Gene Level Analyses Gene Annotation File Creation Date: 07/15/20 Deduplicate Gene Sets: false Data Source: Kidney_10-2 FTOH_Female Work Source: Kidney_10-2 FTOH_Female_williams_0.05_NOMTC_foldfilter1.5_BMD BMDExpress2 Version: BMDExpress 2.30.0507 BETA Timestamp (Start Time): 02/12/2021 22:58.36 Remove Promiscuous Probes: true Remove BMD > Highest Dose from Category Descriptive Statistics: true Remove BMD with p-Value < Cutoff: 0.1 Remove genes with BMDU/BMDL >: 40.0 Remove Genes With Max Fold Change <: 2.0 Identify conflicting probe sets: 0.5 Category Count: 60 Total Run Time: 0 seconds GO/Pathway/Gene Set/Gene ID GO/Pathway/Gene Set/Gene Name All Genes (Expression Data) All Genes (Platform) Input Genes Genes with BMD <= Highest Dose Genes with BMD p-Value >= Genes with BMDU/BMDL <= Genes with max Fold Change >= Genes That Passed All Filters Fisher's A Parameter Fisher's B Parameter Fisher's C Parameter Fisher's D Parameter Fisher's Exact Left P-Value Fisher's Exact Right P-Value Fisher's Exact Two Tail Percentage Entrez Gene IDs Gene Symbols Probe IDs Genes with Conflicting Probesets BMD Mean BMD Median BMD Minimum BMD Standard Deviation BMD wMean BMD wSD BMDL Mean BMDL Median BMDL Minimum BMDL Standard Deviation BMDL wMean BMDL wSD BMDU Mean BMDU Median BMDU Minimum BMDU Standard Deviation BMDU wMean BMDU wSD 5th Percentile Index BMD at 5th Percentile of Total Genes 10th Percentile Index BMD at 10th Percentile of Total Genes BMD List BMDL List BMDU List Probes with Adverse Direction Up Probes with Adverse Direction Down Genes with Adverse Direction Up Genes Up List Genes Up Probes List Genes Up BMD Mean Genes Up BMD Median Genes Up SD Genes Up BMDL Mean Genes Up BMDL Median Genes Up BMDL SD Genes Up BMDU Mean Genes Up BMDU Median Genes Up BMDU SD BMD list (up) BMDL List (up) BMDU List (up) Genes with Adverse Direction Down Genes Down List Genes Down Probes List Genes Down BMD Mean Genes Down BMD Median Genes Down SD Genes Down BMDL Mean Genes Down BMDL Median Genes Down BMDL SD Genes Down BMDU Mean Genes Down BMDU Median Genes Down BMDU SD BMD list (down) BMDL List (down) BMDU List (down) Genes with Adverse Conflict Count Genes Conflict List Genes Conflict Probes List BMD list (Conflict) BMDL list (Conflict) BMDU list (Conflict) Model Counts Mean Fold Change Total Fold Change Min Fold Change Max Fold Change Standard Deviation Fold Change Median Fold Change Lower bound of the 95% confidence interval - BMD Upper bound of the 95% confidence interval - BMD Lower bound of the 95% confidence interval - BMDL Upper bound of the 95% confidence interval - BMDL Lower bound of the 95% confidence interval - BMDU Upper bound of the 95% confidence interval - BMDU Overall Direction Percent Genes With Overall Direction Up Percent Genes With Overall Direction Down Percent Genes With Overall Direction Conflict 24157 acaa1a 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 501072 acaa1b 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 361183 ankrd10 1 1 1 1 0 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 29657 arntl 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 64564 bbox1 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 64564 bbox1 BBOX1_8133 61.3193 61.3193 61.3193 61.3193 39.473 39.473 39.473 39.473 135.622 135.622 135.622 135.622 0.0 61.3193 0.0 61.3193 61.3193 39.473 135.622 1 0 1 64564 BBOX1_8133 61.3193 61.3193 39.473 39.473 135.622 135.622 61.3193 39.473 135.622 0 0 Poly 2,1(1) 2.00858473777771 2.00858473777771 2.00858473777771 2.00858473777771 0.0 2.00858473777771 61.3193 61.3193 39.473 39.473 135.622 135.622 UP 1.0 0.0 0.0 246142 bmf 1 1 1 1 1 0 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 24232 c3 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 58919 ccnd1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 297594 cdca3 1 1 1 1 1 0 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 289057 cfhr1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 306575 ckap2 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 