Readme.md
In NathanSkene/One2One:
One2one Orthologs
Nathan Skene
2018-01-17
This package is used to get 1:1 orthologs based on MGI homology data from http://www.informatics.jax.org/homology.shtml
The data is processed within the package but for key species comparisons is also stored in the data
Get the homolog data
library(One2One)
# Download and format the homolog data from MGI
allHomologs = load.homologs()
## [1] "Species for which homology classes are available:"
## [1] "mouse, laboratory" "human" "chimpanzee"
## [4] "macaque, rhesus" "dog, domestic" "cattle"
## [7] "rat" "frog, western clawed" "zebrafish"
## [10] "chicken"
# Get data on orthology between the two species
species1="human"
species2="mouse"
ortholog_data = analyse.orthology(species1,species2,allHomologs)
## [1] "Selected species: human"
## [1] "Selected species: mouse, laboratory"
## [1] "Full dataset contains 18708 genes from human"
## [1] "Full dataset contains 18995 genes from mouse"
## [1] "1954 genes which are present in human are deleted in mouse"
## [1] "2241 genes which are present in mouse are deleted in human"
## [1] "220 genes are duplicated in human"
## [1] "609 genes are duplicated in mouse"
## [1] "16470 are shared 1:1 between the two species"
# Check the 1:1 homologs
print(ortholog_data$orthologs_one2one[1:10,])
## HomoloGene ID human.symbol mouse.symbol
## 1 100 ETFA Etfa
## 2 1000 CLDN4 Cldn4
## 3 10001 HAUS2 Haus2
## 4 10003 EFHC1 Efhc1
## 5 10004 LRRC8D Lrrc8d
## 6 10005 THAP1 Thap1
## 7 100054 DGKD Dgkd
## 8 10006 ZDHHC4 Zdhhc4
## 9 100071 ANO5 Ano5
## 10 100077 UBALD2 Ubald2
Analyse differences in orthology using EWCE
# Load EWCE package
#install.packages("devtools")
#library(devtools)
#install_github("nathanskene/ewce")
library(EWCE)
data(ctd)
homoIDs_bg = ortholog_data$species2_allGenes
symbols_bg = get.symbol.from.homologID(homoIDs_bg,species1,species2,ortholog_data,species2)
# Which cell types are associated with genes deleted in humans, but present in mice?
homoIDs_target = ortholog_data$species2_present_species1_deleted
symbols_target = get.symbol.from.homologID(homoIDs_target,species1,species2,ortholog_data,species2)
full_results = bootstrap.enrichment.test(sct_data=ctd,hits=symbols_target,bg=symbols_bg,reps=1000,annotLevel=2)
## [1] "Zc3h15" "Spin2c" "Gm13023" "4933415F23Rik"
## [5] "Larp1b" "Dcpp2" "Dcpp3" "Vmn2r54"
## [9] "Cbr2" "Cntnap5b" "Tomm5" "9030025P20Rik"
## [13] "Gm10267" "Zfp955a" "Zfp955b" "Rpl34-ps1"
## [17] "Rpl34" "Trim43b" "2410002F23Rik" "Nptn"
## [21] "Mcts2" "Olfr117" "Skint7" "Dbil5"
## [25] "Doc2g" "Rpl23a" "Olfr944" "Oas1c"
## [29] "Oas1d" "Klra5" "Vmn1r195" "Psg23"
## [33] "Ccdc71" "Bmyc" "Naip5" "Vmn2r29"
## [37] "Ly6a" "Ly6c1" "Ly6c2" "Ly6f"
## [41] "Car15" "Trim30a" "Trim30d" "Cd209f"
## [45] "Vmn2r71" "Gimap9" "Gm3696" "Gm10406"
## [49] "Gm3558" "Gm5796" "Ccnjl" "Serpina3g"
## [53] "Tmsb10" "Tmsb15l" "Tmsb4x" "Calm1"
## [57] "Calm2" "Calm3" "Mettl7a2" "Mettl7a3"
## [61] "Fcna" "Gstm6" "Zfp93" "Zfp108"
## [65] "Zfp747" "Map3k7" "Akr1c13" "Prorsd1"
## [69] "Josd1" "Ccdc163" "Tstd3" "Lrrc9"
## [73] "BC051142" "Sult1a1" "Ms4a6b" "Adam6b"
## [77] "Oasl2" "Akr1b10" "Npcd" "B020004C17Rik"
## [81] "Nebl" "Fam187a" "Aldoart1" "Msl3l2"
## [85] "Zfp956" "4430402I18Rik" "Hmgn2" "Tpm1"
## [89] "Ppp2r5c" "Zkscan4" "Smok3b" "Zfp952"
## [93] "Cntnap5c" "Celf6" "Zfp740" "Sult5a1"
## [97] "2900026A02Rik" "Zfp958" "Vmn2r13" "Vmn2r87"
## [101] "Vmn2r61" "Srp54c" "Cyp4f17" "Gramd1c"
## [105] "Vmn2r2" "Lage3" "Zfp954" "Zim1"
## [109] "Ankrd50" "Smim11" "Zfp949" "Tgtp1"
## [113] "Znrd1as" "Fam193b" "Zeb2os" "Gm4858"
## [117] "Bmp8b" "Ctla2a" "Ctla2b" "Klrc3"
## [121] "Mcpt4" "Pdzph1" "Ms4a6c" "4930519F16Rik"
## [125] "9430038I01Rik" "Cox7b2" "Slco1a4" "Foxp1"
## [129] "Abca8a" "Snhg11" "Tmem191c" "Spink10"
## [133] "Nr1h5" "Tlr13" "1700023F06Rik" "Zfp35"
## [137] "Arxes1" "Arxes2" "Gm14295" "Cyp2j12"
## [141] "Slfn2" "Zfp945" "Zfp944" "Zfp942"
## [145] "Zfp994" "Zfp947" "Zfp995" "1810037I17Rik"
## [149] "0610009B22Rik" "Aldh3b3" "1700011I03Rik" "Snrpa"
## [153] "Olfr695" "Olfr945" "Zfp85" "BC048507"
## [157] "Spag6" "Cox5b" "Hspa1b" "Rnf113a1"
## [161] "Sf3a2" "Srsf5" "Otud5" "Rpl36"
## [165] "Zfp960" "Zfp97" "Rsrc2" "Crip2"
## [169] "Gstt3" "Ccl7" "Qars" "Prr13"
## [173] "Zfp658" "U2af1l4" "Spink2" "Plpp1"
## [177] "Cox6c" "Sf1" "Olfr1331" "Irgm1"
## [181] "Fus" "Zfp708" "Celf1" "Nxpe5"
## [185] "Maml2" "Aldoart2" "Alg13" "Plscr2"
## [189] "Supt20" "Abi3bp" "Afg3l1" "Snrpc"
## [193] "Hmgb3" "Clasrp" "Tpm2" "Zfp873"
## [197] "Sct" "Dmrtc1a" "Zfp943" "Cfhr2"
## [201] "Crb3" "Foxp2" "Vma21" "Dazap1"
## [205] "Prrt1" "Smim26" "Gm1673" "AW146154"
## [209] "Cdkn1c" "9130409I23Rik" "Rbx1" "Nedd4"
## [213] "Mptx2" "Mapre2" "Zfp748" "Akap9"
## [217] "Nxf7" "Ifi27" "Hnrnpa1" "Rbfox3"
## [221] "Ewsr1" "Evi5l" "Fnbp1l" "Setd1b"
## [225] "Rpl22l1" "Gstt1" "Gk" "Aph1c"
## [229] "Uba52" "Tmem115" "Rasl2-9" "Ppp1cc"
## [233] "Zfp874a" "Zfp874b" "Gsta4" "Fmnl1"
## [237] "Nrbp2" "Kcnn2" "Rcor3" "Ppp1r12b"
## [241] "Mamld1" "Nacad" "Pcmt1" "Plekha6"
## [245] "Hmgb1" "Cyp4f16" "Fam13a" "Zfp938"
## [249] "Eif1" "Hist1h1a" "Ifitm1" "Zfp53"
## [253] "Egfem1" "Dcaf12l1" "Perm1" "Foxn3"
## [257] "Rnf138rt1" "Trpc2" "Nos1ap" "Wasl"
## [261] "Nrgn" "Ugt1a7c" "Ehbp1l1" "Pcp4l1"
## [265] "Klf16" "Rpl36a" "E130308A19Rik" "Nisch"
## [269] "Gpihbp1" "Smco4" "Ttll13" "Snrpg"
## [273] "Macf1" "AA414768" "Brd4" "Zfp442"
## [277] "Zfp937" "Elob" "1500009L16Rik" "R3hcc1"
## [281] "Fip1l1" "Gm3604" "Gm5141" "Tchh"
## [285] "C530008M17Rik" "Zfp961" "Zfp229" "Tmem29"
## [289] "Ubap2l" "BC005561" "Zfp651" "Zfp882"
## [293] "Zfp568" "Clec2d" "Clec2g" "Zfp40"
## [297] "Nat8f4" "Ccdc162" "Rps27" "Rps27rt"
## [301] "Gm4832" "Tmem223" "Fhod1" "Apoc1"
## [305] "Kat6b" "Nes" "Zfp939" "2010315B03Rik"
## [309] "Bola2" "Rpl29" "D430019H16Rik" "Rpl31-ps12"
## [313] "Scd2" "Rpl37rt" "Dst" "Srrm3"
## [317] "Gm11780" "Acp5" "Acan" "Atp5k"
## [321] "Hrk" "Ivl" "Nefm" "Ptma"
## [325] "Bex1" "Tcf7" "Ttf1" "Tgoln1"
## [329] "Zfp101" "Zfp185" "Zfp60" "Anp32a"
## [333] "Cdc42" "Irs4" "Krt10" "Srgn"
