Motif activity calculations on UPDATE 010

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Methodology

Motif activities were calculated for all samples for all five organisms using an approach similar to the MARA analysis developed by Erik and Piotr during FANTOM4. First, transcription factor binding sites were predicted in the -300..+100 base pair region around each level-2 promoter in the UPDATE_010 data set. Phylogeny information was included by using the whole-genome alignments from UCSC, but to speed up the calculations no local realignment was done. Note that the species included in the phylogenetic tree depend on what is available from UCSC, and therefore is different for each organism for which we have data. I used the following organisms:

  • Human: hg19, rheMac2, mm9, rn4, bosTau4, equCab2, canFam2, monDom5, galGal3
  • Mouse: mm9, rn4, hg18, rheMac2, bosTau3, equCab1, canFam2, monDom4, galGal3
  • Rat: rn4, mm8, hg18, canFam2, bosTau2, monDom4, galGal2
  • Dog: canFam2, hg17, mm6, rn3
  • Chicken: galGal3, hg18, mm8, rn4, monDom4

Whether phylogeny information should be included at all, and if so, how, is up for debate, but this is what I did for now.

Next, I associated TFBSs to promoters using a distance profile, which models the positions with respect to the promoter at which TFBSs are typically found. This distance profile is estimated for each motif separately and is based on the overall distribution of predicted TFBS positions with respect to level-2 promoters.

The motif activities were then calculated in two ways. First, I applied Motif Activity Response Analysis (MARA) to the promoters with their associated TFBSs and CAGE expression profiles. This calculation is virtually identical to MARA as used in FANTOM4. Note that MARA effectively estimates the motif activities such that it can optimally explain the differences in CAGE expression between the experimental conditions. Therefore, each calculated motif activity depends on the set of conditions on which MARA was performed. To calculate activities independently of each other, I also calculated the motif activities on each condition separately, without the normalization over each condition as is done in MARA. To distinguish this calculation from MARA, I refer to it as MASA (正; Motif Activity State Analysis, as it looks at the motif activities in a single state). Effectively this calculates the TFBS presence near CAGE promoters weighted by the expression of the promoter. Unfortunately this causes a different problem: Ubiquitously expressed genes have high MASA scores, but don't distinguish between cell types (see the MASA pictures below). I therefore also calculated Z-scores for each MASA score with respect to the MASA scores for the same motif in the other cell types (this of course suffers from the same drawback as MARA, and I am not sure yet if we have gained anything here).

To visually represent the motif activities for each organism, I performed complete-linkage hierarchical clustering on the motifs and on the cell types. Heat maps for the MARA activities, MASA activities, and Z-values are below. I then ranked the motifs by their Z-values in each condition for each organism. Below is a table of the first-ranked motif for each organism in each cell type.

Using the MARA activities, I also calculated the predicted regulatory network (using the same approach as in FANTOM4).

I uploaded four types of files:

  • assembly.activities.mara: The motif activities as calculated by MARA
  • assembly.activities.masa: The motif activities as calculated by MASA
  • assembly.zvalues.masa: The Z-values calculated from the MASA scores
  • assembly.network: The transcriptional regulatory network predicted by MARA.

where "assembly" is hg19, mm9, rn4, canFam2, or galGal3.

--Michiel, 2011.03.04

Heatmaps

Organism MARA activities MASA activities MASA Z-values
hg19 Media:hg19.activities.mara.pdf Media:hg19.activities.masa.pdf Media:hg19.zvalues.masa.pdf
mm9 Media:mm9.activities.mara.pdf Media:mm9.activities.masa.pdf Media:mm9.zvalues.masa.pdf
rn4 Media:rn4.activities.mara.pdf Media:rn4.activities.masa.pdf Media:rn4.zvalues.masa.pdf
canFam2 Media:canFam2.activities.mara.pdf Media:canFam2.activities.masa.pdf Media:canFam2.zvalues.masa.pdf
galGal3 Media:galGal3.activities.mara.pdf Media:galGal3.activities.masa.pdf Media:galGal3.zvalues.masa.pdf

