5 and GTEx data are normalized and combined to generate the tissue-based classification, while only GTEx and FANTOM5 data is used for regional classification of the human brain expression. The human regional expression data together with pig and mouse expression data cover 12,999 genes with one-to-one orthologues in both mouse and pig, which are the genes included in the normalization 2.

7

Fig.S6

Fig. S6. Normalized expression values of the 12,999 genes with one-to-one orthologues in all three species. Violin plot showing the distribution of pTPM (a), NX 1 (b) and NX 2 (c) in the 10 brain regions.

8

Fig. S7

Fig. S7. Regional relationship based on global transcript expression in human brain. Uniform Manifold Approximation and Projection (UMAP) plot showing the global expression patterns of all samples (1710) from HPA, GTEx and FANTOM, respectively.

9

Fig. S8

Fig. S8. Detected genes in human brain regions. The bars show the number of detected genes, above cut off (NX=1), in the 10 different regions of the human brain.

10

Fig. S9

Fig. S9. Regional relationship based on global transcript expression in pig brain. Uniform Manifold Approximation and Projection (UMAP) plot of all pig brain samples (119) used for mapping regional transcript expression in the pig brain.

11

Fig. S10

Fig. S10. Detected genes in pig brain regions. The bars show the number of detected genes, above cut off (NX=1), in the 10 different regions of the pig brain. Detected pig genes missing a one-to-one human orthologue are also shown in the upper part of each bar.

12

Fig. S11

Fig. S11. Regional relationship based on global transcript expression in mouse brain. Uniform Manifold Approximation and Projection (UMAP) plot of all mouse brain samples (67) used for mapping regional transcript expression in the mouse brain.

13

Fig. S12

Fig. S12. Detected genes in mouse brain regions. The bars show the number of detected genes, above cut off (NX=1), in the 10 different regions of the mouse brain. Detected mouse genes missing a one to one human orthologue are also shown in the upper part of each bar.

14

Fig. S13

Fig. S13. Correlation between the 10 regions. Heatmaps showing pairwise Spearman correlation between the global expression profile of the 10 regions. (a) Human, (b) pig and (c) mouse.

15

Fig. S14

Fig. S14. Regional expression classification in three mammalian species. (a) The number of regionally elevated genes in the three species, respectively, stratified as enriched, group enriched and enhanced, for the 10 main regions analyzed. (b) The total number of genes classified according to regional specificity in the brain for the three different species.

16

Fig. S15 a, regionally enriched

b, group enriched

c, regionally enhanced

Fig. S15. Regionally elevated genes in human brain. Heatmap showing the expression of regionally enriched (a), group enriched (b) and regionally enhanced (c) genes in the 10 brain regions.

17

Fig. S16 a, regionally enriched

b, group enriched


Fig. S16. Regionally elevated genes in pig brain. Heatmap showing the expression of regionally enriched (a), group enriched (b) and regionally enhanced (c) genes in the 10 pig brain regions.

18

Fig. S17

a, regionally enriched

b, group enriched


Fig. S17. Regionally elevated genes in mouse brain. Heatmap showing the expression of enriched (a), group enriched (b) and regionally enhanced (c) genes in the 10 mouse brain regions.

19

Fig. S18

Fig. S18. Regionally group enriched genes. Chord diagrams showing the relationship of the group enriched genes where each link represents the number of genes that are group enriched in both of the connected regions in (a) human, (b) pig and (c) mouse.

20

Fig. S19

Fig. S19. Comparison of one-to-one orthologue expression in the mammalian brain. (a) Gene orthologue translation resulted in 12,999 human protein-coding genes with a one-to-one orthologue in both mouse and pig. Gene overlap shown in a Venn diagram. (b) Regionally enriched gene expression shared between all three species. The ten main regions are separated into four brain structures; cerebrum (olfactory bulb, cerebral cortex, hippocampus formation, amygdala and basal ganglia), hypothalamus, brainstem (thalamus, midbrain, pons and medulla oblongata) and cerebellum. Venn diagrams are shown for the genes with highest expression in the brain structure in all three species, with the number of genes indicated in parentheses and the number in the Venn diagram showing the number of genes classified as enriched (4-fold higher).

21

Fig. S20

Fig. S20. Regionally enriched genes in the mammalian brain. Heatmap showing the expression profiles of genes with highest expression in the same brain structure (cerebrum, hypothalamus, brainstem or cerebellum) in all three species and enriched expression (4-fold higher) in the same structure compared to the other three brain structures, in at least one of the species. The heatmap includes identical data as Fig 4b but with details about the 10 regions for respective species.

22

Fig. S21

Fig. S21. Differential expression, comparing human and pig brain. Volcano map of differentially expressed genes based on transcript expression data from all 10 regions for human and pig brain, respectively. The X-axis represents log2 fold change and the Y-axis represents log10 (adjusted p-values). Differentially Expressed Genes (DEGs) (Fold Change (FC)>2, adjusted P-value <0.001) are shown as red dots.

ACOT4 SLC44A4DIRC2

ASB5 NME3 XRCC5FUOMDZANK1 SLC16A4 PSMF1PODN CDPF1 FN3K XRCC6BCL2L2−PABPN1 TRPM6 MRPL9 CUTAPPP1CB MYBPHL AMZ2 RPS11TECRCYS1 SLC35B2TMEM106A FBXL5 RPL37ASRP14CLTAFGB FAM96BH2AFJ MIIP TCP1HSPBAP1 ELP5 HMGN3CA13 C5orf15UQCRC1 NENFHECTD3 LPIN1 KXD1NUCKS1 DYNLRB1MED28 HPS1 PSMB4NAA50 STX5SKP2 TBCADDX39B ZFAT ATICNOM1SCUBE3 GPX4SRIC1orf194 IKRASSF1LAT SNRPD2MKS1BIRC6CCDC107 PTH TSR2RPP30ABI3BP SRSF5PDILT PSAPNFYASPCS1RGN HSF5 TKT IP6K2 COX6A1KCTD2 ATRCCT5 VAMP7WAS CIRBPASH1L PIGX QDPRWBP2MMP15PLA2G6FADS2 RALGAPB ARGLU1P4HTMSLC16A2 FAM107ATHRA CST3ID1 CTC1FFAR2 CD74PXKSLC26A11 SNCGILKAPDNA2 SEPT8IKZF5 MTURNMAOAACTG1 TUBB4AEVLNAV2DDB1 CHI3L1ITGA2S100A1 TMEM176A

0

5

10

15

0 50 Log2 fold change

−Lo

g 10

adju

sted

P

DEGsNS

Human vs Pig: Empirical Bayes Statistics, up: 2692, down:2518cutoff: |log2FC|>1, adjP<0.01

23

Fig. S22

Fig. S22. Differential expression, comparing human and mouse. Volcano map of differentially expressed genes based on transcript expression data from all 10 regions for human and mouse brain, respectively. The X-axis represents log2FC and the Y-axis represents log10 (adjusted p-values). DEGs (FC>2, adjusted p-values <0.001) are shown as red dots. Fig. S23

CHMP7

AKR1A1 PTCD2ABCF1PSMD2

DNAJA3 PFN4 SRSF9PHF23 ACE2PFKM USF2CYB5A HPS1VPS35 GORASP2 XRCC5PCK2UBE2S TATDN1NSFL1CCTSB TBC1D17 NCLSLC25A4 UBE2D1 MZF1TSEN34SQSTM1 SF3B5DECR2OGDHNDFIP1 PSKH1 GNB1HSPA8 DALRD3 EXOSC6CHMP4B HNRNPUMOB2 SSFA2ZWINT TACO1PHYH NSRP1IGDCC4POMPDLD PRCPCLMPTIMM8BUBC PUM1IP6K1 TFR2 HMGN3TSPAN3 CLUIRF9CTSS GABARAPZNF865ACOT13COX6C SEC31AVPS53 PMP2UQCRC2 BOD1L1RAB21UQCC2 CD74PPIGTOM1TUBB4B CIRBPSUMF2UFD1 DOCK9DDX24 CNPSEMA6ACEPT1ATP6V0B NASPOTUB2 GFAPUQCR10 CRYABRHOAPEX14 PADI2EFHD1PCYT2MPC1 PON2NT5C QDPRMTUS1ACTG1

0

5

10

15

20

−100 −50 0 50 100 Log2 fold change

−Lo

g 10

adju

sted

P

DEGsNS

Human vs Mouse: Empirical Bayes Statistics, up: 2333, down:2252cutoff: |log2FC|>1, adjP<0.01

24

Fig. S23. Differential expression, comparing pig and mouse. Volcano map of differentially expressed genes based on transcript expression data from all 10 regions for mouse and pig brain, respectively. The X-axis represents log2FC and the Y-axis represents log10 (adjusted p-values). DEGs (FC>2, adjusted p-values <0.001) are shown as red dots.