## [337] "Supt4b" "Zfp59" "Aldh1a7" "Muc1"
## [341] "Cald1" "Rpl32" "Podxl" "Hist1h1e"
## [345] "Hmgn5" "S100a11" "Rplp1" "Slc22a21"
## [349] "Ncoa6" "Fam184b" "Ces1g" "Chtop"
## [353] "Zfp788" "Cmya5" "Scd3" "Bhlhe41"
## [357] "Mxra7" "3300002I08Rik" "Cd209g" "Ap2b1"
## [361] "Rbm33" "Cyp2j9" "4930502E18Rik" "Ccdc30"
## [365] "Zfp773" "Ifi27l2a" "Arhgef38" "Pcdhb18"
## [369] "Pgap2" "Calcb" "Zfp932" "Serpinb1c"
## [373] "Anp32b" "Akr1c14" "Zfp758" "AI661453"
## [377] "Zfp959" "Zfp810" "Pitpnc1" "Cetn4"
## [381] "Hnrnpa3" "Olfr1033" "Krt9" "2810021J22Rik"
## [385] "Zfp871" "Zfp677" "D130040H23Rik" "Diaph2"
## [389] "Serpinb1b" "4930486L24Rik" "Zfp940" "Nrg1"
## [393] "2610524H06Rik" "Zfp120" "Zbed4" "Zfp599"
## [397] "E430018J23Rik" "Bst2" "Zfp933" "Zfp532"
## [401] "Plcxd1" "Zfp81" "U2af1" "Kdm1b"
## [405] "Akap17b" "Aff2" "Gprasp2" "Sel1l2"
## [409] "Lrrc51" "Tmem18" "Mmgt2" "Morc2b"
## [413] "Fer1l4" "Tspyl3" "Efcab10" "Gm266"
## [417] "Pgr15l" "Pln" "Pou3f1" "Esrra"
## [421] "2610002M06Rik" "Lrrfip2" "Ccl6" "Serpinb6b"
## [425] "Acot1" "Igtp" "Map3k7cl" "Gtf2ird2"
## [429] "Lrrc74b" "Hmga2" "Atp6ap1l" "Fbll1"
## [433] "1700061G19Rik" "Fam183b" "Cops2" "Fbxo38"
## [437] "Fbxl22" "Msantd2" "2700097O09Rik" "Pwp2"
## [441] "Gstm3" "Snrpe" "Dync1i2" "Slc35a2"
## [445] "Alyref" "Irx5" "Lmo3" "Nmnat3"
## [449] "3830403N18Rik" "Xlr" "Xlr3b" "Anp32e"
## [453] "Dgcr6" "Ly6g6e" "Gm7903" "Yaf2"
## [457] "Mocs1" "Slc25a1" "Trhr2" "Lao1"
## [461] "Ttc30a2" "Gucy2g" "Zfp352" "Gm13277"
## [465] "Urah" "Cyb5r3" "Siglech" "Zfp870"
## [469] "Adam5" "Glycam1" "Ifi47" "2610028H24Rik"
## [473] "Commd6" "Spaca6" "Folh1" "Arf2"
## [477] "Sh3bgr" "Siah1b" "Zfp68" "Tha1"
## [481] "Fcrls" "Pcdhb4" "Pcdhb6" "Pcdhb11"
## [485] "Rab15" "Ttc39d" "Coa6" "Kctd12b"
## [489] "A430033K04Rik" "Gulo" "Tas2r134" "Ppfia4"
## [493] "Zfp763" "Cutal" "AI413582" "Slc26a10"
## [497] "Rps3a1" "Rrbp1" "Eda" "Setmar"
## [501] "Prps1l3" "H2-T24" "Adam3" "Abcb1b"
## [505] "Cyp2a12" "5031410I06Rik" "Gm21671" "Gm5862"
## [509] "Speer4b" "Ccdc50" "Actl11" "Aox4"
## [513] "Pcdhb14" "Prdx6b" "Csl" "Olfr38"
## [517] "Ahsa2" "4921509C19Rik" "2510002D24Rik" "Cmah"
## [521] "Adam1a" "Ktn1" "Olfr1179" "Olfr1246"
## [525] "Tpm4" "Gja6" "Mup3" "Mup5"
## [529] "Eci3" "Vmn1r13" "Zfp868" "Zfp61"
## [533] "Htr5b" "Lcn3" "Ubb" "Cyp2d22"
## [537] "Igbp1b" "Pdlim3" "Pmaip1" "4931417E11Rik"
## [541] "Mapk1ip1" "Uox" "Nat8f3" "Casp12"
## [545] "Ggta1" "Scd4" "Zfp52" "Acot5"
## [549] "Zfp472" "Slc7a15" "Tmem198b" "Tlr11"
## [553] "4930402F06Rik" "Sik1" "Gm1110" "Fam169b"
## [557] "Olfr1061" "Pvr" "Ggnbp1" "1600015I10Rik"
## [561] "Gm5885" "A630001G21Rik" "Cox7c" "Cbarp"
## [565] "Fbxw17" "Gm13178" "Ccdc74a" "Gm12185"
## [569] "Nrxn3" "Teddm3" "Gm12253" "Rhox3g"
## [573] "Madcam1" "Aldh3b2" "Rbmxl1" "Irs3"
## [577] "Zrsr1" "Vmn2r1" "Tnfrsf23" "Cd209b"
## [581] "Prss32" "Gpr165" "Isoc2b" "Milr1"
## [585] "Gm5127" "1700001J03Rik" "1700018F24Rik" "Actn3"
## [589] "Lipo1" "Cldn34c1" "2610008E11Rik" "Ccl9"
## [593] "Sp100" "Meis1" "Abca17" "Zfp94"
## [597] "Defb30" "Gm6377" "T2" "Mff"
## [601] "Nat8f5" "2310039H08Rik" "Anapc15" "Pcdhb7"
## [605] "Pcdhb9" "Pcdhb12" "AU041133" "4932429P05Rik"
## [609] "Prss1" "Prss3" "Masp1" "Pcdhb8"
## [613] "Rfpl4" "Olfr654" "Aox3" "Acaa1b"
## [617] "Clec4a3" "Otub1" "Alyref2" "Eif2s3y"
## [621] "Cabp1" "Atp8b5"
## [1] "(none)"
## [1] 1
## [1] ""
## [1] "Astro1"
## [1] 0.111
## [1] ""
## [1] "Astro2"
## [1] 0.506
## [1] ""
## [1] "CA1Pyr1"
## [1] 1
## [1] ""
## [1] "CA1Pyr2"
## [1] 0.998
## [1] ""
## [1] "CA1PyrInt"
## [1] 0.982
## [1] ""
## [1] "CA2Pyr2"
## [1] 0.4
## [1] ""
## [1] "Choroid"
## [1] 0.472
## [1] ""
## [1] "ClauPyr"
## [1] 1
## [1] ""
## [1] "Epend"
## [1] 0
## [1] "Fold enrichment: 1.50262729773882"
## [1] "Standard deviations from mean: 4.00966498040887"
## [1] ""
## [1] "Int1"
## [1] 0.096
## [1] ""
## [1] "Int10"
## [1] 0.217
## [1] ""
## [1] "Int11"
## [1] 0.2
## [1] ""
## [1] "Int12"
## [1] 1
## [1] ""
## [1] "Int13"
## [1] 0.622
## [1] ""
## [1] "Int14"
## [1] 1
## [1] ""
## [1] "Int15"
## [1] 0.681
## [1] ""
## [1] "Int16"
## [1] 1
## [1] ""
## [1] "Int2"
## [1] 0.99
## [1] ""
## [1] "Int3"
## [1] 0.979
## [1] ""
## [1] "Int4"
## [1] 0
## [1] "Fold enrichment: 1.30777242003489"
## [1] "Standard deviations from mean: 4.16660208841783"
## [1] ""
## [1] "Int5"
## [1] 0.998
## [1] ""
## [1] "Int6"
## [1] 1
## [1] ""
## [1] "Int7"
## [1] 0.972
## [1] ""
## [1] "Int8"
## [1] 0.993
## [1] ""
## [1] "Int9"
## [1] 0
## [1] "Fold enrichment: 1.30177765590248"
## [1] "Standard deviations from mean: 3.83481628715196"
## [1] ""
## [1] "Mgl1"
## [1] 0.138
## [1] ""
## [1] "Mgl2"
## [1] 0.286
## [1] ""
## [1] "Oligo1"
## [1] 0.968
## [1] ""
## [1] "Oligo2"
## [1] 1
## [1] ""
## [1] "Oligo3"
## [1] 0.566
## [1] ""
## [1] "Oligo4"
## [1] 0.983
## [1] ""
## [1] "Oligo5"
## [1] 0.995
## [1] ""
## [1] "Oligo6"
## [1] 0.853
## [1] ""
## [1] "Peric"
## [1] 0.013
## [1] "Fold enrichment: 1.28498272064174"
## [1] "Standard deviations from mean: 2.59867618305013"
## [1] ""
## [1] "Pvm1"
## [1] 0
## [1] "Fold enrichment: 1.56568184526585"
## [1] "Standard deviations from mean: 5.17543666137627"
## [1] ""
## [1] "Pvm2"
## [1] 0
## [1] "Fold enrichment: 1.86272831441951"
## [1] "Standard deviations from mean: 7.52773806569167"
## [1] ""
## [1] "S1PyrDL"
## [1] 0.979
## [1] ""
## [1] "S1PyrL23"
## [1] 1
## [1] ""
## [1] "S1PyrL4"
## [1] 0.986
## [1] ""
## [1] "S1PyrL5"
## [1] 1
## [1] ""
## [1] "S1PyrL5a"
## [1] 0.85
## [1] ""
## [1] "S1PyrL6"
## [1] 0.004
## [1] "Fold enrichment: 1.11281768827408"
## [1] "Standard deviations from mean: 2.86061883356584"
## [1] ""
## [1] "S1PyrL6b"
## [1] 0.813
## [1] ""
## [1] "SubPyr"
## [1] 0.003
## [1] "Fold enrichment: 1.18967265885381"
## [1] "Standard deviations from mean: 3.51133327908488"
## [1] ""
## [1] "Vend1"
## [1] 0.593
## [1] ""
## [1] "Vend2"
## [1] 0.002
## [1] "Fold enrichment: 1.31743001377535"
## [1] "Standard deviations from mean: 3.59625082030488"
## [1] ""
## [1] "Vsmc"
## [1] 0.115
## [1] ""
print(ewce.plot(full_results$results,mtc_method="BH"))
