Supplementary material Olgert Denas September 24, 2014 List of Figures 1 Workflow of data and experiments. .3 2 The number of TFos for all human and mouse cell types mapped by each of the considered whole genome alignments . .4 3 For each human celltype-factor pair we tested whether the SeqCons rate (of all TFos how many are SeqCons) is higher than expected by a Binomial test . .5 4 For each mouse celltype-factor pair we tested whether the SeqCons rate (of all TFos how many are SeqCons) is higher than expected by a Binomial test . .6 5 The distribution of mouse mappable TFos across cell types ...............7 6 The distribution of human mappable TFos across cell types ..............8 7 The distribution of mouse mappable TFos across transcription factors ........9 8 The distribution of human mappable TFos across transcription factors ........ 10 9 The distribution of mouse mappable TFos nucleotides across cell types ........ 11 10 The distribution of human mappable TFos nucleotides across cell types ........ 12 11 The distribution of mouse mappable TFos nucleotides across transcription factors .. 13 12 The distribution of human mappable TFos nucleotides across transcription factors . 14 13 For each celltype-factor pair we tested whether the (log) binding signal over Funct- Cons or FunctActive elements was significantly different from that over SeqCons elements . 15 14 For each celltype-factor pair we tested whether the (log) binding signal over Funct- Cons or FunctActive elements was significantly different from that over SeqCons elements . 16 15 Classification of mappable elements for all three analogous cell types . 17 16 Classification of mappable elements for all three analogous cell types . 18 17 The plot shows the number of FunctActive elements from a query assay as a function of the subset size . 19 18 The plot shows the number of FunctActive elements from a query assay with respect to a subset of assays from the other species . 20 19 We modeled the situation of a set of assays that have no co-association, thus overlap with an exclusive set of TFos on the other species . 21 20 A mouse Rad21 occupancy site mapped on human chromosome 20. Mapping is guided by the human-mouse whole genome alignments which report 5 insertions in human. We classified this mouse TFos as FunctCons, as its mapped version in human overlapps with Rad21 occupancy sites in K562. 22 List of Tables 1 Peak signal statistics by peak classes . 23 2 Analogous cells . 23 3 Counts of mappable, functionally active, and total TFos. The table reports both the element count and the coverage in mega bases . 24 4 Number of TFos mapped by each alignment for select assays. An element can be mapped if it overlaps DHS elements and shared human mouse DNA by half of its length. 24 1 5 Number of TFos mapped by each alignment for select assays. An element can be mapped if it overlaps DHS elements and shared human mouse DNA by half of its length. Continues ... 25 6 Number of TFos mapped by each alignment for select assays. An element can be mapped if it overlaps DHS elements and shared human mouse DNA by half of its length. 26 2 1 Supplementary figures Figure 1: Workflow of data and experiments. 