PSMD7 FLAD1 BLOC1S6

PSMD2AKR1A1 CHMP7 ACOT4DMAP1 TBL1XR1TUFM RRP15AENDYNLRB1 BCL2L2−PABPN1BBS7LONP1MDH2 ABCF1 USF2GDI2 BRF1GID8 TATDN1MTMR3CSNK1A1 THADARNPEPGSTM3 HNRNPUPQBP1 CYP27B1BMT2 BAK1PEF1 H1FXPSMC1 CTSH SZT2 PUM1ATXN10 SMPD1HSPA8 LATEIF2B2PARK7HSP90AB1 TMA7MRPS24CAPN10 TAF7PSMB1TECR KIF1BP ERG C1orf194UBC COX6C CCNL2NUDCFTSJ3RPS21 RNF111MAN2B2ZWINT SQSTM1 CFLARUBE2J1 CPN2 SF1CAPRIN1 PIWIL4RPL19 DPYSL2SRP19MYL6 CSRNP2PRNP WBP2 OTOSRRS1UQCC2EIF1B C4orf48CD320NDUFS6 TESPA1FMO2GHITMACLYTHBD ATF6BSTMN3 RNASE1NMT2AKIP1DARSMIF GCM1 GPR75ADK CD109COX6A1 LHPPPSPC1PHB CLUQKICPE DIO1CTNNB1 NFIXNSUN5RND2LDHB GPSM3CA2 CD164L2 APOEGAP43 HHIPL1DNM1 SURF6SNAP25 GFAP

0

5

10

15

20

−100 −50 0 50 Log2 fold change

−Lo

g 10

adju

sted

P

DEGsNS

Pig vs Mouse: Empirical Bayes Statistics, up: 3015, down:2933cutoff: |log2FC|>1, adjP<0.01

25

Fig. S24

Fig. S24. Human brain enriched/depleted genes. Significantly differentially expressed genes (FDR < 0.01) of human brain compared to pig and mouse were selected. Log2FC values were determined using pairwise comparisons of average normalized expression (NX) of 10 brain regions in three species. The X-axis represents log2FC of human compared to pig and the Y-axis represents log2FC of human compared to mouse. Only genes both up-regulated or down-regulated in human were shown. The highest up-regulated or down-regulated genes were labeled.

XRCC5

DZANK1

PPP1CB

EDF1

RPL37ASRP14

HMGN3

UQCRC1

DNAJB2

GNB1

PPA1

HNRNPH3

SLC25A3

SLC25A4

VPS35

NCL

MLLT11

CIRBP

SDHA

QDPR

MDH2

CRYAB

EEF1A2

ARGLU1CD74

TSPOAP1

ATP5F1A

NDFIP1

−75

−50

−25

0

25

−20 0 20 40 60Log2FC (human/pig)

Log2

FC (h

uman

/mou

se)

26

Fig. S25

Fig. S25. Pig brain enriched/depleted genes. Significantly differentially expressed genes (FDR < 0.01) of pig brain compared to human and mouse were selected. Log2FC values were determined using pairwise comparisons of average normalized expression (NX) of 10 brain regions in three species. The X-axis represents log2FC of pig compared to human and the Y-axis represents Log2FC of pig compared to mouse. Only genes both up-regulated or down-regulated in pig were shown. The highest up-regulated or down-regulated genes were labeled.

COPS5

DZANK1

NSFL1C

BCL2L2−PABPN1

CUTANAP1L4

EDF1

RPS11TECR

TCF25

RPL37ASRP14

CLTA

PSMD7

CHMP2A

TCP1

NUCKS1

DYNLRB1

PSMB4

AAMP

AGO3C1orf194

UBC

COX6C

PSAP

PSMC1PEA15

NDRG2

CST3POMP

S100A1

−100

−50

0

50

−60 −40 −20 0 20 40Log2FC (pig/human)

Log2

FC (p

ig/m

ouse

)

27

Fig. S26

Fig. S26. Mouse brain enriched/depleted genes. Significantly differentially expressed genes (FDR < 0.01) of mouse brain compared to human and pig were selected. Log2FC values were determined using pairwise comparisons of average normalized expression (NX) of 10 brain regions in three species. The X-axis represents log2FC of mouse compared to human and the Y-axis represents log2FC of mouse compared to pig. Only genes both up-regulated or down-regulated in mouse were shown. The highest up-regulated or down-regulated genes were labeled.

AKR1A1

MDH2PSMD7

PSMD2RRP1

VPS35

GDI2

SDHA

HSPA8

HNRNPU

ZWINT

UBC

CLU

COX6C

TECR

GFAP

RPS11

−50

0

50

100

−50 0 50 100Log2FC (mouse/human)

Log2

FC (m

ouse

/pig

)

28

Fig. S27

33

Fig. S27. Triangular plots showing the relative expression levels in each of the regions of human, pig and mouse brain. Combined scatterplots for respective regions display the fractions of normalized expression (NX) values for all the 12,999 genes with one-to-one orthologue in three species. The genes classified as elevated in either of the species are marked in color.

34

Fig. S28

ob ctx hf am bg hy th mbpm cbrelative expression

Gene IDmax expression (NX)>0.1 >1 >10 >100ob ctx hf am bg hy th mbpm cb

relative expressionGene ID

max expression (NX)>0.1 >1 >10 >100

10.81

34.07

21.76

10.65

16.48

9.68

7.59

24.67

35.55

10.54

3.42

12.24

21.58

28.52

24.66

10.84

22

18.07

9.93

22.39

31.13

0.2

1.47

0.97

0.61

4.95

4.99

17.5

14.43

12.16

21.67

18.98

39.44

2.38

4.99

4.43

0.92

0.71

0.2

9.22

1.06

2.55

8.07

13.19

2.08

7.84

5.41

1.48

12.19

19.12

12.13

3.46

7.92

3.75

1.93

23.14

6.23

5.24

4.64

12.44

10.55

8.69

9.71

24.49

25.88

26.32

10.99

5.53

19.66

2.77

6.47

7.31

5.88

11.48

18.91

13.54

13.71

15.9

1.57

9.7

9.92

0.7

0.79

1.19

13.87

47.82

18.24

9.01

11.2

21.77

32

25.26

30.63

3.62

1.55

11.49

33.43

15.91

53.84

12.61

4.96

2.04

12.17

22.65

13.11

17.27

27.67

19.18

0.48

1.96

0.1

14.94

4.22

6.33

1.55

2.53

4.94

10.95

9.07

10.22

5.17

2.8

8.84

4.46

10.55

28.56

9.82

20.17

22.69

0.27

0.26

0.99

5.13

4.24

2.98

1.03

1.27

4.25

2.63

3.77

7.39

AC008770.2AC023509.3AC092835.1AC118549.1AC138696.1ADNP2ADNPAEBP1AEBP2AHCTF1AHDC1AHRAHRRAIREAKAP8AKAP8LAKNAALX1ALX3ALX4ANKZF1ARARHGAP35ARID2ARID3AARID3BARID3CARID5AARID5BARNT2ARNTARNTL2ARNTLARXASCL1ASCL2ASCL3ASCL4ASCL5ASH1LATF1ATF2ATF3ATF4ATF5ATF6ATF6BATF7ATMINATOH1ATOH7ATOH8BACH1BACH2BARHL1BARHL2BARX1BARX2BATF2BATF3