# Which cell types are associated with genes duplicated in humans, but singletons in mice?
homoIDs_target = ortholog_data$species2_onceOnly_species1_dup
symbols_target = get.symbol.from.homologID(homoIDs_target,species1,species2,ortholog_data,species2)
full_results = bootstrap.enrichment.test(sct_data=ctd,hits=symbols_target,bg=symbols_bg,reps=1000,annotLevel=2)
## [1] "Slx1b" "Coro7" "1110012L19Rik" "F8a"
## [5] "Pramef8" "Arpin" "Nomo1" "Klhl23"
## [9] "Anxa8" "Arhgap8" "Smn1" "D10Jhu81e"
## [13] "Cbs" "Gstt2" "Nbl1" "Prodh"
## [17] "Washc2" "Fcgr4" "Cryaa" "Serf1"
## [21] "Icosl" "Pmf1" "Sgk3" "Ccz1"
## [25] "Ckmt1" "Pom121" "Hspa1a" "Mrpl23"
## [29] "Ankhd1" "Ranbp2" "Asb3" "Gpr89"
## [1] "(none)"
## [1] 0.603
## [1] ""
## [1] "Astro1"
## [1] 0.078
## [1] ""
## [1] "Astro2"
## [1] 0.112
## [1] ""
## [1] "CA1Pyr1"
## [1] 0.601
## [1] ""
## [1] "CA1Pyr2"
## [1] 0.5
## [1] ""
## [1] "CA1PyrInt"
## [1] 0.197
## [1] ""
## [1] "CA2Pyr2"
## [1] 0.717
## [1] ""
## [1] "Choroid"
## [1] 0.874
## [1] ""
## [1] "ClauPyr"
## [1] 0.576
## [1] ""
## [1] "Epend"
## [1] 0.14
## [1] ""
## [1] "Int1"
## [1] 0.077
## [1] ""
## [1] "Int10"
## [1] 0.694
## [1] ""
## [1] "Int11"
## [1] 0.909
## [1] ""
## [1] "Int12"
## [1] 0.56
## [1] ""
## [1] "Int13"
## [1] 0.504
## [1] ""
## [1] "Int14"
## [1] 0.837
## [1] ""
## [1] "Int15"
## [1] 0.753
## [1] ""
## [1] "Int16"
## [1] 0.675
## [1] ""
## [1] "Int2"
## [1] 0.094
## [1] ""
## [1] "Int3"
## [1] 0.727
## [1] ""
## [1] "Int4"
## [1] 0.802
## [1] ""
## [1] "Int5"
## [1] 0.831
## [1] ""
## [1] "Int6"
## [1] 0.902
## [1] ""
## [1] "Int7"
## [1] 0.458
## [1] ""
## [1] "Int8"
## [1] 0.536
## [1] ""
## [1] "Int9"
## [1] 0.687
## [1] ""
## [1] "Mgl1"
## [1] 0.107
## [1] ""
## [1] "Mgl2"
## [1] 0.399
## [1] ""
## [1] "Oligo1"
## [1] 0.93
## [1] ""
## [1] "Oligo2"
## [1] 0.525
## [1] ""
## [1] "Oligo3"
## [1] 0.274
## [1] ""
## [1] "Oligo4"
## [1] 0.911
## [1] ""
## [1] "Oligo5"
## [1] 0.762
## [1] ""
## [1] "Oligo6"
## [1] 0.746
## [1] ""
## [1] "Peric"
## [1] 0.43
## [1] ""
## [1] "Pvm1"
## [1] 0.16
## [1] ""
## [1] "Pvm2"
## [1] 0.549
## [1] ""
## [1] "S1PyrDL"
## [1] 0.51
## [1] ""
## [1] "S1PyrL23"
## [1] 0.234
## [1] ""
## [1] "S1PyrL4"
## [1] 0.68
## [1] ""
## [1] "S1PyrL5"
## [1] 0.998
## [1] ""
## [1] "S1PyrL5a"
## [1] 0.785
## [1] ""
## [1] "S1PyrL6"
## [1] 0.78
## [1] ""
## [1] "S1PyrL6b"
## [1] 0.632
## [1] ""
## [1] "SubPyr"
## [1] 0.452
## [1] ""
## [1] "Vend1"
## [1] 0.016
## [1] "Fold enrichment: 2.18550258806339"
## [1] "Standard deviations from mean: 2.66827596868916"
## [1] ""
## [1] "Vend2"
## [1] 0.147
## [1] ""
## [1] "Vsmc"
## [1] 0.335
## [1] ""
print(ewce.plot(full_results$results,mtc_method="BH"))