3 Wi38 Werirb1 U87 U2os T47d Sknshra Sknsh Sknmc Shsy5y Saec Rptec Raji Pfsk1 Pbdefetal Pbde Panc1 Nt2d1 Nhlf Nhek Nhdfneo Nb4 Mcf7 Mcf10aes K562 Imr90 Hvmf Huvec Hrpe Hre Hpf Hpaf Hmf Hmec Hl60 Hffmyc Hff Hepg2 Helas3 Hek293t Hek293 Hee Hct116 Hcpe Hcm Hcfaa Hbmec Hasp item_class Hac H1hesc Gm19193 Gm19099 epo Gm18951 Gm18526 Gm18505 Gm15510 shared Gm12892 Gm12891 Gm12878 Gm12875 ucsc Gm12874 Gm12873 Gm12872 Gm12865 Gm12864 Gm12801 Gm10847 Gm08714 Cell type (hg19 and mm9) Gm06990 Ecc1 Caco2 Bj Be2c Aoaf Ag10803 Ag09319 Ag09309 Ag04450 Ag04449 A549 Wbrain Thymus Testis Spleen Smint Olfact Mel Megakaryo Mef Lung Liver Limb Kidney Heart G1eer4e2 G1eer4 G1e Ese14 Esb4 Erythrobl Cortex Ch12 Cbellum Bmdm Bmarrow 0e+00 2e+05 4e+05 6e+05 element count Figure 2: The number of TFos for all human and mouse cell types mapped by each of the considered whole genome alignments. Here we show, only those TFos that overlap by half their length with a DHS peak. See supplementary Table 4 for more details. 4 1.00 0.75 significant TRUE 0.50 FALSE 0.25 0.00 0 200 400 1:nrow(a) Figure 3: For each human celltype-factor pair we tested whether the SeqCons rate (of all TFos how many are SeqCons) is higher than expected by a Binomial test. The vertical lines show the estimated 99% confidence interval and the black line indicates the expected rate. The color of the vertical lines indicates whether the interval contains the expected value. 5 0.8 significant TRUE 0.6 0.4 0 40 80 120 1:nrow(a) Figure 4: For each mouse celltype-factor pair we tested whether the SeqCons rate (of all TFos how many are SeqCons) is higher than expected by a Binomial test. The vertical lines show the estimated 99% confidence interval and the black line indicates the expected rate. The color of the vertical lines indicates whether the interval contains the expected value. 6 Wbrain Thymus Olfact Heart Cbellum Megakaryo Smint Limb Cortex Ch12 Spleen Mef Lung Cell Bmdm Liver Testis Bmarrow Mel Kidney G1eer4 Erythrobl Ese14 Esb4 G1eer4e2 G1e 0.7 0.8 0.9 Fraction of elements Figure 5: The distribution of mouse mappable TFos across cell types. The box-plot for each cell type summarizes the distribution of values for the fraction of elements that can be mapped on the other species. Occupied segments for each cell type contribute one value to the distribution. 7 Hek293 Nt2d1 Pfsk1 Sknsh Hct116 Raji U87 Sknmc Hek293t Panc1 Gm10847 Shsy5y Gm15510 Pbdefetal Helas3 H1hesc Pbde Gm12892 Gm18526 Gm18951 Gm18505 Gm19099 Gm19193 A549 Hepg2 Mcf7 Gm12878 Gm12891 Ecc1 Nb4 Gm12801 Huvec Sknshra Nhlf Mcf10aes Hff Wi38 Ag04450 Hac Nhdfneo Cell T47d Ag09309 Hcm K562 Hre Bj Hee Hffmyc Ag10803 Ag09319 Hpf Imr90 Hmf Hasp Gm06990 Hpaf Hvmf Nhek Hmec Hcfaa Aoaf Hl60 Hrpe Gm12874 Gm12865 Be2c Ag04449 Gm12875 Gm12872 Saec Gm12864 Hbmec Hcpe Caco2 Gm12873 Rptec Werirb1 U2os Gm08714 0.5 0.6 0.7 0.8 0.9 Fraction of elements Figure 6: The distribution of human mappable TFos across cell types. The box-plot for each cell type summarizes the distribution of values for the fraction of elements that can be mapped on the other species. 8 Ubfsc13125 Maz Gnc5 Mazab85725 Ubf Gcn5 Fli1sc356 Sin3anb6001263 Pol2 Chd1 Hcfc1 Hcfc1nb10068209 Sin3a Mxi1af4185 Nelfe E2f4 Znfmizdcp1ab65767 Chd1nb10060411 Corestsc30189 Chd2ab68301 Znfmizdcp1 Max Gata2sc9008 Pax5c Usf2 Bhlhe40nb100 Pol2s2 Tf Cmybsc7874 Cmybh141 Zkscan1hpa006672 Ets1 Cjun Nrf2 Bhlhe40 Cmyc Tbp Zc3h11anb10074650 P300sc584 Gata1a Zkscan1 Corest Znf384hpa004051 Jund P300 Tal1 Ctcf Smc3ab9263 Rad21 Znf384 Gata1 Mafkab50322 Ctcfb Pol24h8 Ctcfsc15914 Mafk 0.6 0.7 0.8 0.9 Fraction of elements Figure 7: The distribution of mouse mappable TFos across transcription factors. The box-plot for each transcription factor summarizes the distribution of values for the fraction of elements that can be mapped on the other species. 