BATFBAZ2ABAZ2BBBXBCL6BCL6BBCL11ABCL11BBHLHA9BHLHA15BHLHE22BHLHE23BHLHE40BHLHE41BNC1BNC2

%25&6�í0()�%BPTFBRF2BSXC11orf95CAMTA1CAMTA2CARFCASZ1CBX2CC2D1ACCDC17

&&'&��í62+/+�CDC5LCDX1CDX2CDX4CEBPACEBPBCEBPDCEBPECEBPGCEBPZCENPACENPBCENPBD1CENPSCENPTCENPXCGGBP1CHAMP1CHCHD3CICCLOCKCPEB1CREB1CREB3CREB3L1CREB3L2CREB3L3CREB3L4CREB5CREBL2CREBZF

1.26

1.36

3.12

11.24

14.83

30.17

5.85

20.07

45.02

4.93

15.4

23.49

13.64

25.19

45.36

2.43

2.1

3.52

20.85

20.69

21.03

17.09

14.34

8.96

3.76

1.04

1.98

0.8

0.25

14.4

18.8

24.42

0.19

2.15

0.1

24.2

15.42

17.51

13.46

20.64

40.49

0.36

4.83

4.11

1.66

11.92

10.76

10.91

5.62

1.43

4.56

36.96

18.71

33.84

25.58

21.48

49.15

8.34

31.55

15.06

0.48

0.43

0.99

3.32

5.48

1.69

16.09

15.12

23.59

2.46

3.2

1.06

1.44

3.58

0.18

0.29

1.75

6.85

10.31

3.26

2.25

4.76

7.45

0.38

0.2

0.84

13.65

12.38

13.87

14.66

11.89

13.19

2.68

2.08

0.32

17.21

13.74

37.32

7.31

11.89

8.47

11.24

4.92

21.83

21.29

23.19

25.77

17.86

18.99

36.16

16.44

18.32

12.52

14.61

20.05

19.7

19.11

24.04

19.84

1.7

3.12

3.25

2.07

7.76

9.16

1.87

4

0.26

1.08

6.71

4.43

3.61

8.69

20.92

20.2

20.88

21.44

11.71

20.58

26.41

35





CREMCRXCSRNP1CSRNP2CSRNP3CTCFCTCFLCUX1CUX2CXXC1CXXC4CXXC5DACH1DACH2DBPDBX1DBX2DDIT3DEAF1DLX1DLX2DLX3DLX4DLX5DLX6DMBX1DMRT1DMRT2DMRT3DMRTA1DMRTA2DMRTB1DMRTC2DMTF1DNMT1DNTTIP1DOT1LDPF1DPF3DR1DRAP1DRGXDZIP1E2F1E2F2E2F3E2F4E2F5E2F6E2F7E2F8E4F1EBF1EBF2EBF3EBF4EEA1EGR1EGR2EGR3

6.19

9.4

14.34

0.68

6.56

3.96

10.9

8.4

16.8

18.06

13.69

16.82

19.34

19.95

30.33

24.43

0.53

0.41

0.27

25.79

25.85

37.6

11.59

13.07

8.06

21.24

12.18

32.77

11.63

13.03

13.54

22.31

36.25

52.71

34.9

24.36

25.07

0.41

6.05

7.83

12.52

7.34

22.05

14.85

32.5

21.42

18.63

28.73

23.91

29.27

16.11

14.05

18.76

7.04

0.84

0.15

0.24

2.17

0.6

1

13.81

9.72

7.54

15.15

15.92

15.14

3.21

6.47

1.2

0.2

2.62

3.41

5.73

1.92

1.05

6.49

1.24

2.88

0.69

1.07

1.23

3.45

16.26

23.67

20.94

16.69

11.79

16.36

14.41

13.89

15.91

17.31

14.93

11.98

10.09

22.61

43.53

24.19

19.16

15.58

52.76

27.11

37.63

5.53

6.04

3.43

18.13

39.89

16.84

7.55

2

6.37

0.66

1.33

0.2

10.26

7.72

8.8

16.29

21.1

18.74

16.8

7.11

5.31

9.04

16.57

6.73

3.45

9.02

0.6

1.14

2.4

0.39

10.35

10.97

20.17

9.96

12.98

18.27

4.71

2.08

2.02

9.79

7.59

3.93

5.05

8.06

9.75

31.98

14.55

18.32

4.33

4.71

6.06

13.2

16.83

21.92

EGR4EHFELF1ELF2ELF3ELF4ELF5ELK1ELK3ELK4EMX1EMX2EN1EN2EOMESEPAS1ERFERGESR1ESR2ESRRAESRRBESRRGESX1ETS1ETS2ETV1ETV2ETV3ETV3LETV4ETV5ETV6ETV7EVX1EVX2FAM170AFAM200BFBXL19FERD3LFEVFEZF1FEZF2FIGLAFIZ1FLI1FLYWCH1FOSFOSBFOSL1FOSL2FOXA1FOXA2FOXA3FOXB1FOXB2FOXC1FOXC2FOXD1FOXD2

5.4

8.89

13.34

0.34

1.24

1.17

5.66

9.14

11.6

13.4

44.89

23.15

0.23

0.23

0.26

1.05

2.84

2.99

3.06

19.02

13.53

12.66

34.04

5.02

4.74

9.97

6.01

11.14

12.56

5.62

6.9

9.03

7.04

7.26

11.84

6.05

12.38

8.89

23.08

18.89

17.51

22.51

20.36

13.15

10.22

17.65

23.21

8.09

1.81

6.28

2.68

4.83

0.82

1.8

12.13

1.05

23.56

8.67

8.1

0.61

0.33

0.96

10.47

8.89

35.26

6.03

4.2

3.7

16.14

7.65

22.22

33.23

56.49

69.57

0

3.21

1.23

13.69

6.91

10.13

9.96

3.91

2.24

19.52

19.39

19.28

8.65

5.76

5.59

2.49

2.63

2.17

0.38

2.01

0.19

13.44

12.97

14.35

2.34

14.92

1.4

3.63

5.4

4.92

9.05

7.6

15.53

10.37

10.59

17.66

10.88

7.56

13.15

5.3

6.96

4.87

13.88

7.28

31.8

6.26

3.32

6.06

0.3

8.38

4.69

7.32

8.12

11.34

2.47

6.44

1.61

2.51

6.1

1.15

0.97

4.7

0.3

6.59

8.08

11.92

5

2.7

4.66

3.27

2.65

7.07

36





FOXD3FOXE1FOXE3FOXF1FOXF2FOXG1FOXH1FOXI1FOXI2FOXI3FOXJ1FOXJ2FOXJ3FOXK1FOXK2FOXL1FOXL2FOXM1FOXN1FOXN2FOXN3FOXN4FOXO1FOXO3FOXO4FOXO6FOXP1FOXP2FOXP3FOXP4FOXQ1FOXR1FOXR2FOXS1GABPAGATA1GATA2GATA3GATA4GATA5GATA6GATAD2AGATAD2BGBX1GBX2GCM1GCM2GFI1GFI1BGLI1GLI2GLI3GLI4GLIS1GLIS2GLIS3GLMPGLYR1GMEB1GMEB2

3.46

12.13

1.5

0

1.27

0

1.92

2.21

3.84

3.41

4.63

3.58

2.98

12.54

23.07

14.64

1.02

0.69

1

0.2

0.32

8.29

12.36

14

13.09

18.2

18.35

20.65

22.3

29.58

9.64

11.2

18.31

18.45

13.27

18.61

0.65

0.91

1.22

1.91

4.47

0.85

0.48

2.15

0.14

13.84

21.15

23.97

11.75

36.19

36.28

13.52

16.68

8.33

14.26

21.5

21.66

10.51

11.13

17.76

9.12

8.18

2.74

1.04

1.64

1.71

9.05

6.77

10.09

3.17

1.17

3.59

3.03

7.73

4.51

11.99

10.54

15.06

0.17

1.57

0.54

3.42

5.02

1.74

6.79

10.19

1.05

1.2

2.27

0.26

0.37

5.24

0.81

0.78

0.56

9.84

6.24

13.05

14.49

24.03

25.69

3.59

3.07

1.78

2.97

7.19

9.2

0.94

5.25

0.12

0

2.03

0.18

0.24

0.36

0.43

0.26

4.56

0.18

5.87

4.31

6.39

2.44

2.28

3.47

4.71

12.16

3.92

1.14

4.4

3.02

2.83

9.65

11.67

19.81

9.97

8.62

45.05

30.76

31.09

9.62

12.03

10.44

14.77

8.32

10.49

GPBP1GPBP1L1GRHL1GRHL2GRHL3GSC2GSCGSX1GSX2GTF2BGTF2IGTF2IRD1GTF2IRD2BGTF3AGZF1HAND1HAND2HBP1HDXHELTHES1HES2HES3HES4HES5HES6HES7HESX1HEY1HEY2HEYLHHEXHIC1HIC2HIF1AHIF3AHINFPHIVEP1HIVEP2HIVEP3HKR1HLFHLXHMBOX1HMG20AHMG20BHMGA1HMGA2HMGN3HMX1HMX2HMX3HNF1AHNF1BHNF4AHNF4GHOMEZHOXA1HOXA2HOXA3