# Which cell types are associated with genes duplicated in mice, but singletons in human?
homoIDs_target = ortholog_data$species1_onceOnly_species2_dup
symbols_target = get.symbol.from.homologID(homoIDs_target,species1,species2,ortholog_data,species2)
full_results = bootstrap.enrichment.test(sct_data=ctd,hits=symbols_target,bg=symbols_bg,reps=1000,annotLevel=2)
## [1] "Bglap" "Bglap2" "Pdcd5" "Ywhaq"
## [5] "Gapdh" "3830406C13Rik" "Nutf2" "Serpina3c"
## [9] "Serpina3n" "Rpl17" "Krtap10-4" "Ifi207"
## [13] "Ifi203" "Ifi204" "Ifi211" "Mndal"
## [17] "Gemin6" "Ifit3b" "Ifit3" "Rsph3a"
## [21] "Rsph3b" "Lyz2" "Lyz1" "2700062C07Rik"
## [25] "Amd2" "Ptges3" "Tuba3a" "Trim34a"
## [29] "H2-Bl" "H2-Q4" "H2-Q10" "H2-K1"
## [33] "H2-Q2" "H2-D1" "Olfr287" "Ceacam1"
## [37] "Gbp9" "Zfp110" "Zfp369" "C1ra"
## [41] "C1s1" "C1s2" "Zfp985" "Zfp987"
## [45] "Zfp979" "Zfp984" "Zfp981" "Zfp992"
## [49] "Zfp738" "Zfp729a" "Zfp729b" "Cdv3"
## [53] "Tceal6" "Tceal3" "Zfp975" "Zfp976"
## [57] "H2-T23" "H2-T-ps" "Pirb" "Gm14548"
## [61] "Zfp607b" "Zfp607a" "Gm14325" "Zfp970"
## [65] "Zfp971" "Gm14326" "Gm14305" "Eno1"
## [69] "Zfp931" "Pih1h3b" "Ndufa11" "Oas1g"
## [73] "Serpina1c" "Il4i1" "Pnp" "Pnp2"
## [77] "Srp54a" "Rbm12b2" "Rbm12b1" "Selenbp1"
## [81] "Bcl2a1d" "Bcl2a1b" "Bcl2a1a" "Rpl6"
## [85] "Rnaset2a" "Rbm3" "Bnip3l" "Ndufb4"
## [89] "Csf2rb" "Csf2rb2" "Cisd3" "Eif3j2"
## [93] "Atf1" "Ndufs6" "Gmfg" "Gng5"
## [97] "Sec61g" "Gimap5" "Dnah7b" "Dnah7a"
## [101] "Sap18b" "Sap18" "Mfap1a" "Mfap1b"
## [105] "Slfn8" "Mthfsl" "Mthfs" "Dynlt1a"
## [109] "Dynlt1b" "Cd55" "Evi2b" "Impdh2"
## [113] "Chchd2" "Tmed10" "Mterf1a" "Mterf1b"
## [117] "Esd" "Rpl13" "Acat3" "Acat2"
## [121] "Tmed2" "Trp53rkb" "Trp53rka" "Mrto4"
## [125] "Gstp1" "Klk1b5" "Klk1b27" "H2-DMb1"
## [129] "Olfr110" "Gsta2" "Cd300c2" "Trim12c"
## [133] "Ifit1bl1" "Mgl2" "Clec10a" "Ftl1"
## [137] "Ndufab1" "Rybp" "Llph" "Acot10"
## [141] "Acot9" "Sp110" "Prnd" "Glipr1l1"
## [145] "Ubl4a" "Lilr4b" "Lilrb4a" "Nudt11"
## [149] "Nudt10" "Dnajc19" "Phf11d" "Phf11b"
## [153] "Il11ra1" "Sms"
## [1] "(none)"
## [1] 0.997
## [1] ""
## [1] "Astro1"
## [1] 0.158
## [1] ""
## [1] "Astro2"
## [1] 0.684
## [1] ""
## [1] "CA1Pyr1"
## [1] 1
## [1] ""
## [1] "CA1Pyr2"
## [1] 0.989
## [1] ""
## [1] "CA1PyrInt"
## [1] 1
## [1] ""
## [1] "CA2Pyr2"
## [1] 1
## [1] ""
## [1] "Choroid"
## [1] 0.178
## [1] ""
## [1] "ClauPyr"
## [1] 1
## [1] ""
## [1] "Epend"
## [1] 0.464
## [1] ""
## [1] "Int1"
## [1] 0.954
## [1] ""
## [1] "Int10"
## [1] 1
## [1] ""
## [1] "Int11"
## [1] 0.793
## [1] ""
## [1] "Int12"
## [1] 1
## [1] ""
## [1] "Int13"
## [1] 0.992
## [1] ""
## [1] "Int14"
## [1] 1
## [1] ""
## [1] "Int15"
## [1] 0.991
## [1] ""
## [1] "Int16"
## [1] 1
## [1] ""
## [1] "Int2"
## [1] 0.781
## [1] ""
## [1] "Int3"
## [1] 1
## [1] ""
## [1] "Int4"
## [1] 0.586
## [1] ""
## [1] "Int5"
## [1] 0.863
## [1] ""
## [1] "Int6"
## [1] 0.063
## [1] ""
## [1] "Int7"
## [1] 1
## [1] ""
## [1] "Int8"
## [1] 0.931
## [1] ""
## [1] "Int9"
## [1] 0.991
## [1] ""
## [1] "Mgl1"
## [1] 0
## [1] "Fold enrichment: 2.67912347186028"
## [1] "Standard deviations from mean: 6.5342324736485"
## [1] ""
## [1] "Mgl2"
## [1] 0.001
## [1] "Fold enrichment: 2.16122786010939"
## [1] "Standard deviations from mean: 4.27562902833384"
## [1] ""
## [1] "Oligo1"
## [1] 0.927
## [1] ""
## [1] "Oligo2"
## [1] 0.999
## [1] ""
## [1] "Oligo3"
## [1] 0.029
## [1] "Fold enrichment: 1.25217640356172"
## [1] "Standard deviations from mean: 1.97625341112682"
## [1] ""
## [1] "Oligo4"
## [1] 0.086
## [1] ""
## [1] "Oligo5"
## [1] 0.54
## [1] ""
## [1] "Oligo6"
## [1] 0.505
## [1] ""
## [1] "Peric"
## [1] 0.321
## [1] ""
## [1] "Pvm1"
## [1] 0
## [1] "Fold enrichment: 4.06462314419791"
## [1] "Standard deviations from mean: 13.725418957482"
## [1] ""
## [1] "Pvm2"
## [1] 0
## [1] "Fold enrichment: 2.8017868173953"
## [1] "Standard deviations from mean: 7.44091425335518"
## [1] ""
## [1] "S1PyrDL"
## [1] 0.451
## [1] ""
## [1] "S1PyrL23"
## [1] 1
## [1] ""
## [1] "S1PyrL4"
## [1] 1
## [1] ""
## [1] "S1PyrL5"
## [1] 1
## [1] ""
## [1] "S1PyrL5a"
## [1] 0.828
## [1] ""
## [1] "S1PyrL6"
## [1] 0.981
## [1] ""
## [1] "S1PyrL6b"
## [1] 0.676
## [1] ""
## [1] "SubPyr"
## [1] 0.355
## [1] ""
## [1] "Vend1"
## [1] 0.01
## [1] "Fold enrichment: 1.62933546749876"
## [1] "Standard deviations from mean: 2.87734797032007"
## [1] ""
## [1] "Vend2"
## [1] 0.04
## [1] "Fold enrichment: 1.33204655391656"
## [1] "Standard deviations from mean: 1.8415103360028"
## [1] ""
## [1] "Vsmc"
## [1] 0.229
## [1] ""
print(ewce.plot(full_results$results,mtc_method="BH"))
# Which cell types are associated with genes duplicated in mice and humans?
homoIDs_target = ortholog_data$species2_dup_species1_dup
symbols_target = get.symbol.from.homologID(homoIDs_target,species1,species2,ortholog_data,species2)
full_results = bootstrap.enrichment.test(sct_data=ctd,hits=symbols_target,bg=symbols_bg,reps=1000,annotLevel=2)
## [1] "H3f3a" "H3f3b" "C4b" "C4a" "Spin2d" "Frg2f1"
## [1] "(none)"
## [1] 0.958
## [1] ""
## [1] "Astro1"
## [1] 0.001
## [1] "Fold enrichment: 10.217407386849"
## [1] "Standard deviations from mean: 8.73070982332088"
## [1] ""
## [1] "Astro2"
## [1] 0.114
## [1] ""
## [1] "CA1Pyr1"
## [1] 0.856
## [1] ""
## [1] "CA1Pyr2"
## [1] 0.879
## [1] ""
## [1] "CA1PyrInt"
## [1] 0.643
## [1] ""
## [1] "CA2Pyr2"
## [1] 0.929
## [1] ""
## [1] "Choroid"
## [1] 0.902
## [1] ""
## [1] "ClauPyr"
## [1] 0.975
## [1] ""
## [1] "Epend"
## [1] 0.452
## [1] ""
## [1] "Int1"
## [1] 0.703
## [1] ""
## [1] "Int10"
## [1] 0.603
## [1] ""
## [1] "Int11"
## [1] 0.825
## [1] ""
## [1] "Int12"
## [1] 0.677
## [1] ""
## [1] "Int13"
## [1] 0.64
## [1] ""
## [1] "Int14"
## [1] 0.574
## [1] ""
## [1] "Int15"
## [1] 0.152
## [1] ""
## [1] "Int16"
## [1] 0.934
## [1] ""
## [1] "Int2"
## [1] 0.964
## [1] ""
## [1] "Int3"
## [1] 0.976
## [1] ""
## [1] "Int4"
## [1] 0.951
## [1] ""
## [1] "Int5"
## [1] 0.854
## [1] ""
## [1] "Int6"
## [1] 0.995
## [1] ""
## [1] "Int7"
## [1] 0.986
## [1] ""
## [1] "Int8"
## [1] 0.942
## [1] ""
## [1] "Int9"
## [1] 0.87
## [1] ""
## [1] "Mgl1"
## [1] 0.496
## [1] ""
## [1] "Mgl2"
## [1] 0.17
## [1] ""
## [1] "Oligo1"
## [1] 0.558
## [1] ""
## [1] "Oligo2"
## [1] 0.494
## [1] ""
## [1] "Oligo3"
## [1] 0.239
## [1] ""
## [1] "Oligo4"
## [1] 0.474
## [1] ""
## [1] "Oligo5"
## [1] 0.568
## [1] ""
## [1] "Oligo6"
## [1] 0.29
## [1] ""
## [1] "Peric"
## [1] 0.001
## [1] "Fold enrichment: 9.63297835452611"
## [1] "Standard deviations from mean: 7.75967056788391"
## [1] ""
## [1] "Pvm1"
## [1] 0.16
## [1] ""
## [1] "Pvm2"
## [1] 0.057
## [1] ""
## [1] "S1PyrDL"
## [1] 0.58
## [1] ""
## [1] "S1PyrL23"
## [1] 0.976
## [1] ""
## [1] "S1PyrL4"
## [1] 0.984
## [1] ""
## [1] "S1PyrL5"
## [1] 0.944
## [1] ""
## [1] "S1PyrL5a"
## [1] 0.002
## [1] "Fold enrichment: 4.39774314159853"
## [1] "Standard deviations from mean: 6.8787571122068"
## [1] ""
## [1] "S1PyrL6"
## [1] 0.76
## [1] ""
## [1] "S1PyrL6b"
## [1] 0.051
## [1] ""
## [1] "SubPyr"
## [1] 0.976
## [1] ""
## [1] "Vend1"
## [1] 0.616
## [1] ""
## [1] "Vend2"
## [1] 0.308
## [1] ""
## [1] "Vsmc"
## [1] 0.658
## [1] ""
print(ewce.plot(full_results$results,mtc_method="BH"))
NathanSkene/One2One documentation built on July 14, 2021, 7:48 a.m.