Data files

Organism MARA activities MASA activities MASA Z-values MARA network
hg19 Media:hg19.activities.mara.gz Media:hg19.activities.masa.gz Media:hg19.zvalues.masa.gz Media:hg19.network.gz
mm9 Media:mm9.activities.mara.gz Media:mm9.activities.masa.gz Media:mm9.zvalues.masa.gz Media:mm9.network.gz
rn4 Media:rn4.activities.mara.gz Media:rn4.activities.masa.gz Media:rn4.zvalues.masa.gz Media:rn4.network.gz
canFam2 Media:canFam2.activities.mara.gz Media:canFam2.activities.masa.gz Media:canFam2.zvalues.masa.gz Media:canFam2.network.gz
galGal3 Media:galGal3.activities.mara.gz Media:galGal3.activities.masa.gz Media:galGal3.zvalues.masa.gz Media:galGal3.network.gz

Top-ranked motif per organism and cell type


Spearman correlation between the motif activity and the CAGE expression level of the corresponding transcription factor(s)

These correlations were calculated from the Z-values of the MASA-results above; using the MARA values or using the MASA values directly gives very similar results. The list below is sorted from highest correlation to lowest. Overall, there is no clear tendency for the motif activity and the expression levels to be correlated, as shown by this histogram. However, some motifs, such as E2F1..5, show a clear correlation.