8.74

1.77

1.57

0.26

0.42

0.38

4.62

0.47

2.59

1.12

0.39

0.46

2.83

2.56

6.66

2.36

2.64

3.19

23.09

11.5

21.67

11.51

4.75

6.61

18.54

9.92

26.85

19.56

9.09

11.97

0.27

0.38

0.11

0

1.69

0.35

16.83

14.31

25.97

4.56

10.6

17.9

6.82

5.03

8.17

0.23

4.43

0.26

16.32

4.02

0.26

13.21

7.54

14.68

7.72

9.01

23.93

1.68

2.53

7.26

0.66

7.26

2.57

17.08

11.27

14.96

14.76

5.21

10.62

9.81

12.06

5.29

2.91

2.88

2.84

2.16

2.34

3.73

3.79

5.37

6.37

11.92

22.02

17.88

5.07

11.14

17.21

11.15

15.93

22.05

12.08

9.23

6.61

17.12

21.87

23.06

6.97

7.73

15.72

22.12

20.06

23.13

1.52

1.6

4.87

17.07

20.81

16.77

20.48

21.5

19.08

14.33

3.2

15.8

18.74

12.26

58.48

0.14

3.27

1.92

5.83

4.78

2.76

8.22

6.37

0.39

2.22

0.14

0.13

0.35

0.23

0.52

0.57

0.4

11.93

9.19

6.88

2.81

2.46

3.56

6.69

6.1

11.22

4.66

5.28

4.76

37





HOXA4HOXA5HOXA6HOXA7HOXA9HOXA10HOXA11HOXA13HOXB1HOXB2HOXB3HOXB4HOXB5HOXB6HOXB7HOXB8HOXB9HOXB13HOXC4HOXC5HOXC6HOXC8HOXC9HOXC10HOXC11HOXC12HOXC13HOXD1HOXD3HOXD4HOXD8HOXD9HOXD10HOXD11HOXD12HOXD13HSF1HSF2HSF4HSF5IKZF1IKZF2IKZF3IKZF4IKZF5INSM1INSM2IRF1IRF2IRF3IRF4IRF5IRF6IRF7IRF8IRF9IRX1IRX2IRX3IRX4

9.33

12.11

19.05

12.97

3.07

11.64

3.24

1.7

6.57

0

0.26

0.31

0

0

1.54

1.27

0

0.14

5.86

4.76

9.25

8.24

7.62

1.91

13.25

9.6

18.14

8.81

5.96

0.67

6.65

1.22

2.98

7.06

4.39

5.85

0.42

0.22

0.23

0

0.13

8.57

4.1

21.19

5.93

2.08

6.31

3.33

0.8

5.04

0.64

0.5

0.82

0.62

0

0

0.28

0

0

0.43

0.33

0.61

0.19

3.05

4.88

11.06

5.27

6.28

1.21

2.27

0.16

0.88

0.98

0.3

0.85

0.14

0

0.23

0

0

2.84

0.99

0.29

0.18

16.8

6.28

18.85

21.56

15.8

14.37

7.87

3.37

15.74

1.25

2.62

0.12

4.08

6.53

4.59

1.93

6.04

12.38

0.77

4.96

0.56

6.4

13.14

10.81

12.71

13.02

24.66

1.9

6.54

12

2.84

3.35

4.73

2.98

6.96

7.37

14.71

15.38

20.27

12.25

7.94

18.46

0.88

3.24

0.47

6.29

7

9.61

0.47

3.91

6.65

3.21

4.95

4.87

4.54

12.35

8.16

6.12

12.12

22.86

4.43

5.2

11.51

12.49

5.44

26.31

3.36

1.82

5.56

1.41

3.38

1.93

IRX5IRX6ISL1ISL2ISXJAZF1JDP2JRKJRKLJUNJUNBJUNDKAT7KCMF1KCNIP3KDM2AKDM2BKDM5BKINKLF1KLF2KLF3KLF4KLF5KLF6KLF7KLF8KLF9KLF10KLF11KLF12KLF13KLF14KLF15KLF16KLF17KMT2AKMT2BL3MBTL1L3MBTL3L3MBTL4LBX1LBX2LCORLCORLLEF1LHX1LHX2LHX3LHX4LHX5LHX6LHX8LHX9LIN28ALIN28BLIN54LMX1ALMX1BLTF

4.03

3.61

4.55

1

8.77

0.92

5.43

4.53

5.12

0

0.11

1.76

12.18

10.96

20.84

15.41

11.07

10.93

8.5

7.22

12.06

11.46

2.25

15.37

31.03

35.16

28.6

32.26

18.99

14.25

23.06

17.79

24.26

21.74

18.04

28.24

12.52

9.17

24.03

11.49

15.78

9.82

8.72

10.77

15.32

1.07

0.13

0.43

6.01

7.26

7.26

14.32

9.16

16.78

6.69

1.8

4.45

6.62

1.81

14.5

13.99

6.21

10.75

10.25

13.32

23.32

4.53

3.54

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27.21

19.96

32.95

12.54

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4.87

6.38

9.58

6.37

16.01

19.52

30.48

13.08

11.27

20.58

15.83

13.64

21.06

10.05

23.21

33.85

4.45

11.02

19.33

9.21

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5.54

2.59

4.34

12.33

4.62

3.79

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1.14

3.05

1.22

10.96

12.76

16.99

13.26

12.01

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12.73

15.92

24.39

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0.42

0.14

1.02

0.28

3.33

5.34

5.6

6.45

7.57

7.7

11.56

5.66

8.52

6.21

10.42

15

2.46

2.9

1.8

1.23

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19.4

12.21

3.31

0.66

5.27

4.04

3.14

2.07

1.13

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1.09

38





LYL1MAFMAFAMAFBMAFFMAFGMAFKMAXMAZMBD1MBD2MBD3MBD4MBD6MBNL2MECOMMECP2MEF2AMEF2BMEF2CMEF2DMEIS1MEIS2MEIS3MEOX1MEOX2MESP1MESP2MGAMITFMIXL1MKXMLXMLXIPMLXIPLMNTMNX1MSANTD1MSANTD3MSANTD4MSCMSGN1MSX1MSX2MTERF1MTERF2MTERF3MTERF4MTF1MTF2MXD1MXD3MXD4MXI1MYBMYBL1MYBL2MYCMYCLMYCN