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One2one Orthologs
Nathan Skene 2018-01-17
This package is used to get 1:1 orthologs based on MGI homology data from http://www.informatics.jax.org/homology.shtml
The data is processed within the package but for key species comparisons is also stored in the data
Get the homolog data
library(One2One)
# Download and format the homolog data from MGI
allHomologs = load.homologs()
## [1] "Species for which homology classes are available:"
## [1] "mouse, laboratory" "human" "chimpanzee"
## [4] "macaque, rhesus" "dog, domestic" "cattle"
## [7] "rat" "frog, western clawed" "zebrafish"
## [10] "chicken"
# Get data on orthology between the two species
species1="human"
species2="mouse"
ortholog_data = analyse.orthology(species1,species2,allHomologs)
## [1] "Selected species: human"
## [1] "Selected species: mouse, laboratory"
## [1] "Full dataset contains 18708 genes from human"
## [1] "Full dataset contains 18995 genes from mouse"
## [1] "1954 genes which are present in human are deleted in mouse"
## [1] "2241 genes which are present in mouse are deleted in human"
## [1] "220 genes are duplicated in human"
## [1] "609 genes are duplicated in mouse"
## [1] "16470 are shared 1:1 between the two species"
# Check the 1:1 homologs
print(ortholog_data$orthologs_one2one[1:10,])
## HomoloGene ID human.symbol mouse.symbol
## 1 100 ETFA Etfa
## 2 1000 CLDN4 Cldn4
## 3 10001 HAUS2 Haus2
## 4 10003 EFHC1 Efhc1
## 5 10004 LRRC8D Lrrc8d
## 6 10005 THAP1 Thap1
## 7 100054 DGKD Dgkd
## 8 10006 ZDHHC4 Zdhhc4
## 9 100071 ANO5 Ano5
## 10 100077 UBALD2 Ubald2
Analyse differences in orthology using EWCE
# Load EWCE package
#install.packages("devtools")
#library(devtools)
#install_github("nathanskene/ewce")
library(EWCE)
data(ctd)
homoIDs_bg = ortholog_data$species2_allGenes
symbols_bg = get.symbol.from.homologID(homoIDs_bg,species1,species2,ortholog_data,species2)
# Which cell types are associated with genes deleted in humans, but present in mice?
homoIDs_target = ortholog_data$species2_present_species1_deleted
symbols_target = get.symbol.from.homologID(homoIDs_target,species1,species2,ortholog_data,species2)
full_results = bootstrap.enrichment.test(sct_data=ctd,hits=symbols_target,bg=symbols_bg,reps=1000,annotLevel=2)
## [1] "Zc3h15" "Spin2c" "Gm13023" "4933415F23Rik"
## [5] "Larp1b" "Dcpp2" "Dcpp3" "Vmn2r54"
## [9] "Cbr2" "Cntnap5b" "Tomm5" "9030025P20Rik"
## [13] "Gm10267" "Zfp955a" "Zfp955b" "Rpl34-ps1"
## [17] "Rpl34" "Trim43b" "2410002F23Rik" "Nptn"
## [21] "Mcts2" "Olfr117" "Skint7" "Dbil5"
## [25] "Doc2g" "Rpl23a" "Olfr944" "Oas1c"
## [29] "Oas1d" "Klra5" "Vmn1r195" "Psg23"
## [33] "Ccdc71" "Bmyc" "Naip5" "Vmn2r29"
## [37] "Ly6a" "Ly6c1" "Ly6c2" "Ly6f"
## [41] "Car15" "Trim30a" "Trim30d" "Cd209f"
## [45] "Vmn2r71" "Gimap9" "Gm3696" "Gm10406"
## [49] "Gm3558" "Gm5796" "Ccnjl" "Serpina3g"
## [53] "Tmsb10" "Tmsb15l" "Tmsb4x" "Calm1"
## [57] "Calm2" "Calm3" "Mettl7a2" "Mettl7a3"
## [61] "Fcna" "Gstm6" "Zfp93" "Zfp108"
## [65] "Zfp747" "Map3k7" "Akr1c13" "Prorsd1"
## [69] "Josd1" "Ccdc163" "Tstd3" "Lrrc9"
## [73] "BC051142" "Sult1a1" "Ms4a6b" "Adam6b"
## [77] "Oasl2" "Akr1b10" "Npcd" "B020004C17Rik"
## [81] "Nebl" "Fam187a" "Aldoart1" "Msl3l2"
## [85] "Zfp956" "4430402I18Rik" "Hmgn2" "Tpm1"
## [89] "Ppp2r5c" "Zkscan4" "Smok3b" "Zfp952"
## [93] "Cntnap5c" "Celf6" "Zfp740" "Sult5a1"
## [97] "2900026A02Rik" "Zfp958" "Vmn2r13" "Vmn2r87"
## [101] "Vmn2r61" "Srp54c" "Cyp4f17" "Gramd1c"
## [105] "Vmn2r2" "Lage3" "Zfp954" "Zim1"
## [109] "Ankrd50" "Smim11" "Zfp949" "Tgtp1"
## [113] "Znrd1as" "Fam193b" "Zeb2os" "Gm4858"
## [117] "Bmp8b" "Ctla2a" "Ctla2b" "Klrc3"
## [121] "Mcpt4" "Pdzph1" "Ms4a6c" "4930519F16Rik"
## [125] "9430038I01Rik" "Cox7b2" "Slco1a4" "Foxp1"
## [129] "Abca8a" "Snhg11" "Tmem191c" "Spink10"
## [133] "Nr1h5" "Tlr13" "1700023F06Rik" "Zfp35"
## [137] "Arxes1" "Arxes2" "Gm14295" "Cyp2j12"
## [141] "Slfn2" "Zfp945" "Zfp944" "Zfp942"
## [145] "Zfp994" "Zfp947" "Zfp995" "1810037I17Rik"
## [149] "0610009B22Rik" "Aldh3b3" "1700011I03Rik" "Snrpa"
## [153] "Olfr695" "Olfr945" "Zfp85" "BC048507"
## [157] "Spag6" "Cox5b" "Hspa1b" "Rnf113a1"
## [161] "Sf3a2" "Srsf5" "Otud5" "Rpl36"
## [165] "Zfp960" "Zfp97" "Rsrc2" "Crip2"
## [169] "Gstt3" "Ccl7" "Qars" "Prr13"
## [173] "Zfp658" "U2af1l4" "Spink2" "Plpp1"
## [177] "Cox6c" "Sf1" "Olfr1331" "Irgm1"
## [181] "Fus" "Zfp708" "Celf1" "Nxpe5"
## [185] "Maml2" "Aldoart2" "Alg13" "Plscr2"
## [189] "Supt20" "Abi3bp" "Afg3l1" "Snrpc"
## [193] "Hmgb3" "Clasrp" "Tpm2" "Zfp873"
## [197] "Sct" "Dmrtc1a" "Zfp943" "Cfhr2"
## [201] "Crb3" "Foxp2" "Vma21" "Dazap1"
## [205] "Prrt1" "Smim26" "Gm1673" "AW146154"
## [209] "Cdkn1c" "9130409I23Rik" "Rbx1" "Nedd4"
## [213] "Mptx2" "Mapre2" "Zfp748" "Akap9"
## [217] "Nxf7" "Ifi27" "Hnrnpa1" "Rbfox3"
## [221] "Ewsr1" "Evi5l" "Fnbp1l" "Setd1b"
## [225] "Rpl22l1" "Gstt1" "Gk" "Aph1c"
## [229] "Uba52" "Tmem115" "Rasl2-9" "Ppp1cc"
## [233] "Zfp874a" "Zfp874b" "Gsta4" "Fmnl1"
## [237] "Nrbp2" "Kcnn2" "Rcor3" "Ppp1r12b"
## [241] "Mamld1" "Nacad" "Pcmt1" "Plekha6"
## [245] "Hmgb1" "Cyp4f16" "Fam13a" "Zfp938"
## [249] "Eif1" "Hist1h1a" "Ifitm1" "Zfp53"
## [253] "Egfem1" "Dcaf12l1" "Perm1" "Foxn3"
## [257] "Rnf138rt1" "Trpc2" "Nos1ap" "Wasl"
## [261] "Nrgn" "Ugt1a7c" "Ehbp1l1" "Pcp4l1"
## [265] "Klf16" "Rpl36a" "E130308A19Rik" "Nisch"
## [269] "Gpihbp1" "Smco4" "Ttll13" "Snrpg"
## [273] "Macf1" "AA414768" "Brd4" "Zfp442"
## [277] "Zfp937" "Elob" "1500009L16Rik" "R3hcc1"
## [281] "Fip1l1" "Gm3604" "Gm5141" "Tchh"
## [285] "C530008M17Rik" "Zfp961" "Zfp229" "Tmem29"
## [289] "Ubap2l" "BC005561" "Zfp651" "Zfp882"
## [293] "Zfp568" "Clec2d" "Clec2g" "Zfp40"
## [297] "Nat8f4" "Ccdc162" "Rps27" "Rps27rt"
## [301] "Gm4832" "Tmem223" "Fhod1" "Apoc1"
## [305] "Kat6b" "Nes" "Zfp939" "2010315B03Rik"
## [309] "Bola2" "Rpl29" "D430019H16Rik" "Rpl31-ps12"
## [313] "Scd2" "Rpl37rt" "Dst" "Srrm3"
## [317] "Gm11780" "Acp5" "Acan" "Atp5k"
## [321] "Hrk" "Ivl" "Nefm" "Ptma"
## [325] "Bex1" "Tcf7" "Ttf1" "Tgoln1"
## [329] "Zfp101" "Zfp185" "Zfp60" "Anp32a"
## [333] "Cdc42" "Irs4" "Krt10" "Srgn"
