Organ Annotation VignettePreprocess

Enter the name of the organ you want to analyze.organ_of_interest = "Liver"

We begin by loading a gene by cell matrix A, where Aij is the number of reads (or UMIs) from cell j thataligned to gene i. The Seurat package keeps track of matrices and coordinates derived from A together withmetadata; that information is stored in a large object called tiss. For the sake of explicitness, we describebelow many of the mathematical transformations implemented inside of Seurat.

First, we filter out cells with fewer than 500 genes or 50,000 reads. (For UMI data, we filter out cells withfewer than 500 genes or 1,000 UMIs.)tiss <- FilterCells(object = tiss, subset.names = c("nGene", "nReads"),

low.thresholds = c(500, 50000))

Next, we log-normalize counts for each cell, essentially to log counts per million (for reads) or counts per tenthousand (UMIs). More precisely, we set

Nij = log(

1 +MAij∑j′ Aij′

),

where M = 106 for FACS and M = 104 for droplets. The log is base e. We chose those values of M to beclose to the average number of counts per cell.tiss <- NormalizeData(object = tiss, scale.factor = 1e6)

Then we shift and scale the rows of the normalized matrix, so each gene has mean zero and variance one.

Xij = (Nij − µi)/σi,

where µi is the mean of Nij and σi is the standard deviation of Nij .tiss <- ScaleData(object = tiss)

## [1] "Scaling data matrix"##

|| | 0%||=================================================================| 100%

We select variable genes (those with high standardized log dispersion, given their mean), as they will be moreinformative about differences between cell types in the population.

Concretely, the log dispersion di of a gene i is di = log(vi/mi), where vi is the variance of exp(Nij) and mi

is the mean of exp(Nij). (In other words, mi is 1 plus CPM.) We bin the genes into 20 equal-spaced binsbased on log(mi), then compute the mean and standard deviation of di within each bin. The standardizedlog dispersion d̄i is the dispersion di shifted by the mean and rescaled by the standard deviation of the dk

within its bin. We retain genes with d̄i > 0.5 and log(mi) > 0.1.tiss <- FindVariableGenes(object = tiss, do.plot = TRUE,

x.high.cutoff = Inf, y.cutoff = 0.5, x.low.cutoff = 0.1)

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0610007N19Rik

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1110018G07Rik1110019D14Rik

1110032A04Rik

1110035M17Rik1110038D17Rik1110046J04Rik1110051M20Rik

1110059E24Rik1190002F15Rik

1190002N15Rik1200014J11Rik1300010F03Rik

1500004A13Rik

1500010J02Rik1500031L02Rik

1520402A15Rik

1600010M07Rik

1600016N20Rik1600027N09Rik

1700001G17Rik

1700001K23Rik1700001O22Rik1700001P01Rik

1700003F12Rik

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1700010I14Rik1700012A16Rik1700012B09Rik

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1700029J07Rik1700030C10Rik1700030K09Rik

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2010001M09Rik2010002M12Rik2010002N04Rik

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2310010M20Rik

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2510012J08Rik2510039O18Rik2600006L11Rik

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2810055G20Rik2810403D21Rik2810408A11Rik

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2900002K06Rik

2900005J15Rik2900009J06Rik3110001I22Rik

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3200002M19Rik3300005D01Rik

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9930012K11Rik9930013L23Rik

9930111J21Rik1

9930111J21Rik2A030009H04Rik

A130010J15Rik

A130049A11Rik A1bgA230020J21Rik

A230051G13RikA230056P14RikA230073K19Rik

A230108P19RikA330021E22RikA330041J22Rik

A330049M08Rik

A330050B17Rik

A330069E16RikA3galt2

A430005L14Rik

A430033K04RikA430084P05Rik

A430088P11Rik

A430090L17Rik

A430092G05RikA430093F15Rik

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A430107P09Rik

A4galtA530013C23RikA530032D15Rik

A530054K11Rik

A530064D06Rik

A530072M11RikA530098C11Rik

A530099J19RikA630033H20RikA630089N07Rik

A730008H23Rik

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AA467197

AA543186 AA987161AB124611AF251705

AI118078

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AU040972

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AW549542 AW554918Aaas

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Acot6

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Arhgap30Arhgap39Arhgap4

Arhgap6Arhgap9 Arhgdib

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Bfsp2 BgnBhlha15

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Brd7

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Btbd10

Btbd11 Btbd9Btc

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C030048B08Rik

C130036L24Rik

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C230081A13RikC230096C10RikC2cd4d C330019G07RikC330022C24Rik

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C530028O21Rik C5ar1

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C920021L13Rik

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Capn3Capn5

Capn8

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Car11

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Car13Car15

Car2Car4

Car8Car9 Card10

Card9

Carf Casc3

Casc4

Casc5Cask Casp1

Casp12 Casp4Casp9

Casq1Catsperg1

Cav2

Cbr2Cbx2

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Cc2d2a

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Ccdc109b

Ccdc114

Ccdc120

Ccdc130Ccdc137

Ccdc14

Ccdc142

Ccdc148Ccdc157Ccdc164

Ccdc17Ccdc18

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Ccdc22Ccdc38

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Ccdc68

Ccdc71Ccdc80

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Ccl24Ccl3

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Ccnd1

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Ccnd3Ccndbp1

Ccne1

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Ccr2Ccr3

Ccr4 Ccr6

Ccr7

Ccr8

Ccr9

Ccrl1

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Cd101Cd14

Cd160Cd163

Cd177

Cd180

Cd19

Cd1d2

Cd2

Cd200

Cd200r1Cd200r2

Cd207

Cd209a

Cd209bCd209d Cd22Cd226Cd244

Cd247 Cd24a

Cd27Cd276

Cd28

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Cd300a

Cd300c

Cd300e

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Cd300ld

Cd300lfCd300lg

Cd300lhCd33

Cd34Cd36

Cd37

Cd38Cd3d

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Cd4Cd40

Cd44Cd46

Cd48Cd5

Cd52Cd53

Cd55

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Cd6 Cd68

Cd69Cd7

Cd72

Cd74Cd79aCd79b

Cd80Cd82

Cd83

Cd84Cd86

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Cd9Cd93Cd96Cd97

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Cdk12

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Cdk18 Cdk7

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Cdkl5 Cdkn1cCdkn2aipnlCdkn2b