306575 ckap2 CKAP2_8324 2.60822 2.60822 2.60822 2.60822 0.996983 0.996983 0.996983 0.996983 6.81093 6.81093 6.81093 6.81093 0.0 2.60822 0.0 2.60822 2.60822 0.996983 6.81093 1 0 1 306575 CKAP2_8324 2.60822 2.60822 0.996983 0.996983 6.81093 6.81093 2.60822 0.996983 6.81093 0 0 Exp 4,1(1) 2.2610743045806885 2.2610743045806885 2.2610743045806885 2.2610743045806885 0.0 2.2610743045806885 2.60822 2.60822 0.996983 0.996983 6.81093 6.81093 UP 1.0 0.0 0.0 474143 clec4a 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 474143 clec4a CLEC4A_32636 82.4664 82.4664 82.4664 82.4664 47.8721 47.8721 47.8721 47.8721 265.955 265.955 265.955 265.955 0.0 82.4664 0.0 82.4664 82.4664 47.8721 265.955 1 0 1 474143 CLEC4A_32636 82.4664 82.4664 47.8721 47.8721 265.955 265.955 82.4664 47.8721 265.955 0 0 Poly 2,1(1) 2.183150291442871 2.183150291442871 2.183150291442871 2.183150291442871 0.0 2.183150291442871 82.4664 82.4664 47.8721 47.8721 265.955 265.955 UP 1.0 0.0 0.0 291813 cmtm3 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 25683 col12a1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 25426 cyp1b1 1 1 1 1 0 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 312495 cyp26b1 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 312495 cyp26b1 CYP26B1_8418 238.25 238.25 238.25 238.25 181.323 181.323 181.323 181.323 370.243 370.243 370.243 370.243 0.0 238.25 0.0 238.25 238.25 181.323 370.243 1 0 1 312495 CYP26B1_8418 238.25 238.25 181.323 181.323 370.243 370.243 238.25 181.323 370.243 0 0 Exp 2,1(1) 2.7505569458007812 2.7505569458007812 2.7505569458007812 2.7505569458007812 0.0 2.7505569458007812 238.25 238.25 181.323 181.323 370.243 370.243 UP 1.0 0.0 0.0 24306 cyp4a2 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 298423 cyp4a3 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 316137 adgre1 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 316137 adgre1 EMR1_8558 61.5241 61.5241 61.5241 61.5241 39.6708 39.6708 39.6708 39.6708 132.174 132.174 132.174 132.174 0.0 61.5241 0.0 61.5241 61.5241 39.6708 132.174 1 0 1 316137 EMR1_8558 61.5241 61.5241 39.6708 39.6708 132.174 132.174 61.5241 39.6708 132.174 0 0 Poly 2,1(1) 2.4067232608795166 2.4067232608795166 2.4067232608795166 2.4067232608795166 0.0 2.4067232608795166 61.5241 61.5241 39.6708 39.6708 132.174 132.174 UP 1.0 0.0 0.0 25315 ephx1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 25441 fcer1g 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 24367 fgg 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 290223 fitm1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 361810 fkbp5 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 499537 fyb1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 316033 glb1 1 1 1 1 1 0 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 24426 gstp1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 102552634 loc102552634 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 361580 gtf2h1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 24450 hmgcs2 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 171064 igsf6 1 1 1 1 1 0 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 24494 il1b 1 1 1 1 0 1 1 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 100360623 iqgap2 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 306251 itih1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 293502 kif22 1 1 1 1 0 0 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 684193 loc684193 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 684193 loc684193 LOC684193_9138 468.901 468.901 468.901 468.90099999999995 269.893 269.893 269.893 269.893 1055.43 1055.43 1055.43 1055.43 0.0 468.901 0.0 468.901 468.901 269.893 1055.43 0 1 0 1 684193 LOC684193_9138 468.901 468.901 269.893 269.893 1055.43 1055.43 468.901 269.893 1055.43 0 Power,1(1) 3.5798137187957764 3.5798137187957764 3.5798137187957764 3.5798137187957764 0.0 3.5798137187957764 468.901 468.901 269.893 269.893 1055.43 1055.43 DOWN 0.0 1.0 0.0 292594 lilrb4 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 