## [337] "Supt4b" "Zfp59" "Aldh1a7" "Muc1"
## [341] "Cald1" "Rpl32" "Podxl" "Hist1h1e"
## [345] "Hmgn5" "S100a11" "Rplp1" "Slc22a21"
## [349] "Ncoa6" "Fam184b" "Ces1g" "Chtop"
## [353] "Zfp788" "Cmya5" "Scd3" "Bhlhe41"
## [357] "Mxra7" "3300002I08Rik" "Cd209g" "Ap2b1"
## [361] "Rbm33" "Cyp2j9" "4930502E18Rik" "Ccdc30"
## [365] "Zfp773" "Ifi27l2a" "Arhgef38" "Pcdhb18"
## [369] "Pgap2" "Calcb" "Zfp932" "Serpinb1c"
## [373] "Anp32b" "Akr1c14" "Zfp758" "AI661453"
## [377] "Zfp959" "Zfp810" "Pitpnc1" "Cetn4"
## [381] "Hnrnpa3" "Olfr1033" "Krt9" "2810021J22Rik"
## [385] "Zfp871" "Zfp677" "D130040H23Rik" "Diaph2"
## [389] "Serpinb1b" "4930486L24Rik" "Zfp940" "Nrg1"
## [393] "2610524H06Rik" "Zfp120" "Zbed4" "Zfp599"
## [397] "E430018J23Rik" "Bst2" "Zfp933" "Zfp532"
## [401] "Plcxd1" "Zfp81" "U2af1" "Kdm1b"
## [405] "Akap17b" "Aff2" "Gprasp2" "Sel1l2"
## [409] "Lrrc51" "Tmem18" "Mmgt2" "Morc2b"
## [413] "Fer1l4" "Tspyl3" "Efcab10" "Gm266"
## [417] "Pgr15l" "Pln" "Pou3f1" "Esrra"
## [421] "2610002M06Rik" "Lrrfip2" "Ccl6" "Serpinb6b"
## [425] "Acot1" "Igtp" "Map3k7cl" "Gtf2ird2"
## [429] "Lrrc74b" "Hmga2" "Atp6ap1l" "Fbll1"
## [433] "1700061G19Rik" "Fam183b" "Cops2" "Fbxo38"
## [437] "Fbxl22" "Msantd2" "2700097O09Rik" "Pwp2"
## [441] "Gstm3" "Snrpe" "Dync1i2" "Slc35a2"
## [445] "Alyref" "Irx5" "Lmo3" "Nmnat3"
## [449] "3830403N18Rik" "Xlr" "Xlr3b" "Anp32e"
## [453] "Dgcr6" "Ly6g6e" "Gm7903" "Yaf2"
## [457] "Mocs1" "Slc25a1" "Trhr2" "Lao1"
## [461] "Ttc30a2" "Gucy2g" "Zfp352" "Gm13277"
## [465] "Urah" "Cyb5r3" "Siglech" "Zfp870"
## [469] "Adam5" "Glycam1" "Ifi47" "2610028H24Rik"
## [473] "Commd6" "Spaca6" "Folh1" "Arf2"
## [477] "Sh3bgr" "Siah1b" "Zfp68" "Tha1"
## [481] "Fcrls" "Pcdhb4" "Pcdhb6" "Pcdhb11"
## [485] "Rab15" "Ttc39d" "Coa6" "Kctd12b"
## [489] "A430033K04Rik" "Gulo" "Tas2r134" "Ppfia4"
## [493] "Zfp763" "Cutal" "AI413582" "Slc26a10"
## [497] "Rps3a1" "Rrbp1" "Eda" "Setmar"
## [501] "Prps1l3" "H2-T24" "Adam3" "Abcb1b"
## [505] "Cyp2a12" "5031410I06Rik" "Gm21671" "Gm5862"
## [509] "Speer4b" "Ccdc50" "Actl11" "Aox4"
## [513] "Pcdhb14" "Prdx6b" "Csl" "Olfr38"
## [517] "Ahsa2" "4921509C19Rik" "2510002D24Rik" "Cmah"
## [521] "Adam1a" "Ktn1" "Olfr1179" "Olfr1246"
## [525] "Tpm4" "Gja6" "Mup3" "Mup5"
## [529] "Eci3" "Vmn1r13" "Zfp868" "Zfp61"
## [533] "Htr5b" "Lcn3" "Ubb" "Cyp2d22"
## [537] "Igbp1b" "Pdlim3" "Pmaip1" "4931417E11Rik"
## [541] "Mapk1ip1" "Uox" "Nat8f3" "Casp12"
## [545] "Ggta1" "Scd4" "Zfp52" "Acot5"
## [549] "Zfp472" "Slc7a15" "Tmem198b" "Tlr11"
## [553] "4930402F06Rik" "Sik1" "Gm1110" "Fam169b"
## [557] "Olfr1061" "Pvr" "Ggnbp1" "1600015I10Rik"
## [561] "Gm5885" "A630001G21Rik" "Cox7c" "Cbarp"
## [565] "Fbxw17" "Gm13178" "Ccdc74a" "Gm12185"
## [569] "Nrxn3" "Teddm3" "Gm12253" "Rhox3g"
## [573] "Madcam1" "Aldh3b2" "Rbmxl1" "Irs3"
## [577] "Zrsr1" "Vmn2r1" "Tnfrsf23" "Cd209b"
## [581] "Prss32" "Gpr165" "Isoc2b" "Milr1"
## [585] "Gm5127" "1700001J03Rik" "1700018F24Rik" "Actn3"
## [589] "Lipo1" "Cldn34c1" "2610008E11Rik" "Ccl9"
## [593] "Sp100" "Meis1" "Abca17" "Zfp94"
## [597] "Defb30" "Gm6377" "T2" "Mff"
## [601] "Nat8f5" "2310039H08Rik" "Anapc15" "Pcdhb7"
## [605] "Pcdhb9" "Pcdhb12" "AU041133" "4932429P05Rik"
## [609] "Prss1" "Prss3" "Masp1" "Pcdhb8"
## [613] "Rfpl4" "Olfr654" "Aox3" "Acaa1b"
## [617] "Clec4a3" "Otub1" "Alyref2" "Eif2s3y"
## [621] "Cabp1" "Atp8b5"
## [1] "(none)"
## [1] 1
## [1] ""
## [1] "Astro1"
## [1] 0.111
## [1] ""
## [1] "Astro2"
## [1] 0.506
## [1] ""
## [1] "CA1Pyr1"
## [1] 1
## [1] ""
## [1] "CA1Pyr2"
## [1] 0.998
## [1] ""
## [1] "CA1PyrInt"
## [1] 0.982
## [1] ""
## [1] "CA2Pyr2"
## [1] 0.4
## [1] ""
## [1] "Choroid"
## [1] 0.472
## [1] ""
## [1] "ClauPyr"
## [1] 1
## [1] ""
## [1] "Epend"
## [1] 0
## [1] "Fold enrichment: 1.50262729773882"
## [1] "Standard deviations from mean: 4.00966498040887"
## [1] ""
## [1] "Int1"
## [1] 0.096
## [1] ""
## [1] "Int10"
## [1] 0.217
## [1] ""
## [1] "Int11"
## [1] 0.2
## [1] ""
## [1] "Int12"
## [1] 1
## [1] ""
## [1] "Int13"
## [1] 0.622
## [1] ""
## [1] "Int14"
## [1] 1
## [1] ""
## [1] "Int15"
## [1] 0.681
## [1] ""
## [1] "Int16"
## [1] 1
## [1] ""
## [1] "Int2"
## [1] 0.99
## [1] ""
## [1] "Int3"
## [1] 0.979
## [1] ""
## [1] "Int4"
## [1] 0
## [1] "Fold enrichment: 1.30777242003489"
## [1] "Standard deviations from mean: 4.16660208841783"
## [1] ""
## [1] "Int5"
## [1] 0.998
## [1] ""
## [1] "Int6"
## [1] 1
## [1] ""
## [1] "Int7"
## [1] 0.972
## [1] ""
## [1] "Int8"
## [1] 0.993
## [1] ""
## [1] "Int9"
## [1] 0
## [1] "Fold enrichment: 1.30177765590248"
## [1] "Standard deviations from mean: 3.83481628715196"
## [1] ""
## [1] "Mgl1"
## [1] 0.138
## [1] ""
## [1] "Mgl2"
## [1] 0.286
## [1] ""
## [1] "Oligo1"
## [1] 0.968
## [1] ""
## [1] "Oligo2"
## [1] 1
## [1] ""
## [1] "Oligo3"
## [1] 0.566
## [1] ""
## [1] "Oligo4"
## [1] 0.983
## [1] ""
## [1] "Oligo5"
## [1] 0.995
## [1] ""
## [1] "Oligo6"
## [1] 0.853
## [1] ""
## [1] "Peric"
## [1] 0.013
## [1] "Fold enrichment: 1.28498272064174"
## [1] "Standard deviations from mean: 2.59867618305013"
## [1] ""
## [1] "Pvm1"
## [1] 0
## [1] "Fold enrichment: 1.56568184526585"
## [1] "Standard deviations from mean: 5.17543666137627"
## [1] ""
## [1] "Pvm2"
## [1] 0
## [1] "Fold enrichment: 1.86272831441951"
## [1] "Standard deviations from mean: 7.52773806569167"
## [1] ""
## [1] "S1PyrDL"
## [1] 0.979
## [1] ""
## [1] "S1PyrL23"
## [1] 1
## [1] ""
## [1] "S1PyrL4"
## [1] 0.986
## [1] ""
## [1] "S1PyrL5"
## [1] 1
## [1] ""
## [1] "S1PyrL5a"
## [1] 0.85
## [1] ""
## [1] "S1PyrL6"
## [1] 0.004
## [1] "Fold enrichment: 1.11281768827408"
## [1] "Standard deviations from mean: 2.86061883356584"
## [1] ""
## [1] "S1PyrL6b"
## [1] 0.813
## [1] ""
## [1] "SubPyr"
## [1] 0.003
## [1] "Fold enrichment: 1.18967265885381"
## [1] "Standard deviations from mean: 3.51133327908488"
## [1] ""
## [1] "Vend1"
## [1] 0.593
## [1] ""
## [1] "Vend2"
## [1] 0.002
## [1] "Fold enrichment: 1.31743001377535"
## [1] "Standard deviations from mean: 3.59625082030488"
## [1] ""
## [1] "Vsmc"
## [1] 0.115
## [1] ""
print(ewce.plot(full_results$results,mtc_method="BH"))