3.66

10.68

5.54

12.01

4.01

15.95

2.77

0.7

2.01

6.26

12.38

5.93

3.34

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10.48

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28.32

37.38

45.63

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28.48

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3.69

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28.18

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3.36

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0.64

0.38

1.82

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10.01

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1.59

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22.94

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48.81

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43.59

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4.28

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8.57

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11.51

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1.41

9.57

6.65

5.69

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35.52

54.52

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13.41

24.32

39.76

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0.77

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39.63

29.14

19.66

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8.91

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32.58

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8.98

3.93

10.87

7.99

19.93

26.02

5.58

2.39

6.29

2.03

0.23

1.26

0.61

1.11

0.14

34.12

26.72

23.81

17.03

15.93

11.37

0.89

4.09

0.47

5.24

8.63

9.28

22.42

14.77

14.76

5.15

2.21

4.92

0.26

0.3

0.38

6.19

15.3

14.7

23.54

13.51

31.05

13.86

16.17

35.84

0.62

1.6

4.38

21.26

7.64

9.2

13.39

27.72

5.71

3.49

2.82

14.72

9.23

18.72

3.87

5.7

8.4

21.85

9.9

16.99

7.07

8.96

27.99

2.94

6.81

7.69

10.37

23.92

27.18

9.51

13.99

14.13

0.28

0.48

0.25

14.6

25.43

21.78

2.09

0.6

1.48

8.82

11.81

16.13

20.72

19.85

23.03

4.12

12.74

21.62

7.45

2.74

5.48

6.05

3.95

4.07

1.41

4

6.6

3.05

4.78

6.77

0.28

0.33

2.23

12.88

6.44

7.87

21.2

15.09

19.1

21.96

14.82

10.08

16.16

19.73

39.29

20.11

28.6

39.24

20.03

10.72

17.92

21.18

27.42

23.91

9.69

17.55

5.86

0.89

5.34

0.68

17.23

19.1

14.54

10.21

14.56

15.9

17.97

11.36

12.3

5.84

3.6

1.38

7.93

4.77

10.92

SEBOXSETBP1SETDB1SETDB2SGSM2SHOX2SHOXSIM1SIM2SIX1SIX2SIX3SIX4SIX5SIX6SKISKILSKOR1SKOR2SLC2A4RGSMAD1SMAD3SMAD4SMAD5SMAD9SMYD3SNAI1SNAI2SNAI3SNAPC2SNAPC4SNAPC5SOHLH1SOHLH2SONSOX1SOX2SOX3SOX4SOX5SOX6SOX7SOX8SOX9SOX10SOX11SOX12SOX13SOX14SOX15SOX17SOX18SOX21SOX30SP1SP2SP3SP4SP5SP6

7.95

15.2

12.4

15.12

21.61

16.7

5.94

13.76

11.19

16.68

15.64

41.21

18.41

13.96

7.19

6.04

6.09

2.13

1.78

3.85

2.04

0.18

0.52

3.22

0.53

0.16

1.69

7.21

8.8

26.25

1.51

1.58

3.38

1.09

2.67

3.59

1.18

1.03

2.56

10.21

43.1

26.71

14.44

17.17

11.39

5.32

8.7

13.77

16.01

8.42

15.83

12.08

8.17

9.73

15.76

46.2

22.95

12.94

26.31

21.27

9.28

7.74

12.04

12.17

17.67

20.08

1.49

0.29

3.35

1.45

1.05

3.71

2.64

1.36

2.47

19.82

14.36

14.98

7.49

6.39

15.56

20.95

11.73

24.73

19.53

39.02

38.12

12.46

2.68

6.57

17.05

12.31

28.9

3.62

4.26

4.71

8.08

17.72

8.09

7.11

16.06

3.11

10.52

17.29

28.01

8.69

18.44

28.49

10.68

19.3

39.15

7.41

13.32

4.78

8.87

14.72

21.24

7.58

4.99

12.28

5.97

10.41

5.03

0.96

0.99

5.58

4.51

3.31

1.77

5.85

4

4.39

4.74

6.87

9.06

0.3

0.43

7.42

17.26

23.17

6.92

9.48

22.08

19.4

18.15

20.15

8.99

17.42

20.06

3.04

5.16

1.35

0.99

0.18

1.05

41





SP7SP8SP9SP100SP110SP140SP140LSPDEFSPENSPI1SPIBSPICSPZ1SRCAPSREBF1SREBF2SRFSRYST18STAT1STAT2STAT3STAT4STAT5ASTAT5BSTAT6TAL1TAL2TBPTBPL1TBPL2TBR1TBX1TBX2TBX3TBX4TBX5TBX6TBX10TBX15TBX18TBX19TBX20TBX21TBX22TBXTTCF3TCF4TCF7TCF7L1TCF7L2TCF12TCF15TCF20TCF21TCF23TCF24TCFL5TEAD1TEAD2

14.04

7.83

2.47

19.23

24.43

1.98

8.71

18.98

8.15

1.94

3.63

0.44

8.45

15.74

29.54

5.25

21.02

9.91

15.8

6.7

15.79

21.82

25.59

40.49

10.98

11.23

8.96

18.02

24.15

38.32

11.6

20.47

20.68

14.97

11.2

21.2

16.64

18.32

23.66

1.44

5.19

9.48

1.87

7.22

7.08

13.32

18.12

24.84

6.01

4.15

11.12

10.57

7.96

8.67

27.07

14.55

13.24

15.41

15.44

21.23

2.79

3.11

1.96

0.43

1.25

2.8

3.08

2.38

1.46

1.23

2.96

0.44

0.18

1.09

1.83

2.42

3.56

1.5

1.88

4.56

0.24

2.94

0.93

1.52

3.01

4.22

5.11

0.15

0.19

0.93

1.21

0.52

0.2

12.31

13.11

2.04

1.41

2.62

0.27

0.73

0.4

2.14

8.03

8.31

10.33

28.13

41.34

37.62

6.72

9.27

3.41

5.62

6.86

5.06

23.18

32.27

16.69

20.63

15.86

38.01

2.49

8.68

0.99

0.4

2.27

0.87

1.37

8.61

0.19

2.74

12.64

19.79

8

7.74

8.55

4.22

3.51

4.38

TEAD3TEAD4TEFTERB1TERF1TERF2TET1TET2TET3TFAP2ATFAP2BTFAP2CTFAP2DTFAP2ETFAP4TFCP2TFCP2L1TFDP1TFDP2TFDP3TFE3TFEBTFECTGIF1TGIF2TGIF2LXTHAP1THAP2THAP3THAP4THAP5THAP6THAP7THAP8THAP9THAP10THAP11THAP12THRATHRBTHYN1TIGD1TIGD2TIGD3TIGD4TIGD5TIGD6TIGD7TLX1TLX2TLX3TMF1TOPORSTP53TP63TP73TRAFD1TRERF1TRPS1TSC22D1