Motif expression correlations histogram.png


Motif Transcription factor gene Spearman correlation Scatter plot
E2F1..5 E2F3 0.841683 [[1]]
E2F1..5 E2F1 0.816086 [[2]]
FOS_FOS_B,L1__JUN_B,D_ FOSL1 0.787015 [[3]]
HMGA1,2 HMGA1 0.686243 [[4]]
TFDP1 TFDP1 0.671864 [[5]]
E2F1..5 E2F2 0.627630 [[6]]
IRF1,2 IRF1 0.597349 [[7]]
ELF1,2,4 ELF2 0.569108 [[8]]
E2F1..5 E2F4 0.568816 [[9]]
IRF1,2 IRF2 0.566674 [[10]]
ELF1,2,4 ELF1 0.565809 [[11]]
TEAD1 TEAD1 0.560307 [[12]]
MEF2_A,B,C,D_ MEF2C 0.554162 [[13]]
RFX2..5_RFXANK_RFXAP RFX3 0.546216 [[14]]
SPIB SPIB 0.545655 [[15]]
SMAD1..7,9 SMAD9 0.543776 [[16]]
NFKB1_REL_RELA NFKB1 0.534954 [[17]]
ARNT_ARNT2_BHLHB2_MAX_MYC_USF1 MYC 0.513085 [[18]]
HAND1,2 HAND2 0.465248 [[19]]
NFY_A,B,C_ NFYB 0.458054 [[20]]
NFATC1..3 NFATC1 0.457514 [[21]]
ELK1,4_GABP_A,B1_ ELK1 0.450242 [[22]]
RUNX1..3 RUNX3 0.441659 [[23]]
NFKB1_REL_RELA REL 0.440886 [[24]]
MYFfamily MYOD1 0.439002 [[25]]
RUNX1..3 RUNX1 0.438840 [[26]]
CEBPA,B_DDIT3 CEBPB 0.437270 [[27]]
CEBPA,B_DDIT3 DDIT3 0.436120 [[28]]
SOX17 SOX17 0.431799 [[29]]
FOXO1,3,4 FOXO4 0.427194 [[30]]
YY1 YY1 0.421768 [[31]]
NFY_A,B,C_ NFYC 0.421628 [[32]]
ELK1,4_GABP_A,B1_ GABPB1 0.419064 [[33]]
IRF7 IRF7 0.412893 [[34]]
CREB1 CREB1 0.410191 [[35]]
FOSL2 FOSL2 0.408064 [[36]]
MYFfamily MYF6 0.388749 [[37]]
ELK1,4_GABP_A,B1_ GABPA 0.386305 [[38]]
MEF2_A,B,C,D_ MEF2B 0.380190 [[39]]
SP1 SP1 0.370936 [[40]]
NFY_A,B,C_ NFYA 0.367718 [[41]]
MEF2_A,B,C,D_ MEF2D 0.365749 [[42]]
SOX2 SOX2 0.365530 [[43]]
NRF1 NRF1 0.361426 [[44]]
ZNF143 ZNF143 0.356887 [[45]]
POU6F1 POU6F1 0.356494 [[46]]
FOX_C1,C2_ FOXC2 0.355895 [[47]]
RFX2..5_RFXANK_RFXAP RFXAP 0.354397 [[48]]
ATF4 ATF4 0.353503 [[49]]
ETS1,2 ETS1 0.351178 [[50]]
MEF2_A,B,C,D_ MEF2A 0.347177 [[51]]
ELF1,2,4 ELF4 0.345478 [[52]]
NFE2L1 NFE2L1 0.338455 [[53]]
FOXO1,3,4 FOXO1 0.334483 [[54]]
HNF1A HNF1A 0.329089 [[55]]
HIF1A HIF1A 0.326498 [[56]]
MAFB MAFB 0.319747 [[57]]
EBF1 EBF1 0.316888 [[58]]
SPI1 SPI1 0.313089 [[59]]
MYFfamily MYOG 0.305667 [[60]]
AHR_ARNT_ARNT2 ARNT2 0.296098 [[61]]
JUN JUND 0.295237 [[62]]
ZFP161 ZFP161 0.295189 [[63]]
ESRRA ESRRA 0.294840 [[64]]
HNF4A_NR2F1,2 HNF4A 0.293899 [[65]]
FOXO1,3,4 FOXO3 0.292591 [[66]]
RFX1 RFX1 0.289249 [[67]]