# Which cell types are associated with genes duplicated in humans, but singletons in mice?
homoIDs_target = ortholog_data$species2_onceOnly_species1_dup
symbols_target = get.symbol.from.homologID(homoIDs_target,species1,species2,ortholog_data,species2)
full_results = bootstrap.enrichment.test(sct_data=ctd,hits=symbols_target,bg=symbols_bg,reps=1000,annotLevel=2)
## [1] "Slx1b" "Coro7" "1110012L19Rik" "F8a"
## [5] "Pramef8" "Arpin" "Nomo1" "Klhl23"
## [9] "Anxa8" "Arhgap8" "Smn1" "D10Jhu81e"
## [13] "Cbs" "Gstt2" "Nbl1" "Prodh"
## [17] "Washc2" "Fcgr4" "Cryaa" "Serf1"
## [21] "Icosl" "Pmf1" "Sgk3" "Ccz1"
## [25] "Ckmt1" "Pom121" "Hspa1a" "Mrpl23"
## [29] "Ankhd1" "Ranbp2" "Asb3" "Gpr89"
## [1] "(none)"
## [1] 0.603
## [1] ""
## [1] "Astro1"
## [1] 0.078
## [1] ""
## [1] "Astro2"
## [1] 0.112
## [1] ""
## [1] "CA1Pyr1"
## [1] 0.601
## [1] ""
## [1] "CA1Pyr2"
## [1] 0.5
## [1] ""
## [1] "CA1PyrInt"
## [1] 0.197
## [1] ""
## [1] "CA2Pyr2"
## [1] 0.717
## [1] ""
## [1] "Choroid"
## [1] 0.874
## [1] ""
## [1] "ClauPyr"
## [1] 0.576
## [1] ""
## [1] "Epend"
## [1] 0.14
## [1] ""
## [1] "Int1"
## [1] 0.077
## [1] ""
## [1] "Int10"
## [1] 0.694
## [1] ""
## [1] "Int11"
## [1] 0.909
## [1] ""
## [1] "Int12"
## [1] 0.56
## [1] ""
## [1] "Int13"
## [1] 0.504
## [1] ""
## [1] "Int14"
## [1] 0.837
## [1] ""
## [1] "Int15"
## [1] 0.753
## [1] ""
## [1] "Int16"
## [1] 0.675
## [1] ""
## [1] "Int2"
## [1] 0.094
## [1] ""
## [1] "Int3"
## [1] 0.727
## [1] ""
## [1] "Int4"
## [1] 0.802
## [1] ""
## [1] "Int5"
## [1] 0.831
## [1] ""
## [1] "Int6"
## [1] 0.902
## [1] ""
## [1] "Int7"
## [1] 0.458
## [1] ""
## [1] "Int8"
## [1] 0.536
## [1] ""
## [1] "Int9"
## [1] 0.687
## [1] ""
## [1] "Mgl1"
## [1] 0.107
## [1] ""
## [1] "Mgl2"
## [1] 0.399
## [1] ""
## [1] "Oligo1"
## [1] 0.93
## [1] ""
## [1] "Oligo2"
## [1] 0.525
## [1] ""
## [1] "Oligo3"
## [1] 0.274
## [1] ""
## [1] "Oligo4"
## [1] 0.911
## [1] ""
## [1] "Oligo5"
## [1] 0.762
## [1] ""
## [1] "Oligo6"
## [1] 0.746
## [1] ""
## [1] "Peric"
## [1] 0.43
## [1] ""
## [1] "Pvm1"
## [1] 0.16
## [1] ""
## [1] "Pvm2"
## [1] 0.549
## [1] ""
## [1] "S1PyrDL"
## [1] 0.51
## [1] ""
## [1] "S1PyrL23"
## [1] 0.234
## [1] ""
## [1] "S1PyrL4"
## [1] 0.68
## [1] ""
## [1] "S1PyrL5"
## [1] 0.998
## [1] ""
## [1] "S1PyrL5a"
## [1] 0.785
## [1] ""
## [1] "S1PyrL6"
## [1] 0.78
## [1] ""
## [1] "S1PyrL6b"
## [1] 0.632
## [1] ""
## [1] "SubPyr"
## [1] 0.452
## [1] ""
## [1] "Vend1"
## [1] 0.016
## [1] "Fold enrichment: 2.18550258806339"
## [1] "Standard deviations from mean: 2.66827596868916"
## [1] ""
## [1] "Vend2"
## [1] 0.147
## [1] ""
## [1] "Vsmc"
## [1] 0.335
## [1] ""
print(ewce.plot(full_results$results,mtc_method="BH"))