2.86

2.62

4.22

5.23

2.92

2.3

43.39

45.08

34.79

0.95

4.92

0.16

12.15

14.84

37.4

20.63

18.07

24.94

6.53

25.58

5.48

5.41

14.21

13.51

6.98

12.26

20.1

2.46

1.91

1.73

4.23

5.59

4.49

2.93

1.46

1.17

0.15

2.29

17.04

5.58

8.27

24.47

12.23

20.95

23.13

3.11

3.71

4.99

11.98

12.82

7.65

14.97

16.54

14.01

6.9

12.3

23.31

1.07

4.13

10.1

2.6

6.79

8.56

3.08

3.91

3.44

10.96

12.09

13.06

14.98

9.02

16.65

17.62

11.51

16.84

14.6

7.08

14.72

17.29

14.73

11.64

70.98

26.57

59.19

11.54

17.37

18.66

41.02

12.9

35.33

11.5

6.94

5.58

6.54

4.11

6.66

0.34

2.33

5.64

4.05

9.85

7.37

1.97

2.04

0.36

0

0.54

2.67

4.14

20.16

36.04

10.82

12.55

16.09

10.67

11.68

15.67

11.81

5.54

6.35

3.24

0.13

0.63

2.87

2.53

19.86

14.16

6.44

21.53

8.8

16.48

11.27

69.88

25.29

59.36

42





TSHZ1

TSHZ2

TSHZ3

TTF1

TWIST1

TWIST2

UBP1

UNCX

USF1

USF2

USF3

VAX1

VAX2

VDR

VENTX

VEZF1

VSX1

VSX2

WIZ

WT1

XBP1

XPA

YBX1

YBX2

YBX3

YY1

YY2

ZBED1

ZBED2

ZBED3

ZBED4

ZBED5

ZBED6

ZBED9

ZBTB1

ZBTB2

ZBTB3

ZBTB4

ZBTB5

ZBTB6

ZBTB7A

ZBTB7B

ZBTB7C

ZBTB8A

ZBTB8B

ZBTB9

ZBTB10

ZBTB11

ZBTB12

ZBTB14

ZBTB16

ZBTB17

ZBTB18

ZBTB20

ZBTB21

ZBTB22

ZBTB24

ZBTB25

ZBTB26

ZBTB32

22.25

28.33

20.07

7.18

10.4

10.56

2.53

1.55

1.19

2.58

0.27

0.91

20.37

26.12

30.2

4.97

12.8

34.64

28.61

22.81

23.95

7.89

29.98

47.19

7.29

19.64

10.75

4.81

5.69

14.26

2.92

12.69

2.15

1.9

0.47

6.49

20.09

34.26

0.13

13.19

0.47

0.84

0.7

1.98

1.3

0.74

10.23

14.15

20.74

29.07

13.6

14.71

5.48

3.72

0.48

5.1

3.28

4.43

17.4

16.18

25.96

6.28

7.43

9.08

6.3

8.22

19.12

9.83

10.94

10.29

7.48

6.46

11.15

19.75

25.06

23.31

6.27

6.78

10.91

8.64

14.19

13.71

12.67

24.01

20.36

9.23

10.58

6.8

6.55

4.17

3.02

6.73

14.14

8.62

3.79

12.83

10.5

16.29

21.07

16.93

7.24

7.73

9.19

12.73

9.74

18.78

7.86

12.24

13.93

10.34

9.22

20.19

51.74

53.56

88.41

8.93

28.7

13.39

7.63

7.6

9.58

10.38

4.79

11.16

14.32

23.78

16.67

8.29

10.99

11.44

0.44

1.25

0.14

ZBTB33

ZBTB34

ZBTB37

ZBTB38

ZBTB39

ZBTB40

ZBTB41

ZBTB42

ZBTB43

ZBTB44

ZBTB45

ZBTB46

ZBTB47

ZBTB48

ZBTB49

ZC3H8

ZEB1

ZEB2

ZFAT

ZFHX2

ZFHX3

ZFHX4

ZFP1

ZFP2

ZFP3

ZFP14

ZFP28

ZFP30

ZFP37

ZFP41

ZFP42

ZFP57

ZFP62

ZFP64

ZFP69

ZFP69B

ZFP82

ZFP90

ZFP91

ZFP92

ZFPM1

ZFPM2

ZFX

ZFY

ZGLP1

ZGPAT

ZHX1

ZHX2

ZHX3

ZIC1

ZIC2

ZIC3

ZIC4

ZIC5

ZIK1

ZIM2

ZIM3

ZKSCAN1

ZKSCAN2

ZKSCAN3

15.64

11.9

13.99

5.78

7.26

12.1

4.26

10.75

8.14

13.67

23.93

39.33

5.25

4.14

7.66

6.43

15.17

13.95

2.48

3.28

1.25

15.62

6.22

8.65

5.27

46.21

32.77

12.53

8.68

15.18

13.88

12.34

18.7

9.82

18.86

15.44

10.22

5.71

10.54

5.98

6.01

7.17

8.42

16.79

14.08

16.14

16.06

13.77

24.07

31.79

42.26

4.1

13.94

5.27

6.48

11.68

11.99

4.08

9.4

4.8

7.98

8.2

9.1

14.73

11.58

11.59

16.44

12.44

9.16

11.78

14.43

11.81

8.41

10.13

15.45

14.3

7.07

12.58

0.3

0.5

0.99

16.46

13.68

20.36

9.23

6.58

11.41

8.13

11.5

11.63

6.73

16.14

19

6.97

5.19

5.25

12.34

26.84

51.75

10.74

9.02

15.62

18.43

27.85

22.5

8.05

8.19

18.43

13.21

14.08

20.73

37.47

64.58

96.3

26.39

40.9

48.72

11.12

6.25

39.09

10.33

31.55

40.34

10.47

20.14

37.77

14.58

19.47

25.35

6.39

5.89

6.09

43





ZKSCAN4ZKSCAN5ZKSCAN7ZKSCAN8ZMAT1ZMAT4ZNF2ZNF3ZNF7ZNF8ZNF10ZNF12ZNF14ZNF16ZNF17ZNF18ZNF19ZNF20ZNF22ZNF23ZNF24ZNF25ZNF26ZNF28ZNF30ZNF32ZNF33AZNF33BZNF34ZNF35ZNF37AZNF41ZNF43ZNF44ZNF45ZNF48ZNF57ZNF66ZNF69ZNF70ZNF71ZNF74ZNF75AZNF75DZNF76ZNF77ZNF79ZNF81ZNF83ZNF84ZNF85ZNF90ZNF91ZNF92ZNF93ZNF98ZNF99ZNF100ZNF101ZNF107

6.45

19.08

21.45

21.98

10.39

15.38

7.07

7.69

20.19

12.71

9.92

10.34

18.29

11.83

12.88

22.8

17.6

39.44

9.57

15.51

21.98

41.25

14.03

23.8

7.94

14.88

7.69

9.92

11.99

12.15

18.49

8.54

21.03

ZNF112ZNF114ZNF121ZNF131ZNF132ZNF133ZNF134ZNF135ZNF136ZNF138ZNF140ZNF141ZNF142ZNF143ZNF146ZNF148ZNF154ZNF155ZNF157ZNF160ZNF165ZNF169ZNF174ZNF175ZNF177ZNF180ZNF181ZNF182ZNF184ZNF189ZNF195ZNF197ZNF200ZNF202ZNF205ZNF207ZNF208ZNF211ZNF212ZNF213ZNF214ZNF215ZNF217ZNF219ZNF221ZNF222ZNF223ZNF224ZNF225ZNF226ZNF227ZNF230ZNF232ZNF233ZNF234ZNF235ZNF236ZNF239ZNF248ZNF250

6.73

8.71

15.89

18.57

17.06

19.22

9.25

7.49

17.61

5.71

14.26

19.66

15.42

16.16

36.08

19.42

28.94

14.21

4.53

13.58

14.79

8.24

11.32

17.13

2.98

12.13

14.26

11.27

19.55

18.44

4.08

9.1

9.24

11.44

7.26

13.22

39.93

48.59

39.4

5.58

7.28

10.17

2.14

4.54

3.47

22.71

13.93

17.29

13.21

7.92

10.79

10.52

10.23

11.83

11.49

23.14

23.08

44





ZNF251ZNF253ZNF254ZNF256ZNF257ZNF260ZNF263ZNF264ZNF266ZNF267ZNF268ZNF273ZNF274ZNF275ZNF276ZNF277ZNF280AZNF280BZNF280CZNF280DZNF281ZNF282ZNF283ZNF284ZNF285ZNF286AZNF287ZNF292ZNF296ZNF300ZNF302ZNF304ZNF311ZNF316ZNF317ZNF318ZNF319ZNF320ZNF322ZNF324ZNF324BZNF326ZNF329ZNF331ZNF333ZNF334ZNF335ZNF337ZNF341ZNF343ZNF345ZNF346ZNF347ZNF350ZNF354AZNF354BZNF354CZNF358ZNF362ZNF365

14.39

13.61

20.13

24.33

18.34

14.23

9.9

10.33

20.44

12.39

20.96

6.86

8.09

6.92

16.95

19.66

19.61

13.06

9.48

19.95

4.47

13.14

12.69

18.31

8.05

13.62

16.06

11.53

12.06

10.62

7.24

16.23

24.05

15.25

15.45

17.91

13.47

11.89

19.14

7.18

8.8

9.15

18.84

11.74

11.59

14.86

17.43

25.58

9.97

10

12.33

8.66

14.28

13.88

5.4

16.9

8.1

19.72

9.55

20.72

11.69

12.64

14.98

19.08

15.65

9.96

16.55

12.29

33.3

12.97

18.24

18.95

37.68

15.77

19.67

ZNF366ZNF367ZNF382ZNF383ZNF384ZNF385AZNF385BZNF385CZNF385DZNF391ZNF394ZNF395ZNF396ZNF397ZNF398ZNF404ZNF407ZNF408ZNF410ZNF414ZNF415ZNF416ZNF417ZNF418ZNF419ZNF420ZNF423ZNF425ZNF426ZNF428ZNF429ZNF430ZNF431ZNF432ZNF433ZNF436ZNF438ZNF439ZNF440ZNF441ZNF442ZNF443ZNF444ZNF445ZNF446ZNF449ZNF451ZNF454ZNF460ZNF461ZNF462ZNF467ZNF468ZNF469ZNF470ZNF471ZNF473ZNF474ZNF479ZNF480