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Cep97Cerk

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Chst12Chst15

Chst3

Chst7

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CiitaCish

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Clca1 Clcc1

Cldn10

Cldn15Cldn2

Cldn22Cldn4

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Clec10aClec12a Clec14a

Clec16a

Clec1a

Clec1b

Clec2gClec3b

Clec4a3Clec4d

Clec4e

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Clec4g

Clec4nClec5aClec7a

Clec9aClic4Clic5 Clip1Clk3

Clnk

Clspn

Clstn1Clstn3Cma1

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Cnot2Cnot6

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Cntd1

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Col10a1Col12a1

Col15a1

Col16a1Col17a1Col20a1Col23a1

Col25a1Col3a1

Col4a2

Col4a3bp

Col4a4Col5a1

Col5a2

Col6a2Col6a3Col6a6

Colec10

Colec11

Copb1Copg

Coq2

Coro1a

Coro1bCoro1c

Coro7

Cox10

Cox4i2

Cox6a2

Cox6b2

Cox7a1CpeCpeb1

Cpm Cpne2

Cpne5Cpne7

Cpne9 Cpsf3Cpsf3lCpsf4 Cpt2

Cr2

Cramp1lCreb1

Creb5

Crip1

Crispld2Crk

Crlf1Crlf3

Crmp1

Crocc

Crtam

Crtap

Cryba1

Crygn

Crygs

Csad

Csf1rCsf2

Csf2rbCsf2rb2

Csf3r

Csgalnact1Csrp2bpCst3Cst7

Cstad

CtbsCtdp1Ctdspl2

Ctla2b

Ctla4 Ctnna1Ctnnb1Ctnnbip1Ctnnd1Ctps2Ctr9

Ctrl

Ctsa

Ctsc

CtsdCtsk

CtssCtsw

Cul2Cul9

Cux2

Cuzd1

Cwc22Cx3cr1

Cxcl10

Cxcl11 Cxcl12

Cxcl13

Cxcl16

Cxcl2 Cxcl9

Cxcr2

Cxcr3

Cxcr4

Cxcr5

Cxcr6

Cxxc4

Cyb561d1Cyb5d1Cyb5r3

Cybasc3Cybb

Cyfip1Cyfip2Cyp1a1 Cyp1a2

Cyp21a1

Cyp26b1Cyp2a22Cyp2a4

Cyp2a5

Cyp2ab1

Cyp2b9Cyp2c29

Cyp2c37Cyp2c40

Cyp2c69Cyp2d11

Cyp2d12 Cyp2d9

Cyp2e1

Cyp2f2Cyp2g1

Cyp2r1Cyp2s1

Cyp3a44

Cyp46a1Cyp4a10Cyp4a14

Cyp4b1Cyp4f18

Cyp4f39

Cys1Cysltr1 Cytip

Cytl1

Cyyr1D030056L22RikD10Wsu102e

D130017N08Rik

D130040H23RikD130043K22Rik D14Ertd668e D17Wsu92e

D19Wsu162eD230025D16RikD2Ertd750e

D330022K07Rik

D330028D13Rik

D330050G23Rik

D3Ertd254eD430020J02Rik

D5Ertd605e

D630032N06Rik

D630033O11Rik

D630041G03Rik

D6Mm5e

D730005E14Rik

D7Ertd443e

D830046C22Rik D8Ertd82eD930015E06Rik

D930015M05RikDaam2

Dab2Dact1

Dact2

Daf2

Dapp1

Darc

Dars2

Dbil5

Dcaf13Dcaf5 Dcaf8Dcbld1

Dcdc2a

Dchs1Dck

Dclre1b

Dcn

Dcp1b

Dcst1Dct

Dctn5

Dcun1d2Dcun1d3

Ddi1Ddit4l

Ddr1

Ddr2 Ddx10Ddx19bDdx20

Ddx24

Ddx25

Ddx28

Ddx31Ddx39

Ddx39b

Ddx43Ddx47

Ddx51 Ddx52Ddx54Ddx6

Deaf1Defb1

Degs1Degs2 Dennd1c

Dennd2dDennd3Dennd4b

Depdc1a

Depdc5 DeraDffaDffbDfna5

Dfnb59

Dgat1Dgcr14DgkaDgkd

DgkgDhh

DhodhDhrs3

Dhrs9

Dhx38Dhx40

Diap3

Dido1Dip2a

Disp2

Dkc1Dkk3Dlc1

Dleu7

Dlg4

Dlgap5Dll4

Dmap1

Dmrt2Dmrta1

Dnahc10Dnahc17

Dnajb13

Dnajb7

Dnajc21Dnajc27

Dnajc28

Dnajc7Dnajc9Dnase1l1

Dnase1l2 Dnase1l3Dnase2a

Dnd1

Dnm3

Doc2g

Dock10

Dock11

Dock5

Dok2

Dok3Dok4 Dolpp1

Dopey1DosDpep1Dpep2 Dph2

Dpp4Dpp7

Dpp9Dpt

Dpy19l3 DpysDpysl3

Dqx1

Dscaml1

Dscc1

Dscr3DseDstykDtnbp1

Dtwd2Dtx1 Dus1l

Dus3l Dusp1

Dusp18

Dusp2

Dusp3

Dym

Dync2li1Dyx1c1E030003E18Rik

E030010A14Rik

E030011O05RikE030013I19RikE030018B13Rik

E030030I06Rik

E130112N10Rik

E130203B14Rik

E130215H24RikE130303B06RikE130304I02Rik

E130306D19RikE130307A14Rik

E130309D14Rik

E130310I04RikE130317F20RikE230016K23RikE230016M11Rik

E2f3

E2f5E2f6

E2f7

E330009J07RikE330033B04RikE430018J23Rik

E430025E21RikE4f1Eaf1

Eaf2

Ear2Ebf1

Ebf4

Ebi3

Ecm1

EcscrEcsit

Ect2EdaEda2r

EdaraddEdc3Edn1

Ednrb

Efcab1

Efcab4a

Efcab4b

Efcab7Efemp1 Efemp2

Efhb

Efhd2Efna3

Efna5

Efnb2

Efr3b

Egf

Egfem1

Egfl7

Egfl8

EgflamEgln1

Egln3Egr1

Egr2

Ehd2 Ehd3

Ehf

Ehhadh

Eid3

Eif1aEif2c1

Eif2c2

Eif4a3Eif4h

Eif5a2

Elac1

Elane

Elf3

Elmo1Elmo2

Elmod2Elmod3

Elovl3

Elovl7

Elp2

Elp3

Eltd1

Emb

EmcnEme2

Emid1Emilin1

Emilin2

Eml2Emp1

Emr1

Emr4Enc1

Endod1Eng

Engase

EnkurEno3

Enox2 EnpepEnpp4

Enpp6Enthd1

Entpd1

Entpd6

Eomes

Ep400 Epas1Epb4.1l3

Epb4.1l4a

Epb4.9

Epha4Ephb2

Ephb3

Ephb4

Ephb6Epm2a

Epn2Eral1

Erbb4

Ercc6l

Erich1

Ermn

Esam

Esm1

Espl1

Esrrg Esyt2Ets1

Etv3Evc2 Evi2a

Evi2bEvi5l

Exd1

Exoc2Exoc3Exoc3l

Exoc8Exog

Expi

Extl1Eya2 Eya3Ezh2

EzrF13a1

F2rl1

F2rl2F3

F420014N23RikF630043A04Rik

F630111L10RikF8Fabp3 Fabp4

Fads6

Faim3

Fam102aFam102b Fam105a

Fam105bFam107bFam109bFam110c Fam115aFam117a

Fam118aFam118bFam122b

Fam123a

Fam124aFam129aFam129c

Fam131aFam132b

Fam134cFam151bFam154b

Fam160a1 Fam160b2

Fam161aFam161b

Fam164a

Fam164c

Fam166a

Fam167b

Fam169a

Fam171a1

Fam171b

Fam174b

Fam178b

Fam184a

Fam185a

Fam189a1 Fam189b

Fam193aFam198b

Fam19a3

Fam20bFam20c

Fam23aFam26e

Fam3b

Fam40a

Fam40b Fam49a

Fam54a

Fam55d

Fam59a

Fam63aFam63bFam65b

Fam65c

Fam69b

Fam70aFam71e1Fam72a

Fam73bFam76bFam78a

Fam83d

Fam83fFam83g

Fam84b

Fam92b

Fanca

Fancb

Fancc Far1

Far2

Farp1 Fars2Farsa

Farsb

Fas

Fasl