# Which cell types are associated with genes duplicated in mice, but singletons in human?
homoIDs_target = ortholog_data$species1_onceOnly_species2_dup
symbols_target = get.symbol.from.homologID(homoIDs_target,species1,species2,ortholog_data,species2)
full_results = bootstrap.enrichment.test(sct_data=ctd,hits=symbols_target,bg=symbols_bg,reps=1000,annotLevel=2)
## [1] "Bglap" "Bglap2" "Pdcd5" "Ywhaq"
## [5] "Gapdh" "3830406C13Rik" "Nutf2" "Serpina3c"
## [9] "Serpina3n" "Rpl17" "Krtap10-4" "Ifi207"
## [13] "Ifi203" "Ifi204" "Ifi211" "Mndal"
## [17] "Gemin6" "Ifit3b" "Ifit3" "Rsph3a"
## [21] "Rsph3b" "Lyz2" "Lyz1" "2700062C07Rik"
## [25] "Amd2" "Ptges3" "Tuba3a" "Trim34a"
## [29] "H2-Bl" "H2-Q4" "H2-Q10" "H2-K1"
## [33] "H2-Q2" "H2-D1" "Olfr287" "Ceacam1"
## [37] "Gbp9" "Zfp110" "Zfp369" "C1ra"
## [41] "C1s1" "C1s2" "Zfp985" "Zfp987"
## [45] "Zfp979" "Zfp984" "Zfp981" "Zfp992"
## [49] "Zfp738" "Zfp729a" "Zfp729b" "Cdv3"
## [53] "Tceal6" "Tceal3" "Zfp975" "Zfp976"
## [57] "H2-T23" "H2-T-ps" "Pirb" "Gm14548"
## [61] "Zfp607b" "Zfp607a" "Gm14325" "Zfp970"
## [65] "Zfp971" "Gm14326" "Gm14305" "Eno1"
## [69] "Zfp931" "Pih1h3b" "Ndufa11" "Oas1g"
## [73] "Serpina1c" "Il4i1" "Pnp" "Pnp2"
## [77] "Srp54a" "Rbm12b2" "Rbm12b1" "Selenbp1"
## [81] "Bcl2a1d" "Bcl2a1b" "Bcl2a1a" "Rpl6"
## [85] "Rnaset2a" "Rbm3" "Bnip3l" "Ndufb4"
## [89] "Csf2rb" "Csf2rb2" "Cisd3" "Eif3j2"
## [93] "Atf1" "Ndufs6" "Gmfg" "Gng5"
## [97] "Sec61g" "Gimap5" "Dnah7b" "Dnah7a"
## [101] "Sap18b" "Sap18" "Mfap1a" "Mfap1b"
## [105] "Slfn8" "Mthfsl" "Mthfs" "Dynlt1a"
## [109] "Dynlt1b" "Cd55" "Evi2b" "Impdh2"
## [113] "Chchd2" "Tmed10" "Mterf1a" "Mterf1b"
## [117] "Esd" "Rpl13" "Acat3" "Acat2"
## [121] "Tmed2" "Trp53rkb" "Trp53rka" "Mrto4"
## [125] "Gstp1" "Klk1b5" "Klk1b27" "H2-DMb1"
## [129] "Olfr110" "Gsta2" "Cd300c2" "Trim12c"
## [133] "Ifit1bl1" "Mgl2" "Clec10a" "Ftl1"
## [137] "Ndufab1" "Rybp" "Llph" "Acot10"
## [141] "Acot9" "Sp110" "Prnd" "Glipr1l1"
## [145] "Ubl4a" "Lilr4b" "Lilrb4a" "Nudt11"
## [149] "Nudt10" "Dnajc19" "Phf11d" "Phf11b"
## [153] "Il11ra1" "Sms"
## [1] "(none)"
## [1] 0.997
## [1] ""
## [1] "Astro1"
## [1] 0.158
## [1] ""
## [1] "Astro2"
## [1] 0.684
## [1] ""
## [1] "CA1Pyr1"
## [1] 1
## [1] ""
## [1] "CA1Pyr2"
## [1] 0.989
## [1] ""
## [1] "CA1PyrInt"
## [1] 1
## [1] ""
## [1] "CA2Pyr2"
## [1] 1
## [1] ""
## [1] "Choroid"
## [1] 0.178
## [1] ""
## [1] "ClauPyr"
## [1] 1
## [1] ""
## [1] "Epend"
## [1] 0.464
## [1] ""
## [1] "Int1"
## [1] 0.954
## [1] ""
## [1] "Int10"
## [1] 1
## [1] ""
## [1] "Int11"
## [1] 0.793
## [1] ""
## [1] "Int12"
## [1] 1
## [1] ""
## [1] "Int13"
## [1] 0.992
## [1] ""
## [1] "Int14"
## [1] 1
## [1] ""
## [1] "Int15"
## [1] 0.991
## [1] ""
## [1] "Int16"
## [1] 1
## [1] ""
## [1] "Int2"
## [1] 0.781
## [1] ""
## [1] "Int3"
## [1] 1
## [1] ""
## [1] "Int4"
## [1] 0.586
## [1] ""
## [1] "Int5"
## [1] 0.863
## [1] ""
## [1] "Int6"
## [1] 0.063
## [1] ""
## [1] "Int7"
## [1] 1
## [1] ""
## [1] "Int8"
## [1] 0.931
## [1] ""
## [1] "Int9"
## [1] 0.991
## [1] ""
## [1] "Mgl1"
## [1] 0
## [1] "Fold enrichment: 2.67912347186028"
## [1] "Standard deviations from mean: 6.5342324736485"
## [1] ""
## [1] "Mgl2"
## [1] 0.001
## [1] "Fold enrichment: 2.16122786010939"
## [1] "Standard deviations from mean: 4.27562902833384"
## [1] ""
## [1] "Oligo1"
## [1] 0.927
## [1] ""
## [1] "Oligo2"
## [1] 0.999
## [1] ""
## [1] "Oligo3"
## [1] 0.029
## [1] "Fold enrichment: 1.25217640356172"
## [1] "Standard deviations from mean: 1.97625341112682"
## [1] ""
## [1] "Oligo4"
## [1] 0.086
## [1] ""
## [1] "Oligo5"
## [1] 0.54
## [1] ""
## [1] "Oligo6"
## [1] 0.505
## [1] ""
## [1] "Peric"
## [1] 0.321
## [1] ""
## [1] "Pvm1"
## [1] 0
## [1] "Fold enrichment: 4.06462314419791"
## [1] "Standard deviations from mean: 13.725418957482"
## [1] ""
## [1] "Pvm2"
## [1] 0
## [1] "Fold enrichment: 2.8017868173953"
## [1] "Standard deviations from mean: 7.44091425335518"
## [1] ""
## [1] "S1PyrDL"
## [1] 0.451
## [1] ""
## [1] "S1PyrL23"
## [1] 1
## [1] ""
## [1] "S1PyrL4"
## [1] 1
## [1] ""
## [1] "S1PyrL5"
## [1] 1
## [1] ""
## [1] "S1PyrL5a"
## [1] 0.828
## [1] ""
## [1] "S1PyrL6"
## [1] 0.981
## [1] ""
## [1] "S1PyrL6b"
## [1] 0.676
## [1] ""
## [1] "SubPyr"
## [1] 0.355
## [1] ""
## [1] "Vend1"
## [1] 0.01
## [1] "Fold enrichment: 1.62933546749876"
## [1] "Standard deviations from mean: 2.87734797032007"
## [1] ""
## [1] "Vend2"
## [1] 0.04
## [1] "Fold enrichment: 1.33204655391656"
## [1] "Standard deviations from mean: 1.8415103360028"
## [1] ""
## [1] "Vsmc"
## [1] 0.229
## [1] ""
print(ewce.plot(full_results$results,mtc_method="BH"))
# Which cell types are associated with genes duplicated in mice and humans?
homoIDs_target = ortholog_data$species2_dup_species1_dup
symbols_target = get.symbol.from.homologID(homoIDs_target,species1,species2,ortholog_data,species2)
full_results = bootstrap.enrichment.test(sct_data=ctd,hits=symbols_target,bg=symbols_bg,reps=1000,annotLevel=2)
## [1] "H3f3a" "H3f3b" "C4b" "C4a" "Spin2d" "Frg2f1"
## [1] "(none)"
## [1] 0.958
## [1] ""
## [1] "Astro1"
## [1] 0.001
## [1] "Fold enrichment: 10.217407386849"
## [1] "Standard deviations from mean: 8.73070982332088"
## [1] ""
## [1] "Astro2"
## [1] 0.114
## [1] ""
## [1] "CA1Pyr1"
## [1] 0.856
## [1] ""
## [1] "CA1Pyr2"
## [1] 0.879
## [1] ""
## [1] "CA1PyrInt"
## [1] 0.643
## [1] ""
## [1] "CA2Pyr2"
## [1] 0.929
## [1] ""
## [1] "Choroid"
## [1] 0.902
## [1] ""
## [1] "ClauPyr"
## [1] 0.975
## [1] ""
## [1] "Epend"
## [1] 0.452
## [1] ""
## [1] "Int1"
## [1] 0.703
## [1] ""
## [1] "Int10"
## [1] 0.603
## [1] ""
## [1] "Int11"
## [1] 0.825
## [1] ""
## [1] "Int12"
## [1] 0.677
## [1] ""
## [1] "Int13"
## [1] 0.64
## [1] ""
## [1] "Int14"
## [1] 0.574
## [1] ""
## [1] "Int15"
## [1] 0.152
## [1] ""
## [1] "Int16"
## [1] 0.934
## [1] ""
## [1] "Int2"
## [1] 0.964
## [1] ""
## [1] "Int3"
## [1] 0.976
## [1] ""
## [1] "Int4"
## [1] 0.951
## [1] ""
## [1] "Int5"
## [1] 0.854
## [1] ""
## [1] "Int6"
## [1] 0.995
## [1] ""
## [1] "Int7"
## [1] 0.986
## [1] ""
## [1] "Int8"
## [1] 0.942
## [1] ""
## [1] "Int9"
## [1] 0.87
## [1] ""
## [1] "Mgl1"
## [1] 0.496
## [1] ""
## [1] "Mgl2"
## [1] 0.17
## [1] ""
## [1] "Oligo1"
## [1] 0.558
## [1] ""
## [1] "Oligo2"
## [1] 0.494
## [1] ""
## [1] "Oligo3"
## [1] 0.239
## [1] ""
## [1] "Oligo4"
## [1] 0.474
## [1] ""
## [1] "Oligo5"
## [1] 0.568
## [1] ""
## [1] "Oligo6"
## [1] 0.29
## [1] ""
## [1] "Peric"
## [1] 0.001
## [1] "Fold enrichment: 9.63297835452611"
## [1] "Standard deviations from mean: 7.75967056788391"
## [1] ""
## [1] "Pvm1"
## [1] 0.16
## [1] ""
## [1] "Pvm2"
## [1] 0.057
## [1] ""
## [1] "S1PyrDL"
## [1] 0.58
## [1] ""
## [1] "S1PyrL23"
## [1] 0.976
## [1] ""
## [1] "S1PyrL4"
## [1] 0.984
## [1] ""
## [1] "S1PyrL5"
## [1] 0.944
## [1] ""
## [1] "S1PyrL5a"
## [1] 0.002
## [1] "Fold enrichment: 4.39774314159853"
## [1] "Standard deviations from mean: 6.8787571122068"
## [1] ""
## [1] "S1PyrL6"
## [1] 0.76
## [1] ""
## [1] "S1PyrL6b"
## [1] 0.051
## [1] ""
## [1] "SubPyr"
## [1] 0.976
## [1] ""
## [1] "Vend1"
## [1] 0.616
## [1] ""
## [1] "Vend2"
## [1] 0.308
## [1] ""
## [1] "Vsmc"
## [1] 0.658
## [1] ""
print(ewce.plot(full_results$results,mtc_method="BH"))
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