TP53 TP53 0.288418 [[68]]
JUN JUN 0.287065 [[69]]
STAT1,3 STAT1 0.285049 [[70]]
LEF1_TCF7_TCF7L1,2 TCF7L1 0.282803 [[71]]
FOXP1 FOXP1 0.280522 [[72]]
RFX2..5_RFXANK_RFXAP RFX2 0.280221 [[73]]
SMAD1..7,9 SMAD6 0.279935 [[74]]
MYFfamily MYF5 0.277773 [[75]]
TFAP2_A,C_ TFAP2C 0.276803 [[76]]
DBP DBP 0.274124 [[77]]
SRF SRF 0.272955 [[78]]
HBP1_HMGB_SSRP1_UBTF HMGB2 0.270943 [[79]]
bHLH_family MXD3 0.266357 [[80]]
NFATC1..3 NFATC2 0.261042 [[81]]
FOS_FOS_B,L1__JUN_B,D_ JUNB 0.258667 [[82]]
HBP1_HMGB_SSRP1_UBTF HBP1 0.258615 [[83]]
bHLH_family HES6 0.255850 [[84]]
SNAI1..3 SNAI3 0.252970 [[85]]
DMAP1_NCOR_1,2__SMARC SMARCA5 0.251573 [[86]]
NFKB1_REL_RELA RELA 0.250287 [[87]]
SMAD1..7,9 SMAD4 0.248788 [[88]]
SOX_8,9,10_ SOX9 0.248325 [[89]]
SMAD1..7,9 SMAD1 0.247502 [[90]]
SOX_8,9,10_ SOX8 0.243049 [[91]]
AHR_ARNT_ARNT2 ARNT 0.240579 [[92]]
NFIL3 NFIL3 0.236421 [[93]]
ETS1,2 ETS2 0.235928 [[94]]
EP300 EP300 0.234088 [[95]]
RUNX1..3 RUNX2 0.229801 [[96]]
ARNT_ARNT2_BHLHB2_MAX_MYC_USF1 MAX 0.224185 [[97]]
NHLH1,2 NHLH2 0.222854 [[98]]
MYB MYB 0.215738 [[99]]
GTF2A1,2 GTF2A2 0.214222 [[100]]
GTF2I GTF2I 0.211486 [[101]]
STAT2,4,6 STAT6 0.205898 [[102]]
TAL1_TCF_3,4,12_ TCF3 0.205632 [[103]]
VSX1,2 VSX1 0.203498 [[104]]
TFAP2_A,C_ TFAP2A 0.202943 [[105]]
NKX3-1 NKX3-1 0.201749 [[106]]
HIC1 HIC1 0.201551 [[107]]
POU2F1..3 POU2F1 0.201246 [[108]]
GTF2A1,2 GTF2A1 0.197263 [[109]]
POU3F1..4 POU3F2 0.194055 [[110]]
VSX1,2 VSX2 0.189519 [[111]]
TLX1..3_NFIC_dimer_ TLX1 0.187962 [[112]]
PITX1..3 PITX1 0.186101 [[113]]
FOXA2 FOXA2 0.183837 [[114]]
POU2F1..3 POU2F3 0.182298 [[115]]
POU2F1..3 POU2F2 0.177903 [[116]]
FOXP3 FOXP3 0.177792 [[117]]
ARNT_ARNT2_BHLHB2_MAX_MYC_USF1 USF1 0.176758 [[118]]
EGR1..3 EGR2 0.176213 [[119]]
FOX_F1,F2,J1_ FOXJ1 0.173193 [[120]]
RORA RORA 0.172773 [[121]]
POU3F1..4 POU3F4 0.172656 [[122]]
HNF4A_NR2F1,2 NR2F2 0.157303 [[123]]
FOXD3 FOXD3 0.154134 [[124]]
ATF2 ATF2 0.153517 [[125]]
ADNP_IRX_SIX_ZHX ADNP 0.153422 [[126]]
PDX1 PDX1 0.152632 [[127]]
NR1H4 NR1H4 0.148988 [[128]]
PRRX1,2 PRRX2 0.148726 [[129]]
NKX2-2,8 NKX2-2 0.148446 [[130]]
RXRA_VDR_dimer_ VDR 0.146062 [[131]]
FOXL1 FOXL1 0.145980 [[132]]
LEF1_TCF7_TCF7L1,2 TCF7L2 0.143538 [[133]]
XBP1 XBP1 0.142011 [[134]]