Fastkd5 Fat4Fbln2

Fbln5 Fbxl15

Fbxl16

Fbxl18

Fbxl19Fbxl2

Fbxl21Fbxl22

Fbxl8

Fbxo11Fbxo17Fbxo2 Fbxo21

Fbxo27

Fbxo28

Fbxo32Fbxo34

Fbxo44

Fbxo5

Fbxw17 Fbxw2

Fcer1g

Fcer2a

Fcgr1 Fcgr2bFcgr3Fcgr4Fcho1

Fchsd1 Fchsd2

Fcna

Fcrl1Fcrla

Fcrlb Fem1b

Fem1cFen1

Fermt3

Fert2Fes

FevFfar2Fgd1

Fgd2 Fgd6

Fgf12Fgf13

Fgf7

Fgfbp3Fgfr1op

FggFgl2

FgrFhad1 Fhdc1

Fhl1

Fhl2

Fhl3Fhod1

Fhod3 FicdFignl1

Fitm2

Fkbp10

Fkbp9FlcnFlii

Flna

Flnb

FlncFlot1

Flrt1Flrt2

Flrt3

Flt1Flywch1Fmn2

Fmo3

Fndc5

Fndc7 Fndc8Folr1

Folr2

Folr4 FosFoxa1

Foxa2

Foxd2Foxd4Foxe1Foxf1a

Foxj3

Foxk1Foxm1 Foxo1

Foxo3 Foxp1

Foxp2Foxp3

Foxq1

Foxr1Foxred1

Foxred2

Foxs1Fpr1

Fpr2

Fras1 Frmd4aFrmd6

Frmd7

Frmd8

Frs3

FrylFrzbFsd1l

Fsd2

Fsip1

Fst

Fstl1Fstl3Ftsj2

Ftsjd2Fuca2Fut4

Fut8

Fv1

Fxyd2

Fxyd3

Fxyd5FybFyco1

FynFzd1

Fzd10Fzd3

Fzd9

Fzr1G2e3

G6pdx

Gaa

Gab1

Gab2Gab3

Gabbr1

Gabbr2 Gadd45a

Gadd45bGal3st1

Gal3st4Gale

Galk1Galk2

GalmGalnsGalnt10

Galnt12Galnt6Galnt7

Galnt9

Galntl2

Galntl4GapdhsGapt

Gas2l3

Gas6Gas7

Gas8Gata3

Gata4

GatmGba

Gba2

Gbf1

Gbgt1

Gbp1 Gbp2Gbp3Gbp4Gbp5Gbp6

Gbp7Gbp8Gbp9 Gcap14Gcc2

Gck

Gcm2

Gcnt2Gcnt3

Gcnt7

GdaGdf10

Gdf11

Gdf2

Gdf3Gdf9

Gdpd1Gem

Gemin5Gemin8

Gen1Gfm2Gfpt1

Gfpt2

Gfra2

Gga2

Ggt5

Ggt6

Ghdc

Gimap1

Gimap3

Gimap5Gimap6Gimap7Gins3 Gipc1

Gipc2

Gipc3Gipr

Gja1

Gja4Gja5

Gjc1Gjc3Gk5

Gla Glb1

Gli1

Glipr2 Gls2Glt1d1 Gltpd1

GlulGm10007

Gm10012Gm10069

Gm10190 Gm10248

Gm10336

Gm10345

Gm10373Gm10433

Gm10451

Gm10509Gm10556

Gm106Gm10638

Gm10767

Gm10790

Gm10791

Gm10804Gm10872

Gm10941

Gm11201

Gm11346

Gm11428Gm11435

Gm11648Gm11992

Gm12185

Gm12216

Gm12238

Gm12250

Gm12253Gm12359

Gm12657

Gm129Gm13139

Gm13238

Gm13251

Gm1337Gm13375Gm13476

Gm13483Gm13807

Gm13845

Gm14023

Gm14047Gm14057

Gm14139

Gm14295Gm14306 Gm14326Gm14327Gm14378

Gm14393 Gm14446Gm14718

Gm14827

Gm14872Gm15348

Gm15441Gm15471

Gm15545

Gm156Gm1564Gm15663

Gm15706Gm15708Gm15760

Gm15787

Gm15880

Gm15915

Gm16119

Gm16516

Gm16523

Gm166 Gm16675

Gm16701

Gm16702

Gm1673

Gm16793

Gm16880

Gm16973

Gm16998Gm17359Gm17455

Gm17762Gm17769Gm18756Gm1943

Gm19461

Gm19557

Gm19705

Gm19710Gm2011

Gm20199Gm20257Gm2027

Gm20604Gm20605

Gm2061

Gm2518Gm3336Gm3435

Gm4532

Gm4636

Gm4787Gm4841Gm4890

Gm4902

Gm4980

Gm5

Gm5069

Gm5086

Gm5113

Gm5150

Gm527

Gm5431

Gm5465Gm5468

Gm5512

Gm5535Gm5544

Gm5595Gm5643

Gm5820Gm6034

Gm6251

Gm6277

Gm6377Gm6402

Gm6568

Gm684Gm6904

Gm7854

Gm826

Gm8817Gm8979

Gm9047Gm9079

Gm9159

Gm9199

Gm960Gm962

Gm9733Gm9833Gm9895Gm9920

Gm9958Gm9992

Gmfb

Gml

Gmpr

Gna11Gna14

Gna15

Gnai1Gnao1

Gnaq

Gnb1l

Gngt1

Gnl1

Gnl3 Gnpda1Gnpda2

Gnrh1Golga3

Golph3lGon4l

Gopc

Gorab

Gosr1Gp1ba

Gp1bb

Gp49a

Gpat2Gpbar1

Gpc1Gpc4Gpd2

Gphb5

Gpi1

Gpihbp1

GpkowGpm6b Gpn1Gpn3

Gpnmb

Gpr107Gpr108

Gpr114

Gpr116

Gpr126Gpr128

Gpr133 Gpr137b

Gpr141Gpr143

Gpr150

Gpr153

Gpr17

Gpr171

Gpr174

Gpr18

Gpr180Gpr182

Gpr183Gpr20

Gpr39Gpr4Gpr55

Gpr64

Gpr68

Gpr82

Gpr84

Gpr97Gprc5aGprc5b

Gprin3Gpsm1Gpsm3

Gpt2Gpx3Gpx6

Gpx8

Gramd1aGramd4 Grap

Grap2

Grb10Greb1lGrem2

Grhl1

Grhl3

Gria3Grid1

Grik5

Grin2d

Grin3b

Grk5

Grlf1

Grm8Grn

Grwd1

Gsdmc2

Gsdmd

Gsg1

Gsg2GsnGstcd

Gstm3 Gstp1Gstt3Gtdc1 Gtf2h2

Gtf3c1

Gtf3c3

Gtf3c4Gtf3c5

Gtpbp2Guca2aGucy1a3

Gucy2c

Gulo

Gyk

Gyltl1b

GypcGys1

Gys2

Gzma

Gzmb

GzmcGzmkGzmm

H1foo

H2−Aa

H2−Ab1H2−DMa

H2−DMb1

H2−DMb2

H2−Ea−ps

H2−Eb1

H2−Eb2

H2−M3H2−Oa

H2−Ob

H2−Q4 H2−Q6

H2−Q7H2−T24

H2afy2

H47

H60b

Hace1 HampHamp2Hand2

Hao2

Hap1 Hars2Has1

Has3Haus4

Haus5 Haus8

Havcr2

Hbb−b1Hbs1l

Hcfc1

Hck

Hcls1

Hcn3Hcrtr2Hdac1

Hdac10

Hdac2Hdac3Hdac8

Hdc

Hdx Heatr2Heatr5bHeatr7b1

Heatr8Hebp2

Hectd3Hecw2Helb

HellsHelq

Helz

Hepacam2

HephHerc1 HexaHexim1

Hey1Heyl

Hfe

Hfm1HhipHic2

Hif1anHif3a Hilpda

Hinfp

Hip1Hip1r

Hipk1

Hist1h1a

Hist1h1b

Hist1h1cHist1h2ac

Hist1h2ad

Hist1h2ahHist1h2aiHist1h2ak

Hist1h2an

Hist1h2ao

Hist1h2bb

Hist1h2bg

Hist1h2bjHist1h2bn

Hist1h3b

Hist1h3cHist1h3d

Hist1h3f

Hist1h4aHist1h4b

Hist1h4i

Hist1h4mHist1h4nHist2h2bbHist2h4Hist3h2ba

Hk3

Hmbox1 HmbsHmg20a

Hmga2−ps1

Hmgn3 Hmgxb4

Hmha1

Hmox1

Hn1Hn1lHnf1b

Hnrnpa1

HnrnpmHoga1Hook3

Hoxa1

Hoxa7Hoxa9

Hoxb4Hoxb6Hoxb7

HpHpcal1

Hpdl

HpgdHpgds

Hps1Hps5Hps6Hpx

Hrh1

Hs2st1

Hs3st1Hs3st6

Hsd17b6Hsd17b7Hsdl1

Hsf2bp

Hsf4

Hsf5

Hsh2dHspa12aHspa12b

Hspa1bHspa1l

Hspa4l

Hspb2

Hspb9 Hspbap1

Htatsf1

Htr2b

Htra1Htra3

Htra4Htt

HunkHus1

Hvcn1

Hyal1Hyal2

Hyal3

Hyal5

I830012O16RikI830077J02Rik IbtkIca1Ica1l

Icam1

Icam2Icam4 Icos Id3Id4Idh3gIduaIffo2

Ifi30

Ifi35Ifi44 Ifi47

Ifit1

Ifit2

Ifit3

Ifitm1

Ifitm5

Ifitm6

Ifng

Ifngr1Ift140

Igf2

Igf2as

Igf2bp3

Igf2rIgfbp5Igfbp6

Igfbp7

Igsf10

Igsf3

Igsf6Igsf9Igtp

Ihh Ikbkg

Ikzf4

Il10

Il10raIl10rb

Il12a