4.57

11.3

5.3

7.91

4.6

21.36

5.84

17.56

15.77

13.27

18.48

27.94

7.27

13.56

24.72

19.04

29.37

25.5

14.52

19.5

14.71

12.14

8.71

12.69

5.75

11.19

9.97

14.69

9.16

32.37

9.35

12.91

20

7.35

21.68

12

6.43

3.36

9.24

15.61

5.01

16.67

18.35

12.99

18.7

11.29

27.37

8.88

11.6

23.75

29.7

13.53

18.05

10.54

5.84

7.44

10.97

9.92

4.53

13.71

26.3

15.73

12.77

5.66

12.19

8.95

15.79

16.56

20.19

9.19

9.32

15.98

11.43

15.79

19.65

31.4

9.3

10.79

2.52

7.49

7.56

45





ZNF483ZNF484ZNF485ZNF486ZNF487ZNF488ZNF490ZNF491ZNF492ZNF493ZNF496ZNF497ZNF500ZNF501ZNF502ZNF503ZNF506ZNF507ZNF510ZNF511ZNF512ZNF512BZNF513ZNF514ZNF516ZNF517ZNF518AZNF518BZNF519ZNF521ZNF524ZNF525ZNF526ZNF527ZNF528ZNF529ZNF530ZNF532ZNF534ZNF536ZNF540ZNF541ZNF543ZNF544ZNF546ZNF547ZNF548ZNF549ZNF550ZNF551ZNF552ZNF554ZNF555ZNF556ZNF557ZNF558ZNF559ZNF560ZNF561ZNF562

20.74

35.22

27.75

7.67

7.01

8.82

4.93

6.76

5.39

8.77

13.35

14.26

22.79

19.24

14.3

11.36

11.34

11.1

12.97

12.09

15.94

4.6

10.33

6.62

9.71

14.1

12.42

13.67

24.5

53.39

5.36

8.57

11.22

17.82

17.53

34.48

9.14

8.9

16.94

5.12

19.12

11.36

ZNF563ZNF564ZNF565ZNF566ZNF567ZNF568ZNF569ZNF570ZNF571ZNF572ZNF573ZNF574ZNF575ZNF576ZNF577ZNF578ZNF579ZNF580ZNF581ZNF582ZNF583ZNF584ZNF585AZNF585BZNF586ZNF587ZNF587BZNF589ZNF592ZNF594ZNF596ZNF597ZNF598ZNF599ZNF600ZNF605ZNF606ZNF607ZNF608ZNF609ZNF610ZNF611ZNF613ZNF614ZNF615ZNF616ZNF618ZNF619ZNF620ZNF621ZNF623ZNF624ZNF625ZNF626ZNF627ZNF628ZNF629ZNF630ZNF639ZNF641

5.16

15.02

17.54

10.71

15.87

12.06

4.44

18.13

9.5

4.4

8.09

21.27

9.24

15.48

22.23

16.27

6.7

8.25

10.19

16.16

14.09

12.76

13.79

22.62

13.17

25.43

13.23

3.68

2.5

14.89

9.47

10.82

14.1

5.77

5.05

6.42

11.86

13.22

12.88

27.84

18.34

19.62

6.4

7.15

16.63

46





ZNF644ZNF646ZNF648ZNF649ZNF652ZNF653ZNF654ZNF655ZNF660ZNF662ZNF664ZNF665ZNF667ZNF668ZNF669ZNF671ZNF672ZNF674ZNF675ZNF677ZNF678ZNF680ZNF681ZNF682ZNF683ZNF684ZNF687ZNF688ZNF689ZNF691ZNF692ZNF695ZNF696ZNF697ZNF699ZNF700ZNF701ZNF703ZNF704ZNF705AZNF706ZNF707ZNF708ZNF709ZNF710ZNF711ZNF713ZNF714ZNF716ZNF717ZNF721ZNF724ZNF726ZNF728ZNF729ZNF730ZNF732ZNF736ZNF737ZNF740

16.8

44.18

27.01

10.19

6.91

9.47

9.22

14.18

21.99

8.64

7.77

14.77

5.68

9.16

14.44

23.38

13.48

24.06

15.96

24.26

36.32

6.09

8.63

9.41

13.55

12.96

14.43

13.92

12.91

12.78

7.18

7.3

11.29

5.14

12.73

7.59

7.77

11.58

13.7

15.38

8.86

23.7

5.53

6.75

6.13

9.91

17.38

7.43

11.89

15.05

19.69

47.44

17.57

37.13

7.39

14.33

4.51

7.54

14.48

9.27

22.73

14.82

18.43

14.03

8.66

12.08

0.78

0.41

0.14

8.66

8.96

13.3

16.51

11.14

16.32

7.17

11.01

15.72

17.75

12.53

5.78

4.89

5.91

4.02

6.02

10.04

9.27

11.09

7.96

4.31

7.95

8.52

23.45

10.07

18.44

14.43

10.22

16.77

24.47

3.28

9.4

1.23

14.64

19.73

20.8

9.35

20.39

28.82

4.4

6.82

2.39

4.71

11.94

14.42

ZNF746ZNF747ZNF749ZNF750ZNF763ZNF764ZNF765ZNF766ZNF768ZNF770ZNF771ZNF772ZNF773ZNF774ZNF775ZNF776ZNF777ZNF778ZNF780AZNF780BZNF781ZNF782ZNF783ZNF784ZNF785ZNF786ZNF787ZNF788ZNF789ZNF790ZNF791ZNF792ZNF793ZNF799ZNF800ZNF804AZNF804BZNF805ZNF808ZNF813ZNF814ZNF816ZNF821ZNF823ZNF827ZNF829ZNF830ZNF831ZNF835ZNF836ZNF837ZNF841ZNF843ZNF844ZNF845ZNF846ZNF850ZNF852ZNF853ZNF860

47

Fig. S28. Expression heatmap across regions and three species for transcription factors. Heatmaps showing the relative expression across the 10 brain regions and three species. The maximum expression across the 10 regions in each of the three species is also shown as bars showing the brain expression levels between species. Expression level and absolute values are only shown for genes with regional classification data in human (requires available GTEx and FANTOM data) as well as human one-to-one orthologues for mouse and pig expression profile.


Gene IDmax expression (NX)>0.1 >1 >10 >100

4.32

7.25

9.54

10.14

7.38

5.56

1

2.12

6.19

20.01

9.41

4.8

7.55

7.01

11.26

6.82

14.32

10.26

12.77

14.55

13.66

10.25

13.56

ZNF865ZNF878ZNF879ZNF880ZNF891ZSCAN1ZSCAN2ZSCAN4ZSCAN5AZSCAN9ZSCAN10ZSCAN12ZSCAN16ZSCAN18ZSCAN20ZSCAN21ZSCAN22ZSCAN23ZSCAN25ZSCAN26ZSCAN29ZSCAN30ZSCAN31ZSCAN32ZUFSPZXDC

48

Fig S29.

Figure S29. Expression heatmap across regions and three species for genes involved in neurotransmission. Heatmaps showing the relative expression across the 10 brain regions and three species. The maximum expression across the 10 regions in each of the three species is also shown as bars showing the brain expression levels between species. Expression level and absolute values are only shown for genes with regional classification data in human (requires available GTEx and FANTOM data) as well as human one-to-one orthologues for mouse and pig expression profile.

49

Fig. S30

53

Figure S30. Expression heatmap across regions and three species for G-protein coupled receptor (GPCR) genes. Heatmaps showing the relative expression across the 10 brain regions and three species. The maximum expression across the 10 regions in each of the three species is also shown as bars showing the brain expression levels between species. Expression level and absolute values are only shown for genes with regional classification data in human (requires available GTEx and FANTOM data) as well as human one-to-one orthologues for mouse and pig expression profile.

54

Fig. S31

Fig. S31. Brain elevated genes compared to other tissue types. The highest expression value based on all of the human brain regions including spinal cord and corpus callosum represented the brain as a tissue type for tissue-based classification on the whole human body level. A four-fold difference in expression level is used for defining genes as elevated in either one or a group of tissue types. Tissue specificity (a) and tissue distribution (b) categories show that 33 genes are only detected in brain and 2587 genes are classified as brain elevated. 16,227 genes are in total detected in the human brain. Description of the different classification rules is found in table S4 and table S8. The combination of a and b is summarized in table S7.

55

Fig. S32

Fig S32. Brain elevated genes and co-expression clusters with peripheral tissues. (a) Heatmap showing the expression of all the 2587 brain elevated genes in all the 37 tissue types, including brain at the top. A selection of genes from five sub-clusters (marked at the bottom of the heatmap in color) are exemplified by IHC images from different tissue types (b-e).