SOX_8,9,10_ SOX10 0.141618 [[135]]
RXR_A,B,G_ RXRG 0.138791 [[136]]
EGR1..3 EGR3 0.137448 [[137]]
SMAD1..7,9 SMAD3 0.133554 [[138]]
NKX2-2,8 NKX2-8 0.130732 [[139]]
PRDM1 PRDM1 0.130111 [[140]]
RBPJ RBPJ 0.126726 [[141]]
CEBPA,B_DDIT3 CEBPA 0.121052 [[142]]
bHLH_family HEY1 0.119493 [[143]]
AHR_ARNT_ARNT2 AHR 0.117428 [[144]]
ESR1 ESR1 0.115442 [[145]]
ZIC1..3 ZIC1 0.113777 [[146]]
NR5A1,2 NR5A2 0.109033 [[147]]
bHLH_family OLIG2 0.104603 [[148]]
FOX_F1,F2,J1_ FOXF2 0.104598 [[149]]
HNF4A_NR2F1,2 NR2F1 0.103058 [[150]]
NR6A1 NR6A1 0.100385 [[151]]
NANOG_mouse_ NANOG 0.099938 [[152]]
SOX5 SOX5 0.099262 [[153]]
ADNP_IRX_SIX_ZHX SIX2 0.095746 [[154]]
HMX1 HMX1 0.092173 [[155]]
HAND1,2 HAND1 0.091690 [[156]]
E2F1..5 E2F5 0.091342 [[157]]
ARNT_ARNT2_BHLHB2_MAX_MYC_USF1 ARNT 0.090402 [[158]]
STAT5_A,B_ STAT5B 0.089589 [[159]]
GFI1 GFI1 0.088742 [[160]]
STAT2,4,6 STAT2 0.088383 [[161]]
TLX1..3_NFIC_dimer_ TLX3 0.086683 [[162]]
ARID5B ARID5B 0.084674 [[163]]
CRX CRX 0.084349 [[164]]
KLF4 KLF4 0.079121 [[165]]
RXR_A,B,G___NR1H2,PPAR_dimers NR1H2 0.077426 [[166]]
HOX_A4,D4_ HOXA4 0.076449 [[167]]
RFX2..5_RFXANK_RFXAP RFX5 0.076444 [[168]]
bHLH_family HEY2 0.076300 [[169]]
RFX2..5_RFXANK_RFXAP RFX4 0.075448 [[170]]
HSF1,2 HSF1 0.073449 [[171]]
PAX2 PAX2 0.070847 [[172]]
NANOG NANOG 0.070369 [[173]]
ADNP_IRX_SIX_ZHX SIX5 0.070160 [[174]]
TFCP2 TFCP2 0.068274 [[175]]
MYBL2 MYBL2 0.067085 [[176]]
HBP1_HMGB_SSRP1_UBTF HMGB3 0.066710 [[177]]
SREBF1,2 SREBF2 0.062794 [[178]]
bHLH_family MITF 0.062051 [[179]]
ADNP_IRX_SIX_ZHX ZHX1 0.060156 [[180]]
DMAP1_NCOR_1,2__SMARC NCOR1 0.059172 [[181]]
GFI1B GFI1B 0.057878 [[182]]
ALX4 ALX4 0.057049 [[183]]
ZBTB6 ZBTB6 0.056235 [[184]]
STAT2,4,6 STAT4 0.054894 [[185]]
NR5A1,2 NR5A1 0.052045 [[186]]
MSX1,2 MSX1 0.051234 [[187]]
POU3F1..4 POU3F1 0.050175 [[188]]
ZIC1..3 ZIC3 0.048955 [[189]]
bHLH_family ARNTL 0.048502 [[190]]
RXR_A,B,G___NR1H2,PPAR_dimers RXRB 0.045964 [[191]]
bHLH_family OLIG1 0.045872 [[192]]
KLF12 KLF12 0.045677 [[193]]
POU3F1..4 POU3F3 0.044229 [[194]]
NKX2-3_NKX2-5 NKX2-5 0.043547 [[195]]
NHLH1,2 NHLH1 0.042690 [[196]]
BACH2 BACH2 0.042438 [[197]]
GATA6 GATA6 0.041663 [[198]]
LHX3,4 LHX3 0.040380 [[199]]
RXR_A,B,G___NR1H2,PPAR_dimers RXRA 0.039914 [[200]]