Il12rb1Il13ra2

Il16

Il17aIl17c

Il17f

Il17rd

Il18bpIl18rap

Il1a

Il1b

Il1f9

Il1rl2

Il1rn

Il2Il20rb Il21r

Il22ra1

Il27ra

Il2rb

Il2rgIl31ra

Il34

Il4

Il4ra

Il5ra

Il6stIl7r

Ilvbl

Impg2 Ing1Ing3Inpp1Inpp4b

Inpp5eInpp5j Inpp5k

InsrInts9 Ipo11

Ipo4Ipo7Iqcg

Iqck

Iqgap1

Iqgap3

Irak4Irf1

Irf4Irf5 Irf7

Irf8

Irf9

Irg1

Irgm1

Irgq

Islr

Islr2

IspdIsyna1Itch Itfg1Itga1

Itga4

Itga9

ItgaeItgal

Itgam

ItgaxItgb1bp1

Itgb2Itgb3

Itgb4

Itgb5Itgb7

ItkItm2a

ItpkaItpkbItpkcItpr3

Ivl

Jag1

Jakmip1 Jam2

Jmjd1cJmjd4Jmjd5

Jmjd7

Jph3

JrkJun

Junb

KarsKatnb1

Kazald1

Kbtbd4

Kbtbd7

Kbtbd8

Kcnab1

Kcnc1

Kcne3

Kcng2Kcnh3Kcnh4

Kcnj10Kcnj15Kcnj2

Kcnj8Kcnj9

Kcnk1Kcnk10

Kcnk3

Kcnk7Kcnmb1Kcnmb2

Kcnq1ot1Kcnq5

Kcns2

Kcns3Kcnt2Kcp

Kctd10

Kctd11Kctd12

Kctd12b

Kctd14

Kctd15Kctd18

Kctd21

Kctd4

Kctd7

Kdelc1

Kdelr3 Kdm3a

Kdm4dKdm5b

Kdm6a

KdrKeap1

Khdc1a

Kif15

Kif18a Kif19a

Kif20a Kif21bKif22

Kif23

Kif24

Kif26a

Kif3cKif4Kif5bKifc1

Kifc2

Kirrel3

Kiss1Kiss1r

Kit

Klb

Klc1

Klc2

Klc3

Klf1

Klf11Klf4Klf5

Klf6

Klf8

Klhdc1Klhdc8a

Klhl10

Klhl11 Klhl13

Klhl14

Klhl15 Klhl18 Klhl20Klhl22

Klhl23

Klhl24

Klhl28Klhl32 Klhl36Klhl6

Klk1

Klk1b27

Klk9

Klra1

Klra17

Klra18

Klra2

Klra23Klra3

Klra5Klra7

Klra8

Klra9

Klraq1Klrb1a

Klrb1b

Klrb1c

Klrc1Klrc2 Klrd1

Klre1

Klrg1

Klri2

Klrk1Kptn

Kremen2

Kri1

Krt14Krt17Krt19

Krt20Krt7

Krt80Krtap9−1

Krtcap3L3mbtl2LOC100038947

LOC100503280LOC100503496

LOC100504703LOC100642166

LOC100859962LOC106740

LOC330599

LOC622167

LOC626693

Lag3

Lair1

Lama1Lama4

Lama5Lamb1 Lamb2

Lamb3Lancl3

Laptm5

Large Lars2Las1l

Lass3

Lass4Lass5LatLat2Lax1

Lca5

Lck

Lcn12Lcn2

Lcn4 Lcp1Ldb2Ldhb

Ldlrap1

Ldoc1l

Lect1

Lef1 Lefty1

Lenep

Leng9 Leo1LeprLepre1

Leprel1Leprel2 Leprot

Lgals2 Lgals3

Lgals3bpLgmn

Lhfp

Lhfpl2Lifr

Lig1Lig4 Lilra5

Lilra6

Lilrb3Lilrb4

Limch1 Limd2Lime1

Limk2

Lins

Lipt1Lix1

Lix1lLmbr1l Lmbrd2

Lmcd1

Lmf1LmlnLmo1

Lnx1Lonp1Lor

Loxl1

Loxl3

Lpar2

Lpar4Lpar5

Lpar6Lpcat2Lpin3

LplLpxnLrat

Lrch1

Lrch2

Lrdd

Lrfn4

Lrg1Lrit2

LrmpLrp11Lrp2Lrp8

Lrr1Lrrc10b

Lrrc14

Lrrc19

Lrrc2

Lrrc20

Lrrc25

Lrrc27

Lrrc32

Lrrc33

Lrrc4

Lrrc42Lrrc46

Lrrc48

Lrrc49

Lrrc56

Lrriq3

Lrrk2

Lrtm1

Lrwd1

Lsamp

Lsm14aLsm6

Lsp1

LssLta

LtbLtb4r1

Ltb4r2

Ltbp1

Ltbp4Luc7l2

Lum Ly6aLy6c1

Ly6c2

Ly6dLy6f

Ly6g5b

Ly6g6d Ly6iLy6k

Ly86

Ly9Lyn

Lynx1

Lypd3

Lypd6b

Lysmd3

Lyst

Lyve1Lyz1

Lyz2

Mab21l2 Macf1Mad1l1

Madd

Maea

Maff

MafkMag Maged2

Magi2

Mal Mal2Malt1

Mamdc2

Maml3Mamld1

Man2a1Man2b1ManeaMaoaMap3k14

Map3k15

Map3k3Map3k6

Map4k1Map4k4

Map4k5Mapk11

Mapk12

Mapk13

Mapk4 Mapk7Mapk8ip3

Mapkapk3

March1

March9

Marco

Mark3

Mars2

Marveld2Marveld3

Mast3Mat2bMatk

Matn2 Matr3Mau2

Mavs

Mbnl3

Mboat1Mboat4

Mboat7McamMcart1McatMccc1

Mcl1Mcm2

Mcm3Mcm3ap

Mcm5

Mcm6

Mcm7Mcm8

Mcoln3

Mcph1Mctp1Mdfi

Mdfic

Mdga1

Mdk

Mdm1

Med20Med27Med9 Mef2c

MefvMeg3

Megf8 Meis1Meis3

Melk

Memo1Men1 MertkMesdc2

MetrnlMettl15Mettl2Mettl21aMettl3

Mex3b

Mfap3

Mfap4

Mfap5Mfge8

MfngMfsd10

Mfsd12

Mfsd2b

Mfsd3Mfsd7a Mfsd7b

Mfsd7c

Mfsd9 Mgat1Mgat2Mgat4a

Mgst1

Mia1

Mib2

Mical2Micalcl

Mier2 Mier3Mif4gd

MiipMipol1

Mir1191Mir1199Mir132

Mir133a−1Mir146

Mir16−1

Mir181b−2

Mir1843Mir1894

Mir1904Mir1932

Mir1949Mir1956

Mir199a−1Mir1b

Mir24−2Mir26a−1

Mir3061

Mir30bMir30e

Mir325Mir326

Mir339Mir340

Mir3470a

Mir3471−1Mir3473

Mir466iMir5098Mir5135

Mir684−1

Mir695

Mir744Mirlet7f−1Mis12Mis18bp1 Mki67

Mknk1

Mkrn3Mks1

Mlf1Mlkl

Mll5Mllt3 Mllt6

Mlph

Mlxipl

MmabMmadhcMmgt2

Mmp11

Mmp12Mmp13

Mmp14Mmp24

Mmp27

Mmp28

Mmp3

Mmp8

Mmp9

Mmrn2Mms22l

Mns1Mob3a

Mob3c

MocosMogat1

Morc4Morn1

Morn5

Mov10

Mpeg1

Mpp2Mpp4

Mpp7

Mpped2

Mpv17Mpzl1

Mpzl3Mrgpra2b

Mrgpre

Mrps7

Mrrf

Mrvi1

Ms4a1

Ms4a15Ms4a4b

Ms4a4cMs4a4d

Ms4a6bMs4a6cMs4a6d

Ms4a8aMsh2

Msh4

Msh5 Msh6Msl1 Msn

Msr1

Mst1r

Msto1

Msx1 Mtap1s

Mtap4

Mtap9

Mtbp

Mtch1

Mterf

Mterfd2Mthfsd

Mtl5

Mtm1Mtmr11

Mtmr12

Mtmr14Mtnr1a

MtrMtrr

Mtus2Muc1Muc13

Muc6 Mum1

Mum1l1

Mup10

Mup14Mup20

Mup3

Mup6

Mup7Mup9

Mus81MuskMutyh

Mxd1

Mxd3Mxra8Myadm

Mybbp1a

Mybl1Mybpc2

Myc

Mycbpap

Mycn

Myg1

Myh11Myh7bMyl6b

Myl7 Myl9 MylipMylpf Myo10Myo18a

Myo1c

Myo1eMyo1f

Myo1g

Myo7a

Myo7bMyo9aMyo9bMyom1

Myom3

Myoz1

Myst1Myst3

Mzf1

N28178 N4bp1

N4bp3Naaa

Naalad2

Nacc1Nadk

Nagpa

Naip1

Naip6

Nanos1

NanpNans

Nap1l3

NapbNapepld

Naprt1

Napsa

NarfNarg2Nat14

Nav3

Nbas

Nbl1

Ncam1

Ncam2

Ncapg

Ncaph Ncaph2

Ncbp1

Ncdn

Ncf1Ncf2Ncf4

Nck2Nckap1l

Ncoa6

Ncr1

Ndc80 Nde1

Ndn

Ndor1

Ndrg1

Ndufa4l2

Necap2

Nedd9Nefh Neil1

Neil2

Neil3

Nek2Nek3

Nek8NepnNeto2

Neu2Neurl1a

Neurl1b

Neurl3

Nf2Nfam1Nfasc

Nfatc1Nfatc3Nfe2 NfkbiaNfkbid

Nfrkb Nfx1Nfya

Ngfr

Ngly1Nhlrc1Nhsl2Niacr1

Nid1Nid2

Nipal4