9 Grp20 Suz12 Ctbp2 Irf3 E2f1 Spt20 Cebpz Brca1a300 Hae2f1 Sin3anb6001263 Hmgn3 Elk4 E2f4 Nfya Ccnt2 Sin3ak20 Chd1a301218a Mazab85725 Sp2 Nrf1 Sp2sc643 Taf1 Mxi1 Chd2 Ubfsc13125 Yy1c Elk112771 Srebp1 Baf170 Foxp2 Ubtfsab1404509 Creb1sc240 Tcf7l2 Mxi1af4185 Brca1 Baf155 Pol2 Sp4v20 Gata3sc269sc269 Gtf2f1 Tr4 Yy1sc281 Ini1 Brg1 Chd2ab68301 Gtf2b E2f6 Six5 P300sc582 Ets1 Gabp Corestsc30189 Zkscan1hpa006672 Egr1 Ap2alpha Tcf7l2c9b92565 Tbp Taf7sc101167 Zbtb7a Gtf2f1ab28179 Rfx5200401194 Cebpdsc636 Max Zbtb7asc34508 Ap2gamma Pol24h8 Cmyc Pgc1a Sp1 Pmlsc71910 Kap1 Yy1 Nrsf Bhlhe40 Irf1 Stat1 Znf263 Whip Nfyb Erra Atf3 Ehdac8 Thap1sc98174 Znf143166181ap Mybl2sc81192 Rxra Gata3 Nelfe Hdac2sc6296 Elf1sc631 P300 Bclaf101388 Pol2s2 Zeb1sc25388 Gata1 Mbd4sc271530 Bhlhe40c Zbtb33 Ikzf1iknucla Tblr1ab24550 Nfkb Nanogsc33759 Bach1 Elf1 Tf Gata3sc269 Arid3anb100279 Atf2sc81188 Gr Egata2 Stat2 Znf217 Fosl1sc183 Gata2 Srf Usf1sc8983 Eralphaa Tblr1nb600270 Mta3sc81325 Hnf4a Tcf12 Nficsc81335 Bhlhe40nb100 Foxm1sc502 Tcf3 Corestab24166 Nfe2sc22827 Eraa Mef2csc13268 Gata3sc268 Stat3 Pou2f2 P300b Enr4a1 Znf143 Cfos Hnf4gsc6558 Usf2 Pbx3 Ejunb Smc3ab9263 Cjun Ejund Prdm19115 Stat5asc74442 P300sc584sc584 Pax5n19 Foxa1sc6553 Bach1sc14700 Nfatc1sc17834 Mef2a Nr2f2sc271940 Arid3asc8821 Ctcf Tead4sc101184 Atf106325 Rad21 Zzz3 Ctcfb Ebf1sc137065 Jund Foxa1 Ctcfc Bcl3 Pax5c20 Ctcfsc15914c20 Hnf4asc8987 Efos Ctcflsc98982 Cbx3sc101004 Irf4sc6059 Mafk Trim28sc81411 Foxa1sc101058 Fosl2 Runx3sc101553 Foxa2sc6554 Ctcfsc5916 Bcl11a Maffm8194 Mafksc477 Usf1 Rfx5 Cebpb Mafkab50322 Pu1 Maff Cebpbsc150 Sirt6 Srebp2 Tal1sc12984 Nfe2 Pou5f1sc9081 Batf Gcn5 Gata2sc267 Esr Hsf1 Znf274m01 Setdb1 Brf2 Znf274 Tf3c110 Rpc155 Bdp1 Brf1 Pol3 0.25 0.50 0.75 Fraction of elements Figure 8: The distribution of human mappable TFos across transcription factors. The box-plot for each transcription factor summarizes the distribution of values for the fraction of elements that can be mapped on the other species. 10 Wbrain Thymus Olfact Heart Cbellum Megakaryo Smint Cortex Ch12 Mef Limb Lung Liver Cell Bmdm Spleen Bmarrow Testis Mel Kidney Erythrobl Esb4 G1eer4 Ese14 G1eer4e2 G1e 0.60 0.65 0.70 0.75 0.80 0.85 Fraction of bases Figure 9: The distribution of mouse mappable TFos nucleotides across cell types. The box-plot for each cell type summarizes the distribution of values for the fraction of nucleotides that can be mapped on the other species. 11 Nt2d1 Hek293 Sknsh Pfsk1 Shsy5y Hct116 Sknmc U87 H1hesc Raji Hek293t Gm10847 Gm12892 Panc1 Helas3 Gm15510 Pbdefetal Gm18526 Pbde Gm18951 A549 Ecc1 Gm19099 Hepg2 Gm18505 Gm19193 Sknshra Huvec Mcf7 Mcf10aes Gm12878 Gm12891 Nb4 T47d Nhlf K562 Hff Hac Gm12801 Nhdfneo Cell Hcm Ag04450 Imr90 Bj Wi38 Ag09319 Hre Hffmyc Ag10803 Ag09309 Hee Hpf Hpaf Nhek Hvmf Hmec Hasp Ag04449 Aoaf Hmf Hcfaa Be2c Saec Gm06990 Hrpe Hcpe Hbmec Gm12874 Gm12865 Rptec Gm12872 Gm12864 Gm12875 Hl60 Gm12873 Caco2 U2os Werirb1 Gm08714 0.5 0.6 0.7 Fraction of bases Figure 10: The distribution of human mappable TFos nucleotides across cell types.