HOX_A4,D4_ HOXD4 0.038547 [[201]]
POU5F1 POU5F1 0.037087 [[202]]
POU1F1 POU1F1 0.036855 [[203]]
ARNT_ARNT2_BHLHB2_MAX_MYC_USF1 ARNT2 0.035919 [[204]]
JUN JUNB 0.035788 [[205]]
HLF HLF 0.034341 [[206]]
OCT4_SOX2_dimer_ POU5F1 0.031286 [[207]]
MZF1 MZF1 0.031243 [[208]]
TBX4,5 TBX5 0.026384 [[209]]
FOS_FOS_B,L1__JUN_B,D_ FOSB 0.021261 [[210]]
TFAP4 TFAP4 0.019944 [[211]]
PATZ1 PATZ1 0.018723 [[212]]
ZNF238 ZNF238 0.018716 [[213]]
HBP1_HMGB_SSRP1_UBTF UBTF 0.016290 [[214]]
RXR_A,B,G___NR1H2,PPAR_dimers PPARG 0.011687 [[215]]
GATA4 GATA4 0.010309 [[216]]
SMAD1..7,9 SMAD2 0.009052 [[217]]
SMAD1..7,9 SMAD5 0.007724 [[218]]
SPZ1 SPZ1 0.007261 [[219]]
ADNP_IRX_SIX_ZHX IRX5 0.006931 [[220]]
NFATC1..3 NFATC3 0.006887 [[221]]
HBP1_HMGB_SSRP1_UBTF SSRP1 0.006680 [[222]]
NKX2-1,4 NKX2-1 0.002890 [[223]]
TAL1_TCF_3,4,12_ TCF12 0.002631 [[224]]
FOXQ1 FOXQ1 0.001169 [[225]]
ONECUT1,2 ONECUT2 -0.001663 [[226]]
MSX1,2 MSX2 -0.002938 [[227]]
LMO2 LMO2 -0.004032 [[228]]
CDC5L CDC5L -0.004116 [[229]]
ATF5_CREB3 ATF5 -0.004958 [[230]]
OCT4_SOX2_dimer_ SOX2 -0.006791 [[231]]
ADNP_IRX_SIX_ZHX IRX4 -0.007307 [[232]]
PAX6 PAX6 -0.011055 [[233]]
RXR_A,B,G_ RXRB -0.013317 [[234]]
TFAP2B TFAP2B -0.016931 [[235]]
NFE2L2 NFE2L2 -0.017743 [[236]]
RXR_A,B,G___NR1H2,PPAR_dimers PPARA -0.018180 [[237]]
bHLH_family HEYL -0.019438 [[238]]
ADNP_IRX_SIX_ZHX ZHX3 -0.021360 [[239]]
MYOD1 MYOD1 -0.027445 [[240]]
NKX2-3_NKX2-5 NKX2-3 -0.027771 [[241]]
SNAI1..3 SNAI1 -0.032412 [[242]]
REST REST -0.033128 [[243]]
HSF1,2 HSF2 -0.034159 [[244]]
LEF1_TCF7_TCF7L1,2 TCF7 -0.042013 [[245]]
NFE2 NFE2 -0.043868 [[246]]
CDX1,2,4 CDX2 -0.044348 [[247]]
bHLH_family MXD4 -0.044784 [[248]]
EGR1..3 EGR1 -0.045478 [[249]]
ONECUT1,2 ONECUT1 -0.046304 [[250]]
FOX_D1,D2_ FOXD1 -0.048518 [[251]]
AIRE AIRE -0.051075 [[252]]
GCM1,2 GCM2 -0.051530 [[253]]
FOX_F1,F2,J1_ FOXF1 -0.054904 [[254]]
CUX2 CUX2 -0.055846 [[255]]
LHX3,4 LHX4 -0.056027 [[256]]
HOX_A5,B5_ HOXB5 -0.066447 [[257]]
NKX2-1,4 NKX2-4 -0.073380 [[258]]
PPARG PPARG -0.074323 [[259]]
STAT1,3 STAT3 -0.075259 [[260]]
HOXA9_MEIS1 HOXA9 -0.081168 [[261]]
bHLH_family MXI1 -0.083253 [[262]]
NR3C1 NR3C1 -0.091658 [[263]]
ATF6 ATF6 -0.094819 [[264]]
DMAP1_NCOR_1,2__SMARC SMARCC2 -0.096414 [[265]]