NkaplNkd2

Nkg7

Nkx2−6Nlgn2

Nlgn3

Nlrc3Nlrc4

Nlrp1a

Nlrp1b

Nlrp1c−psNmnat2

Nnat

Noa1 Noc4l

Nod2Nodal

Nol3

Nomo1 NonoNop16

Nop58

Nos2Notch3

Noxo1

Npb

Npdc1

Npff

Nphp1

Nphp4

Nploc4Nppa

Nprl2

Nqo1

Nr1h5

Nr1i3

NraddNrap NrasNrbp1Nrf1

Nrg1

Nrg2

Nrip1

Nrip2 Nrm

Nron

Nrp1

Nrtn

Nrxn1

Nrxn2Nsd1

Nsl1

Nsmaf

Nsun4Nsun5

Nt5c2

Nt5dc3

Nt5e

Ntm Ntn4Ntrk2

Nuak2Nubp2

Nudcd1

Nudcd3

Nudt15

Nudt16l1

Numbl

Nup107 Nup153

Nup210Nup210l

Nup35Nup43 Nup62

Nup62cl

Nup85Nup88Nup93Nupl1

Nupl2

Nusap1

NvlO3far1

Oas1b

Oas1c

Oas1gOas1h

Oas3

Oasl1

Oasl2OatOaz3

Obfc1

Obscn

Obsl1

Ocstamp

Odf3l1Odz1

Ogn

Oit1Oit3

Olfm1Olfm2Olfm3

Olfml1

Olfml3Olfr1034

Olfr1393

Olfr1396

Olfr164

Olfr455

Olfr56Olfr750

Olfr76

Olig1

Olr1

Omg

Omp

Opa3

Opn1sw

Opn3

Optc

Orai3Orc2 Orm2

Osbpl10

Osbpl2

Osbpl5Osbpl7

Osbpl8Osgin1OsmOstb

Otos

Otud3 Otud7b

Ovgp1Ovol1

Oxct1

P2rx1P2rx2

P2ry10P2ry12P2ry13P2ry14P2ry6

Padi2

Padi4

Pak1ip1

Pak6

Palm3Pam

Pamr1

Pan2Pank2Papln

Paqr3

Paqr4Paqr5Paqr8

Pard6g

Parp10ParvgPatl1

Pax5Pax6Paxip1

Pbk

Pbld2Pbx4

Pbxip1

Pcbp3

PccaPcdh1

Pcdh12Pcdh15Pcdha11Pcdhb10

Pcdhb11Pcdhb12Pcdhb13

Pcdhb14Pcdhb17

Pcdhb20Pcdhb21

Pcdhb22

Pcdhb4

Pcdhb5Pcdhga1Pcdhga11

Pcdhga2

Pcdhga3Pcdhga6

Pcdhga7

Pcdhga8Pcdhgb5

Pcdhgb8

Pcdhgc4

Pcgf2

Pcid2

Pcif1Pck2

Pclo Pcolce2Pcsk4Pdcd1

Pdcd11Pdcd1lg2 Pddc1Pde10aPde1a

Pde1b

Pde1cPde2a

Pde4aPde4b

Pde4d

Pde4dipPde5a

Pde6cPde6g

Pde8bPdgfb

Pdgfra

PdgfrlPdk3

Pdlim3 Pdlim4

Pdp1

Pdpn Pdxp

Pdzd4

Pdzrn3 Pea15aPear1

Pepd

Pes1

Pex5Pfkfb4

Pfkp

Pgam2

Pgam5

Pgap1Pgap2Pgap3

Pgd

Pgf

Pggt1b

Pglyrp1

Pgm1 Pgm2Pgm3 Pgpep1Pgs1

Phactr1

Phc1

Phf10Phf11

Phf19 Phf21a

Phf21b

Phf5a

Phf7Phf8

Phgdh

Phgr1

Phka1Phldb2Phlpp1

Phrf1Phxr4

Pias4

Pigh Pigk

Pigm

PigqPigs

Pigu

Pigv

Pigz

Pih1d2Pik3ca

Pik3cdPik3cg

Pik3ip1Pik3r3

Pik3r5

PilraPilrb1Pilrb2

Pim2

Pion

Pip4k2c

Pip5k1b

Pira2

Pisd−ps3

Pitpna

Pitpnc1Pitpnm1

Piwil2

Pkd1l2Pkd1l3

Pkd2l2

Pkdcc Pkib Pkm2Pknox2

Pkp3

Pla1aPla2g15

Pla2g4a

Pla2g4cPla2g4dPla2g4f

Pla2g6Pla2g7

Pla2r1

Plac8

Plag1

Plagl1

PlatPlau Plbd1

Plcb2

Plcd3Plcd4

Plcg2

Plcl1

Plcxd1

Pld2Pld3

Pld4

Pld6

Pldi

Plec

PlekPlek2

Plekha2

Plekha4

Plekha7

Plekhb1

Plekhb2

Plekhf1Plekhg5

Plekhh1

Plekhh3Plekhm1Plekhm3Plin4

Plk1

Plk2

Plk3Plk4

PlnPlod2

Plrg1Pls1

Plscr4

Pltp

Plvap

Plxdc1

Plxna3

Plxnc1

Pmaip1

Pmel

Pmp22

PmpcbPnck

Pnkp

Pnma1

Pnpla5 Poc1aPoc5

Podn

Podnl1 Podxl

PogkPoglut1

Pogz

Pola2Pold1Pold2

PolePolh

PollPolm

Polq

Polr1b

Polr2k

Pomgnt1Pomt2

Pop1 PorPot1a

Pou2af1Pou4f1

Pou6f1Ppan

Ppap2aPpap2bPpapdc3

Ppara

PpatPpic

Ppil1Ppil6

Ppip5k1

Ppm1dPpm1e Ppm1j

Ppme1Ppp1r13b

Ppp1r13l

Ppp1r36

Ppp1r3a

Ppp1r3dPpp1r3e

Ppp1r3f

Ppp1r9bPpp2r3a

Ppp2r3d

Ppp2r5b Ppp2r5cPpp2r5d

Ppp3cb

Ppp3ccPpp4r1l−ps Ppt1Pqlc2Pqlc3Pramef8

Prc1

Prdm11Prdm15Prdm16 Prelp

Prf1

Prickle1Prickle2

Prkab2Prkag1

Prkar1b

Prkar2b

Prkca

Prkcb

Prkcc

PrkcdPrkcdbp Prkx

Prl2c3

Prmt10Prmt2Prmt3Prmt5Prmt6

Prmt7

Proca1Procr

Prok1Prom1 Pros1

Prosapip1

Prox2 Prpf31Prps1l1Prpsap1

Prr18Prr22

Prr3 Prr5l Prrc2b

Prrg4

Prrt1

Prrt3

Prss2

Prss30

Prss48Prss53

Prune2 PsapPsat1Psd4

Psen1Psma8 Psmd3Psmd9

Psmg3Pstpip1

PtafrPtbp2Ptch1

Ptdss1

Ptdss2

Ptger3

Ptges

PtgfrnPtgir

Ptgis Ptgs1

Pth1rPtk6

Ptp4a3

Ptpdc1

Ptplad2Ptpn1

Ptpn11Ptpn13

Ptpn14Ptpn4

Ptpn6

Ptpn7Ptpn9 Ptprb

PtprcPtprcapPtprePtprm

Ptprr

Ptprs

PtprtPtpru

Ptprv

Ptprz1

Ptrh1

Purg

Pus3Pvrl4

Pwp2Pwwp2b Pxdn

Pycr1

Pydc3PygbPyglPygm

Pygo2Pyhin1

PyyQpctlQser1

Qtrt1

R74862 Rab11fip1Rab11fip5

Rab19

Rab23Rab25

Rab31Rab32

Rab38Rab39 Rab3bRab3gap1

Rab3il1

Rab3ip

Rab40b

Rab40cRab44

Rab6bRab7l1

Rabepk

Rac2Rac3

Rad21Rad50

Rad51Rad51ap1

Rad51cRad51l3Rad54bRad54l Rae1

Raet1a Raf1Ralgapa2

Ralgps1

Ralgps2RalyRamp1 Ramp2

Ramp3Ranbp10

Ranbp9Rangap1

Rap1gapRap1gap2

Rap1gds1Rapgef1

Rapgef3Rapgef4Rapgef5

RapsnRarb

RarsRars2

Rasa3

Rasal1

Rasal3 Rasd1

Rasgef1aRasgrf1Rasgrp1

Rasgrp4 Rasip1

Rasl12Rasl2−9−ps

Rassf1

Rassf4

Rassf5Raver1−fdx1l

Rb1

Rbak

Rbck1

Rbl1 Rbm10

Rbm19Rbm20

Rbm44Rbm46

Rbm4bRbm5

Rbms1

Rbms2

RbmxRcan3Rcbtb2

Rcc1Rcn1

Rcn2Rcn3Rcor3 Rcsd1Rd3

RdbpRdh1

Rdh12Rdh18−ps

Rec8

Reck

Recql4

Reep1 Reep4

Reg4

Relb

RelnRelt Renbp

Rep15

Retnla

Retnlg

Rev3lRexo4

Rfc3

Rfc5

Rfpl4

Rftn1

Rfx1

Rfx2

Rfx3Rfx4

Rg9mtd2

Rgag4

Rgs1Rgs12

Rgs14

Rgs18

Rgs19Rgs2

Rgs4

Rgs5

Rhbdd3Rhbdf1

Rhbdf2Rhbdl1

Rhbdl3

Rhd

Rhebl1

Rhof

RhogRhoh

Rhox5Rian

Ribc1

Ric3

Ric8Ric8b

Riiad1

RimklaRims2

Rims3Rin1

Rin2

Rin3 Ripk1Ripk2

Ripk3RlfRln3

Rltpr

Rmnd5bRnase10

Rnase13

Rnase6Rnd2Rnd3

Rnf113a2Rnf121Rnf122

Rnf123

Rnf135Rnf14Rnf144a

Rnf145

Rnf146

Rnf157

Rnf166Rnf169

Rnf208

Rnf215

Rnf217Rnf220

Rnf4Rnf41Rngtt

Rnh1