56

Fig. S33

Fig. S33. Expression profiles of cell type signature genes. Heatmaps showing the expression of the cell type signature gene expression across the 10 brain regions. The different cell type signature genes are color coded in the top row.

57

Fig. S34

Fig. S34. Scatterplot of the regional expression levels of the cell type signature genes. The X-axis represents the 10 brain regions in human and the Y-axis represents the normalized expression (NX) of each gene in each region. The signature genes are color coded by cell types and the most abundance ones in respective region are indicated by gene names.

KCNAB2CAMK2A

CAMK2A

CAMK2A

CAMK2A FA2H

CALB1

CALB1

SLC17A7

SLC17A7 SLC17A7

SLC17A7

ATP1A3

ATP1A3

ATP1A3

ATP1A3

ATP1A3

SH3GL2

RGS4

RGS4

APOE

APOE

APOE

APOE

APOE

MTSS1LMTSS1LMTSS1L

MTSS1L

MTSS1L

MTSS1L MTSS1L

MTSS1L

HAPLN2

HAPLN2

ANO3

TJAP1

S100A1 S100A1

S100A1

S100A1

CAMKVCERCAM

CERCAMCERCAM

KLK6

NPTX1

ZCCHC12

RELN

MOG

0

30

60

90

olfa

ctor

y re

gion

cere

bral

cor

tex

hipp

ocam

pal f

orm

atio

n

amyg

dala

basa

l gan

glia

hypo

thal

amus

thal

amus

mid

brai

n

pons

and

med

ulla

cere

bellu

m

Regions

NX

Cell typesa

a

a

a

astrocytesmicroglianeuronsoligodendrocyte

58

Fig. S35

Fig. S35. Expression profiles of cell type signature genes. Heatmap showing the expression of the cell type signature genes in peripheral tissue types grouped in corresponding way as seen in Fig 7, based on cell type signature genes. The different cell type signature genes are color coded in the top row.

59

Table S4. Classification rules used to categories gene expression in tissues and brain regions Specificity category Description

Elevated

tissue enriched/ regional enriched

NX level in a particular tissue/brain region at least four times any other tissue/brain region

group enriched NX levels of a group (of 2-‐5 tissue or brain regions) at least four times any other tissue/brain region

tissue enhanced/ regional enhanced

NX levels of a group (of 1-‐5 tissues or brain regions) at least four times the mean of all tissues/brain regions

low tissue specificity/ low regional specificity

NX 1 in at least one tissue/brain region but not elevated in any tissue/brain region

not detected NX less than 1 in all tissues/brain regions Table S7. All protein coding genes and tissue classification from a brain-‐perspective

Categories including

expression above cut off (NX 1) in brain.

Distribution category Only

detected in brain

Detected in some

Detected in many

Detected in all

Not detected in

brain Total

Specificity category

Brain enriched 19 135 313 21 -‐ 488

Group enriched -‐ 222 261 13 -‐ 496

Brain enhanced 14 328 956 305 -‐ 1603 Elevated in other tissue than brain

-‐ 700 2742 1856 -‐ 5298

Low tissue specificity and detected in brain

-‐ 15 884 7443 -‐ 8342

Not detected -‐ -‐ -‐ -‐ 3443 3443

Total 33 1400 5156 9638 3443 19670

60

Table S8. Classification rules used to categorize genes expression based on tissue distribution (expression above cut of NX=1). Category Description Detected in single Detected in a single tissue

Detected in some Detected in more than one but less than one third of the different tissues

Detected in many Detected in at least a third but not all tissues types

Detected in all Detected in all tissues Not detected NX < 1 in all tissues

Table S10. Tissue specificity category for the 420 cell type signature genes listed in table S9

Cell type # Signature genes

Brain elevated only

Group/enhanced incl Brain

Elevated in other tissue than brain

Low tissue specificity

Neuron 196 59 69 46 22 Oligodendrocyte 65 8 26 17 14 Astrocyte 108 8 7 59 34 Microglia 51 1 2 36 12

61

Table S13. Antibody ID and information of the antibodies used for protein localization showing in figure 3,4,5,6 and 7. Antibody specificity was determined using PrEST array (PrEST, affinity to random protein fragments, western blot (wb, selective affinity for protein of predicted size), paired antibodies (paired, independent antibodies with similar patterns) and orthogonal validation (ortho, staining pattern supported by mRNA distribution profiles. Detailed antibody information is available in version 19 of the human protein atlas. Gene name Antibody ID included

in figure dilution factor

conc (mg/ml)

validation

IGFBP5 HPA070407 3 100 0.0505 PrEST, Ortho

NECAB1 HPA023629 3 3000 0.2025 Prest, wb,

paired, ortho

SLC6A2 AMAb91116 3 300 n/a Prest, paired,

ortho ADCYAP1 HPA065887 3 1400 0.3251 PrEST, ortho GPR151 HPA065728 3 0.4394 PrEST, ortho GNAL HPA051160 4 1000 0.3445 PrEST, ortho

TMEM266 HPA041921 4 5000 0.9623 PrEST, paired,

ortho SCGN AMAb90630 4 1000 n/a paired, ortho TFAP2B HPA034683 4 250 0.3445 PrEST, ortho GPR37L1 HPA064454 5 1600 0.1845 PrEST, ortho GPR162 HPA055135 5 35 0.0288 PrEST, ortho

GPRC5C HPA029776 5 135 0.3326 PrEST, wb,

ortho

ARHGEF33 HPA041051 6 3000 0.3046 PrEST, paired,

ortho

ATP1A3 HPA056446 6 950 0.072 PrEST, paired,

ortho

CRYAB HPA057100 6 450 0.0263 PrEST, wb,

paired, ortho

RFX2 HPA048969 6 80 0.0707 PrEST, wb,

ortho AIF1 HPA049234 6 400 0.2954 PrEST, ortho ACSL4 HPA005552 6 100 0.08 PrEST, wb

ADORA2A HPA075997 6 1300 0.4042 PrEST, paired,

ortho CACNG3 HPA077238 6 50 0.1116 PrEST, ortho ANK1 HPA004842 6 300 0.085 PrEST, ortho

GFAP HPA056030 6 550 0.1105 PrEST, paired,

ortho

ALDH6A1 HPA029074 6 800 0.2298 PrEST, wb,

paired, ortho

62

AKAP17A HPA043247 6 1000 0.1155 PrEST ALOX5 HPA071285 7 50 0.0163 PrEST, ortho

ITGB2 HPA016894 7 75 0.0625 PrEST, wb,

paired, ortho

PYCARD HPA049074 7 55 0.0282 PrEST, wb,

paired, ortho SLC13A5 HPA044343 7 100 0.1319 PrEST, wb

ALDH1L1 HPA050139 7 6000 0.3436 PrEST, wb,

paired, ortho SNTA1 CAB037059 7 1000 n/a KCNAB2 CAB001975 7 50 n/a ortho

KCNB1 HPA042434 7 750 0.1661 PrEST, paired,

ortho

PDE1B HPA018492 7 75 0.0375 PrEST, wb,

ortho

MAG HPA012499 7 50 0.095 PrEST, paired,

ortho

PPP1R14A HPA042097 7 600 0.1167 PrEST, paired,

ortho ENPP6 HPA042740 7 10 0.0335 PrEST

Table S1. List of all 1710 human brain samples included in the analysis. Table S2. List of all the 119 pig brain samples included in the analysis. Table S3. List of all the 67 mouse brain samples included in the analysis. Table S5. List of the 537 genes with highest expression in same brain structure of all three mammalian species and classified as enriched (fourfold higher NX in one structure compared to the other) in either of the three species. Table S6a. List of genes related to fig. S21 volcano plot comparing expression in human and pig brain. Table S6b. List of genes related to fig. S22 volcano plot comparing expression in human and mouse brain. Table S6c. List of genes related to fig. S23 volcano plot comparing expression in pig and mouse brain. Table S9. List of the 420 cell type signature genes. Table S11. Sample information related to RNA-‐seq quality control of mouse brain samples. Table S12. Sample information related to RNA-‐seq quality control of pig brain samples. Movie S1. iDISCO+ volume immunostaining of a whole mouse brain for GPR151 receptor.

supplementary materials for...2 fig. s1 fig. s1. schematic drawing, indicating the anatomical...

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