AR AR -0.097115 [[266]]
GATA1..3 GATA3 -0.098243 [[267]]
NKX6-1,2 NKX6-1 -0.100540 [[268]]
bHLH_family MLXIPL -0.101816 [[269]]
PAX3,7 PAX7 -0.108886 [[270]]
BPTF BPTF -0.115037 [[271]]
ALX1 ALX1 -0.117144 [[272]]
PAX8 PAX8 -0.118184 [[273]]
FOS_FOS_B,L1__JUN_B,D_ FOS -0.118335 [[274]]
MAZ MAZ -0.119779 [[275]]
TBP TBP -0.121494 [[276]]
FOX_I1,J2_ FOXJ2 -0.126419 [[277]]
DMAP1_NCOR_1,2__SMARC DMAP1 -0.126591 [[278]]
FOX_I1,J2_ FOXI1 -0.133892 [[279]]
PAX1,9 PAX9 -0.134310 [[280]]
ADNP_IRX_SIX_ZHX ZHX2 -0.140813 [[281]]
CDX1,2,4 CDX1 -0.141211 [[282]]
bHLH_family MNT -0.143438 [[283]]
PITX1..3 PITX2 -0.144940 [[284]]
FOXM1 FOXM1 -0.151562 [[285]]
PAX5 PAX5 -0.153646 [[286]]
RXR_A,B,G_ RXRA -0.157331 [[287]]
HOX_A6,A7,B6,B7_ HOXB7 -0.161903 [[288]]
NKX6-1,2 NKX6-2 -0.162829 [[289]]
ZNF384 ZNF384 -0.165298 [[290]]
SREBF1,2 SREBF1 -0.177228 [[291]]
HOX_A6,A7,B6,B7_ HOXA7 -0.181028 [[292]]
PITX1..3 PITX3 -0.184486 [[293]]
SNAI1..3 SNAI2 -0.186187 [[294]]
TLX2 TLX2 -0.186753 [[295]]
TAL1_TCF_3,4,12_ TCF4 -0.188978 [[296]]
GATA1..3 GATA1 -0.193447 [[297]]
GLI1..3 GLI3 -0.196351 [[298]]
bHLH_family ARNTL2 -0.199272 [[299]]
HOX_A5,B5_ HOXA5 -0.199518 [[300]]
IKZF2 IKZF2 -0.208705 [[301]]
bHLH_family CLOCK -0.214325 [[302]]
GATA1..3 GATA2 -0.215999 [[303]]
PAX3,7 PAX3 -0.216099 [[304]]
GCM1,2 GCM1 -0.220920 [[305]]
bHLH_family NPAS2 -0.242346 [[306]]
FOS_FOS_B,L1__JUN_B,D_ JUND -0.243666 [[307]]
GLI1..3 GLI1 -0.243813 [[308]]
TEF TEF -0.251727 [[309]]
PBX1 PBX1 -0.263422 [[310]]
RXR_A,B,G___NR1H2,PPAR_dimers RXRG -0.284354 [[311]]
ZIC1..3 ZIC2 -0.286441 [[312]]
MTF1 MTF1 -0.288082 [[313]]
HOX_A6,A7,B6,B7_ HOXB6 -0.289895 [[314]]
ATF5_CREB3 CREB3 -0.296706 [[315]]
bHLH_family TFE3 -0.298604 [[316]]
ZBTB16 ZBTB16 -0.305596 [[317]]
RREB1 RREB1 -0.308151 [[318]]
ZNF148 ZNF148 -0.324099 [[319]]
bHLH_family ID1 -0.326107 [[320]]
TOPORS TOPORS -0.343149 [[321]]
IKZF1 IKZF1 -0.353840 [[322]]
ZEB1 ZEB1 -0.356777 [[323]]
PAX1,9 PAX1 -0.406964 [[324]]
DMAP1_NCOR_1,2__SMARC SMARCA1 -0.413524 [[325]]
HOXA9_MEIS1 MEIS1 -0.423077 [[326]]
TAL1_TCF_3,4,12_ TAL1 -0.436151 [[327]]
HES1 HES1 -0.441240 [[328]]
TGIF1 TGIF1 -0.486870 [[329]]
NFIX NFIX -0.607094 [[330]]
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