Rnpc3Rnu11Rnu12

Robo2Robo3 Robo4

RogdiRor1 Rorc

Rp2h Rpa1Rpa2Rpf2Rpgrip1Rpgrip1l

Rph3alRpl31−ps12Rpl39l

Rpp14Rpp40

Rpph1

Rprd1a

Rps15a−ps4Rps19−ps3

Rps6ka1Rps6ka2

Rps6kc1

Rps6kl1

Rqcd1Rrad

Rraga

Rragd

Rrm1Rrm2

Rrp1bRrp7a

Rrp9Rsad2

Rsph1

Rsph4aRsph9Rspo3

Rsrc1

Rtel1

Rtn1

Rtn2 Rtn4 Rtp4

Rufy4

Rundc1

Rundc3b

Runx2Rxrg

S100a11S100a3

S100a4

S100a6

S100a8S100a9

S100b

S100pbp

S1pr3

S1pr4

S1pr5Saa1

Saa2Safb

Sag

Samd12Samd5Samhd1

Samsn1

Sarm1Sars

Sart3Sash3

Sat1Satb1

Sbf2

Sbk2Sbsn

Scamp2

Scamp4 Scarb2

Scarf1

Scarf2Scarna2Scarna3aScarna3bSccpdh

Scd1Scd2

Scd4

Scfd2Scg2

Scg3Schip1

Sclt1Scn3aScn3b

Scn4aScn8a Sdc3

Sdcbp2 Sdccag8Sdpr

Sebox

Sec14l4

Sec16b

Sec31a

Sectm1a

Sectm1b

Sel1l3Selenbp2

Sell

Selp

Selplg

Sema4aSema4d

Sema4f

Sema5b

Sema6aSenp5Senp8Sepn1

Sept3

Sept4

Sept6Sept8Serac1

SerhlSerinc4

Serinc5

Serp2 Serpina3cSerpina3f

Serpina3g

Serpina3hSerpina3i

Serpina9

Serpinb10−ps

Serpinb1a

Serpinb6aSerpinb6b

Serpinb7

Serpinb8Serpinb9

Serpinb9bSerpine1Serpine3Serpini1

Sertad3

Sertad4

Sesn1Sestd1Setbp1

Setd1a Setd2Setd5

Setdb1Sf3a1

Sf3b3

Sfmbt1Sfpi1

Sftpa1Sftpb

SftpcSftpd Sfxn2

Sfxn3Sfxn4

Sgca

SgcbSgce

Sgip1

Sgk1Sgms1

Sgol2Sgpl1

Sgpp2

Sgsh

SgtbSh2b3

Sh2d2a

Sh2d3c

Sh2d5

Sh2d7

Sh3bgr

Sh3bgrl3Sh3bp2Sh3bp5lSh3gl3

Sh3kbp1Sh3tc1Sh3tc2

Shank1

Shank2Shc1

Shc4

Shcbp1SheShf

Shisa4

Shisa5Shisa9

Shroom1

Shroom2Shroom4Siae

Sidt1

SigirrSiglec1

Siglecg

Siglech

Sipa1Sirpa

Sirpb1a

Sirpb1bSirt5

Sit1

Skap1Skint3 Sla

Slain1Slamf1

Slamf6

Slamf7Slamf8

Slamf9

Slc10a3

Slc10a6

Slc10a7

Slc11a1

Slc11a2Slc12a2

Slc12a4Slc12a5Slc12a8

Slc13a5

Slc14a1Slc15a2 Slc15a3

Slc15a4Slc16a3

Slc16a9Slc17a9Slc18a1Slc18a2Slc19a1

Slc1a2

Slc1a4

Slc1a5Slc20a2

Slc22a13b

Slc22a27

Slc22a29

Slc22a3

Slc23a3

Slc24a5

Slc25a18

Slc25a19Slc25a26

Slc25a31

Slc25a34 Slc25a35Slc25a36Slc25a43

Slc25a44Slc26a10Slc26a2

Slc26a6Slc27a1

Slc27a3

Slc27a6

Slc28a1Slc29a1

Slc29a2

Slc29a3Slc29a4 Slc2a3

Slc2a6

Slc2a8

Slc30a3Slc30a6 Slc31a2Slc34a2

Slc35a2 Slc35a4

Slc35c2

Slc35f1

Slc36a4Slc37a2Slc38a1

Slc39a11

Slc39a12

Slc39a2

Slc39a5 Slc39a6Slc39a9 Slc3a2

Slc40a1

Slc41a3Slc43a2

Slc43a3

Slc44a1Slc44a2Slc44a3

Slc45a4Slc46a1Slc4a2

Slc4a7Slc4a8Slc52a3

Slc5a11

Slc5a4b

Slc6a1Slc6a19Slc6a20b

Slc6a6Slc6a8

Slc7a1

Slc7a10Slc7a11

Slc7a15Slc7a4

Slc7a6osSlc7a7Slc8a1 Slc9a1 Slc9a3r2

Slc9a5

Slc9a7

Slc9a9

Slco2a1Slco3a1

Slco4a1

Slfn1Slfn10−ps

Slfn2Slfn4Slfn9

Slpi

Slx4

Smad3

Smarca2

Smarca5−ps

Smarcal1Smarcd3Smc1b Smc2

Smc4Smchd1Smg1

Smoc2

SmoxSmpd3

Smpdl3aSmpdl3b

Smtn Smu1

Smug1Smurf1

Snai3Sned1Snhg11 Snhg4

Snhg9

Snora20

Snora30Snora65Snora70Snora78

Snora7aSnora81

Snord118

Snord15aSnord17Snord2Snord49a

Snord52Snord55

Snord8Snord87Snord89Snord92

SnrkSnrnp200Snx16 Snx17Snx19

Snx20

Snx27

Snx30Snx6Snx8Soat1

Sod3Sorl1SostSox12

Sox15

Sox18

Sox5

Sox6 Sox7Sp100

Sp3

Sp5Spaca1Spag4Spag5

Spag9 Sparc

Spata21

Spata22Spata24 Spata7Spdya

Specc1

Specc1lSpg11

Spib

Spic

Spice1

Spink3

Spint1Spire1

Spire2

SpnSpnb2

Spnb4

Spns1

Spns3Spo11

Spock2Spon1 Spp1

SprnSprr1a

Spry4

Sptlc2

Srd5a3 Srgn

Srl

Srp54b

Srpk3

Srpx2

Srsf2Ssbp2

Ssfa2SspnSspo

Sstr1

Sstr2

Sstr4

St14 St3gal6

St6galnac2St6galnac4

St7

St8sia3

St8sia4

St8sia6

Stab1 Stab2Stac2

Stag2Stambpl1Stap1

Stard3

Stard6

Stard8Stat4Stat5a Stat6Stc1Steap1

Stil

Stim1

Stk17bStk25

Stk3Stk30

Stk32cStk36

Stk4Stmn1

Stmn2

Stoml1Stox2Strn Strn4Stx11

Stx19

Stx1b Stx5a

Stxbp2Stxbp4

Stxbp5l

Sufu Sugt1Sulf1 Sult1d1

Sult2a1Sult2a2Sult2b1

Sult6b1

Sumf1

Sumo1

Sun1Sun2

Sun3

Supt16h

Surf6Susd1

Susd2

Suv420h1

Sv2c

Swap70Sycp2 Syde1Syde2

Syk

Syn1Syn2

Syn3

Syne1Syngr1Syngr3

Syngr4

Synpo

Synpo2

Syp

Syt12

Syt15Syt4Syt9

Sytl4Sytl5 Tab1 Tab2

Tacc3Tacstd2 Taf1

Taf1bTaf4aTaf4b

Taf8

Tagap

Tagln2Tanc1Taok2Tap1Tap2Tapbpl

Tarm1Tars2Tarsl2

Tasp1Tatdn2 Tbc1d1Tbc1d10b

Tbc1d10c

Tbc1d12Tbc1d14

Tbc1d17Tbc1d20

Tbc1d22aTbc1d2bTbc1d4Tbc1d9b

Tbl1xTbrg3

Tbx2

Tbx20

Tbx21 Tbxa2rTbxas1

Tc2nTceal3

Tcerg1Tcf12

Tcf19Tcf4

Tchh

Tcirg1 Tcn2

Tcp11

Tcp11l2

Tctn1

Tctn2Tctn3

Tdp1Tead4

TecTek

Terf2ipTert TesTespa1

Tet1

Tet2Tex12

Tex14

Tfap4Tfcp2l1

TfecTfip11 Tfpi

Tg

Tgfb3TgfbiTgfbr1

Tgfbrap1Tgs1Th1lThada

Thbs1Thbs2

Themis

Thg1l

Thnsl1 Thoc6

Thsd7a

ThtpaThumpd1

Ticam1

Ticam2

Tie1Tigit Timd4

Timm44

Timp1

Timp2

Timp3Tinagl1

TiparpTk1Tk2 Tkt

Tlcd1

Tle2 Tle4Tle6

Tlr1Tlr13Tlr5

Tlr6

Tlr7

Tlr9

Tm4sf1

Tm6sf1Tmbim1Tmc6

Tmc7Tmco3

Tmco4Tmed1

Tmed7Tmeff2

Tmem102Tmem106a

Tmem116Tmem117Tmem121

Tmem123Tmem132a

Tmem132eTmem136

Tmem138

Tmem139

Tmem149

Tmem154Tmem158

Tmem161aTmem173Tmem175

Tmem177

Tmem181a

Tmem181b−ps

Tmem181c−ps

Tmem186Tmem192Tmem194

Tmem198b Tmem2

Tmem20

Tmem204

Tmem206

Tmem22Tmem221

Tmem229a Tmem229b

Tmem35

Tmem38a

Tmem43

Tmem44

Tmem45b

Tmem47Tmem51Tmem65 Tmem66

Tmem68

Tmem71

Tmem79

Tmem80

Tmem81Tmem86aTmem87b

Tmem88

Tmem8b

Tmem91 Tmem9b

Tmie

Tmigd1

Tmod4

Tmprss4Tmsb15b1Tmsb15lTmtc1

Tmtc2Tmtc3Tmtc4

Tmub2

Tmx2Tnf Tnfaip1

Tnfaip2

Tnfaip3Tnfaip6

Tnfaip8Tnfaip8l2Tnfaip8l3

Tnfrsf10b

Tnfrsf11aTnfrsf11b

Tnfrsf13c

Tnfrsf18

Tnfrsf19 Tnfrsf1b

Tnfrsf23

Tnfrsf25

Tnfrsf26

Tnfrsf4Tnfrsf9

Tnfsf11

Tnfsf13b

Tnfsf14Tnfsf4

Tnfsf9Tnip2Tnip3

Tnk1

Tnni2

Tnni3

Tnpo3

Tnrc18

Tns1Tns4

TnxbToe1 TollipTom1l1

Tomm34Tonsl Top1mtTop2a

ToporsTor3a

ToxTox2Tpcn2 Tpd52l2

Tpk1 Tpm4Tpp1Tppp

Tppp3

TprglTpst1 Tpst2Tpx2 TrabdTraf1Traf2Traf3Traf3ip1Traf3ip3 Traf7

Traip

Trappc4Trappc9Trdmt1

Treh

Trem1

Trem3

Treml2

Treml4Trex1

Trhde Trim16

Trim17

Trim27

Trim29

Trim3 Trim30a

Trim30b

Trim35

Trim36

Trim45

Trim46

Trim47

Trim6Trim62

Trim66

Trim68

Trim69

Trio

Trip13

Trip4Trmt11

Trmt2a

Trmt2bTrmt6

Trmt61aTrmu Trove2

Trp53bp1Trp53i11Trp53i13

Trpm2

Trpm3

Trpm4Trpm5

Trpv2

Trpv4

Tsc22d1Tsc22d3Tsen2Tsen54

Tshb

Tshz3

Tslp

Tsnax

Tsnaxip1Tspan1

Tspan13Tspan14

Tspan15

Tspan18Tspan2Tspan3

Tspan32

Tspan4

Tspan6

Tspan7

Tspan8

Tssk6

Ttc12

Ttc19Ttc23

Ttc25Ttc26

Ttc3Ttc30a1

Ttc30a2

Ttc33Ttc4

Ttc5Ttf2 Tti1

TtkTtll11

Ttll13

Ttll4

Ttll5Ttn

Ttyh1Tub

Tuba1a

Tuba3a

Tuba8

Tubb2b

Tubb5Tubd1

Tube1Tubg1

Tubgcp3

Tubgcp4Tubgcp6

Tuft1Tulp2 Tut1 Twf2

TxkTxlnb

TxnipTyr

Tyro3

Tyrobp

Tyw1Uaca

Uap1

Uap1l1Uba7Ubac1Ubap1Ubash3a

UbdUbe2cUbe2cbp Ube2fUbe2g2Ube2t

Ube4bUbl3Ublcp1

Ubr3

Ubr5Ubxn11

Uchl1Uchl4

Uckl1 Ucp2Ufm1

Uggt2

Ugt1a10 Uhmk1

Uhrf1

Uhrf1bp1Uimc1

Ulbp1 Ulk2

Ulk4Umodl1

Unc119Unc119bUnc13a

Unc45a

Unc5b

Unc5clUnc79

Unc93b1Upf2

Upf3a

Upk1aUpk1bUpk3a

Upp1

Urb1Urb2 UrgcpUsh1g

Ushbp1

Usp11

Usp14Usp18Usp20 Usp21Usp22

Usp27x

Usp30

Usp31

Usp32Usp33

Usp40

Usp46Usp54

Utf1

Utp18Vac14Vamp1 Vangl1

Vangl2

Vash1Vaultrc5 Vav1

Vav2

Vcam1

VcanVcl

Vcpip1VegfcVill Vim

Vipr1

VldlrVmn2r96

Vnn1

Vpreb3

Vps13dVps16

Vps18Vps37d Vps39

Vps41Vps8 Vrk3Vsig10

Vsig4

Vti1aVwa1 Vwa5a

VwfWasf1 Wdfy4

Wdhd1Wdr1

Wdr13

Wdr19Wdr24

Wdr3Wdr31

Wdr4Wdr43

Wdr45Wdr45l

Wdr47Wdr48

Wdr55Wdr5b Wdr6

Wdr73 Wdr74Wdr8Wdr85

Wdr86

Wdr89Wdr91Wdr93

Wdr96

Wdyhv1

Wfdc1

Wfikkn1

Wfikkn2

Wfs1

Whsc1Whsc2

Wipf3

Wipi2

Wisp1Wls

Wnk4

Wnt10a

Wnt10bWnt2

Wnt2bWnt4

Wnt5aWnt9a

Wscd1

Wscd2

Wwtr1X99384 Xab2Xcl1

Xcr1

XdhXirp1 Xkr8

Xlr3b

Xlr4c Xpnpep1Xpo5Xrcc3

Xrra1Xylt2

Ydjc Yes1

Ypel1

Ythdf2Zap70Zbtb16Zbtb17

Zbtb3

Zbtb32

Zbtb37

Zbtb40

Zbtb41Zbtb43Zbtb45

Zbtb46

Zbtb5

Zbtb6Zbtb7c

Zbtb9Zc3h12d Zc3h15

Zc3hav1Zc3hc1

Zcchc18Zcchc3

Zdhhc14

Zdhhc15

Zdhhc2 Zdhhc7Zfat Zfc3h1

Zfp101Zfp105

Zfp106Zfp108Zfp109

Zfp11 Zfp110Zfp111

Zfp112Zfp12

Zfp128Zfp13Zfp14 Zfp142

Zfp146Zfp157

Zfp169Zfp174

Zfp180Zfp189

Zfp202

Zfp212

Zfp217

Zfp239

Zfp26 Zfp263Zfp266Zfp27

Zfp28Zfp280b Zfp280dZfp287Zfp296 Zfp3Zfp30

Zfp300Zfp345

Zfp35

Zfp354bZfp354c

Zfp358Zfp369

Zfp382

Zfp385a

Zfp39Zfp395

Zfp407

Zfp41Zfp418

Zfp420Zfp423

Zfp426Zfp444Zfp446Zfp455

Zfp456

Zfp458

Zfp46Zfp462

Zfp472Zfp493

Zfp498

Zfp51Zfp513Zfp516 Zfp518a

Zfp521

Zfp524

Zfp526

Zfp532Zfp54

Zfp551Zfp563

Zfp566Zfp580

Zfp583Zfp59

Zfp599

Zfp605

Zfp607Zfp61 Zfp62

Zfp623Zfp646Zfp647Zfp651 Zfp655

Zfp658Zfp661Zfp68

Zfp688Zfp689Zfp692

Zfp7 Zfp704

Zfp707Zfp71−rs1Zfp712

Zfp72

Zfp747

Zfp759

Zfp763 Zfp764Zfp772

Zfp773

Zfp777Zfp78

Zfp783 Zfp784Zfp788Zfp791

Zfp808

Zfp81

Zfp82Zfp820Zfp821

Zfp827

Zfp846

Zfp866

Zfp87Zfp871

Zfp872Zfp873

Zfp882Zfp93

Zfp934

Zfp935

Zfp939Zfp940Zfp941

Zfp947

Zfp951 Zfp959Zfp964 Zfpm2 Zfyve1Zfyve20Zfyve21Zfyve27

Zfyve28

Zglp1

Zgpat Zhx1Zkscan14Zkscan17

Zkscan3Zkscan4

Zkscan6

Zmat1

Zmiz2Zmym1

Zmynd10

Zmynd19Znfx1

Zpbp2Zscan10Zscan2

Zscan20

Zscan29Zswim5

Zwilch

ZxdcZyg11aZyx

Cells are projected onto a low-dimensional subspace using principal component analysis on the scaledexpression X of the variable genes.tiss <- RunPCA(object = tiss, do.print = FALSE)tiss <- ProjectPCA(object = tiss, do.print = FALSE)

We can visualize top genes in each principal component.PC 1

Msn

Srgn

Cd38

Sparc

Pla1a

Rapgef4

Sec16b

Mlxipl

PC 2

Scd1

Mgst1

Alb

Apoa2

Tspan7

Nrp1

Snrk

Ppap2b

PC 3

Apoa2

Mup3

Hamp

Alb

Cd52

Coro1a

Rac2

Ptprc

2

We then project onto just the top principal components. This has the effect of keeping the major directionsof variation in the data and, ideally, supressing noise. A decent rule of thumb is to pick the elbow in the plotbelow.PCElbowPlot(object = tiss)

5

10

15

5 10 15 20PC

Sta

ndar

d D

evia

tion

of P

C

Choose the number of principal components to use.n.pcs = 11

Cluster

The clustering is performed on a shared-nearest-neighbors graph on the cells.

The shared-nearest-neighbors graph was constructed based on the Euclidean distance in the low-dimensionalsubspace; cells are connected if their k-neighborhoods overlap. Indeed, let N (j) denote the k-nearestneighborhood (k = 30) for a cell j. The shared-nearest-neighbor graph G has a vertex for each cell and anedge of weight

wjk = |N (j) ∩N (k)||N (j) ∪N (k)|

between cells j and k. Cells were clustered using a modified version of the Louvain method for modularitymaximization. The modularity has a resolution parameter γ,

Q =∑

ij

(Aij − γ

kikj

2m

)δ(ci, cj),

where Aij is the weighted adjacency matrix, ki and kj are the weighted degrees of cells i and j, m is thetotal weight of edges in the graph, ci denotes cluster membership, and δ(ci, cj) is 1 if i and j are in the samecluster, and 0 otherwise.

3

The resolution γ is a tuneable parameter in this analysis that sets the tradeoff between in-group connectionsand between-group connections. High resolution favors smaller clusters.# Set resolutionres.used <- 1

tiss <- FindClusters(object = tiss, reduction.type = "pca", dims.use = 1:n.pcs,resolution = res.used, print.output = 0, save.SNN = TRUE)

We use tSNE solely to visualize the data.tiss <- RunTSNE(object = tiss, dims.use = 1:n.pcs, seed.use = 10, perplexity=30)

TSNEPlot(object = tiss, do.label = T, pt.size = 1.2, label.size = 4)

0

1

23

4

5

6

7

8

−20

0

20

−20 −10 0 10 20

tSNE_1

tSN

E_2

0

1

2

3

4

5

6

7

8

Label clusters using marker genes

Check expression of genes useful for indicating cell type.genes_hep = c('Alb', 'Ttr', 'Apoa1', 'Serpina1c') #hepatocytegenes_endo = c('Pecam1', 'Nrp1', 'Kdr','Oit3') # endothelialgenes_kuppfer = c('Emr1', 'Clec4f', 'Cd68', 'Irf7') # Kuppfer cellsgenes_nk = c('Zap70', 'Il2rb', 'Nkg7', 'Cxcr6') # Natural Killer cellsgenes_b = c('Cd79a', 'Cd79b', 'Cd74', 'Cd19') # B Cells

genes_all = c(genes_hep, genes_endo, genes_kuppfer, genes_nk, genes_b)

In the tSNE plots below, the intensity of each point represents the log-normalized gene expression Nij .

4

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0

3

6

9

Alb

Alb

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.0

2.5

5.0

7.5

Ttr

Ttr

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.02.55.07.510.0

Apoa1

Apoa1

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.0

2.5

5.0

7.5

Serpina1c

Serpina1c

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

02468

Pecam1

Pecam1

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

02468

Nrp1

Nrp1

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

02468

Kdr

Kdr

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

02468

Oit3

Oit3

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

02468

Emr1

Emr1

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.02.55.07.510.0

Clec4f

Clec4f

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

02468

Cd68

Cd68

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0

2

4

6

Irf7

Irf7

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0

2

4

6

Zap70

Zap70

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

02468

Il2rb

Il2rb

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.0

2.5

5.0

7.5

Nkg7

Nkg7

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.0

2.5

5.0

7.5

Cxcr6

Cxcr6

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.0

2.5

5.0

7.5

Cd79a

Cd79a

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.0

2.5

5.0

7.5

Cd79b

Cd79b

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

0.02.55.07.510.0

Cd74

Cd74

−20

0

20

−20 −10 0 10 20tSNE_1

tSN

E_2

02468

Cd19

Cd19

Dotplots show, for each cluster and gene, the fraction of cells with at least one read for the gene (circle size)and the average scaled expression for that gene among the cells expressing it (circle color).

5

0

1

2

3

4

5

6

7

8C

d19

Cd7

4C

d79b

Cd7

9aC

xcr6

Nkg

7Il2

rbZ

ap70

Irf7

Cd6

8C

lec4

fE

mr1

Oit3

Kdr

Nrp

1P

ecam

1S

erpi

na1c

Apo

a1T

trA

lb

−1

0

1

2

avg.exp.scale

pct.exp0.000.250.500.751.00

The low but nonzero levels of Albumin present in all clusters is consistent with a small amount of leakage,either through physical contamination or index hopping. Nevertheless, the absolute levels of expressionconfirm a sharp difference between the hepatocyte clusters and the others.

0e+00

1e+05

2e+05

3e+05

0 1 2 3 4 5 6 7 8

Identity

Alb

To confirm the identity of a cluster, you can inspect the genes differentially expressed in that cluster comparedto the others.clust.markers7 <- FindMarkers(object = tiss, ident.1 = 7,

only.pos = TRUE, min.pct = 0.25, thresh.use = 0.25)

The top markers for cluster 7 include histocompatibility markers H2-*, consistent with the expression of other

6

B-cell markers seen above.head(clust.markers7)

## p_val avg_logFC pct.1 pct.2 p_val_adj## H2-DMb2 9.768214e-101 7.042620 0.902 0.024 2.279999e-96## Pou2af1 1.585456e-100 6.108999 0.732 0.006 3.700612e-96## Spib 1.271751e-88 6.278530 0.707 0.010 2.968394e-84## Cd19 1.240657e-87 7.018641 0.756 0.016 2.895818e-83## H2-Oa 6.025345e-85 5.833053 0.683 0.010 1.406376e-80## H2-Ob 1.236266e-83 5.860218 0.780 0.022 2.885569e-79

Using the markers, we can confidentaly label the clusters. We provide both a free annotation (where anyname can be used) and a cell ontology class. The latter uses a controlled vocabulary for easy comparisonbetween studies and different levels of the taxonomy.tiss <- StashIdent(object = tiss, save.name = "cluster.ids")

cluster.ids <- c(0, 1, 2, 3, 4, 5, 6, 7, 8)

free_annotation <- c("endothelial cell","hepatocyte","hepatocyte","hepatocyte","hepatocyte","kuppfer","hepatocyte","B cell","NK/NKT cells")

cell_ontology_class <-c("endothelial cell of hepatic sinusoid","hepatocyte","hepatocyte","hepatocyte","hepatocyte","Kupffer cell","hepatocyte","B cell","natural killer cell")

tiss = stash_annotations(tiss, cluster.ids, free_annotation, cell_ontology_class)

Checking for batch effects

Color by metadata, like plate barcode, to check for batch effects. Here we see that the clusters are segregatedby sex.

7

TSNEPlot(object = tiss, do.return = TRUE, group.by = "mouse.id")

−20

0

20

−20 −10 0 10 20

tSNE_1

tSN

E_2

3_11_M

3_56_F

3_57_F

3_9_M

Nevertheless, every cluster contains cells from multiple mice.table(FetchData(tiss, c('mouse.id','ident')) %>% droplevels())

## ident## mouse.id 0 1 2 3 4 5 6 7 8## 3_11_M 160 0 59 29 51 47 0 31 32## 3_56_F 0 46 0 11 0 0 25 0 0## 3_57_F 0 46 0 5 0 0 28 0 0## 3_9_M 22 1 32 37 20 14 1 10 7

Final coloring

Color by cell ontology class on the original tSNE.TSNEPlot(object = tiss, group.by = "cell_ontology_class")

8

−20

0

20

−20 −10 0 10 20

tSNE_1

tSN

E_2

B cell

endothelial cell of hepatic sinusoid

hepatocyte

Kupffer cell

natural killer cell

Save the Robject for later

#filename = here('00_data_ingest', '04_tissue_robj_generated',# paste0("facs_", organ_of_interest, "_seurat_tiss.Robj"))#print(filename)#save(tiss, file=filename)

# To reload a saved object#filename = here('00_data_ingest', '04_tissue_robj_generated',# paste0("facs_", organ_of_interest, "_seurat_subtiss.Robj"))#load(file=filename)

Export the final metadata

#save_annotation_csv(tiss, organ_of_interest, "facs")

9