292594 lilrb4 LILRB4_9000 350.991 350.991 350.991 350.991 212.248 212.248 212.248 212.248 1011.69 1011.69 1011.69 1011.69 0.0 350.991 0.0 350.991 350.991 212.248 1011.69 1 0 1 292594 LILRB4_9000 350.991 350.991 212.248 212.248 1011.69 1011.69 350.991 212.248 1011.69 0 0 Linear,1(1) 2.2846055030822754 2.2846055030822754 2.2846055030822754 2.2846055030822754 0.0 2.2846055030822754 350.991 350.991 212.248 212.248 1011.69 1011.69 UP 1.0 0.0 0.0 313977 lpin1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 291327 mrc1 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 291327 mrc1 MRC1_33067 1.46016E-12 1.46016E-12 1.46016E-12 1.46016E-12 1.46016E-12 1.46016E-12 1.46016E-12 1.46016E-12 1.46017E-12 1.46017E-12 1.46017E-12 1.46017E-12 0.0 1.46016E-12 0.0 1.46016E-12 1.46016E-12 1.46016E-12 1.46017E-12 0 1 0 1 291327 MRC1_33067 1.46016E-12 1.46016E-12 1.46016E-12 1.46016E-12 1.46017E-12 1.46017E-12 1.46016E-12 1.46016E-12 1.46017E-12 0 Hill,1(1) 2.0781304836273193 2.0781304836273193 2.0781304836273193 2.0781304836273193 0.0 2.0781304836273193 1.46016E-12 1.46016E-12 1.46016E-12 1.46016E-12 1.46017E-12 1.46017E-12 DOWN 0.0 1.0 0.0 497009 naaa 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 114519 nfil3 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 114519 nfil3 NFIL3_9304 422.204 422.204 422.204 422.204 301.507 301.507 301.507 301.507 506.933 506.933 506.933 506.933 0.0 422.204 0.0 422.204 422.204 301.507 506.933 1 0 1 114519 NFIL3_9304 422.204 422.204 301.507 301.507 506.933 506.933 422.204 301.507 506.933 0 0 Poly 2,1(1) 2.106243133544922 2.106243133544922 2.106243133544922 2.106243133544922 0.0 2.106243133544922 422.204 422.204 301.507 301.507 506.933 506.933 UP 1.0 0.0 0.0 65052 pik3c3 1 1 1 1 0 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 363465 pir 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 288583 plod3 1 1 1 0 0 0 1 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 315988 rbm15b 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 619560 rup2 1 1 1 1 1 0 1 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 25044 sds 1 1 1 1 1 0 1 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 192247 sez6 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 29483 slc1a3 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 303879 slc51a 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 303879 slc51a SLC51A_33157 37.1342 37.1342 37.1342 37.1342 11.0074 11.0074 11.0074 11.0074 108.745 108.745 108.745 108.745 0.0 37.1342 0.0 37.1342 37.1342 11.0074 108.745 1 0 1 303879 SLC51A_33157 37.1342 37.1342 11.0074 11.0074 108.745 108.745 37.1342 11.0074 108.745 0 0 Hill,1(1) 2.156353235244751 2.156353235244751 2.156353235244751 2.156353235244751 0.0 2.156353235244751 37.1342 37.1342 11.0074 11.0074 108.745 108.745 UP 1.0 0.0 0.0 24902 sult2a6 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 360243 top2a 1 1 1 1 0 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 308768 ticrr 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 688621 tslp 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 315852 ttk 1 1 1 1 1 0 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 292008 txnl4b 1 1 1 0 0 0 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 29623 ugt2b37 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 29623 ugt2b37 UGT2B15_33121 32.501 32.501 32.501 32.501 7.51954 7.51954 7.51954 7.519539999999999 103.327 103.327 103.327 103.327 0.0 32.501 0.0 32.501 32.501 7.51954 103.327 1 0 1 29623 UGT2B15_33121 32.501 32.501 7.51954 7.51954 103.327 103.327 32.501 7.51954 103.327 0 0 Hill,1(1) 3.2770063877105713 3.2770063877105713 3.2770063877105713 3.2770063877105713 0.0 3.2770063877105713 32.501 32.501 7.51954 7.51954 103.327 103.327 UP 1.0 0.0 0.0 286989 ugt2b7 1 1 1 1 1 1 1 1 1 11 0 2767 1.0 0.0043181 0.0043181 100.0 286989 ugt2b7 UGT2B7_33032 54.3141 54.3141 54.3141 54.3141 15.595 15.595 15.595 15.595 186.641 186.641 186.641 186.641 0.0 54.3141 0.0 54.3141 54.3141 15.595 186.641 1 0 1 286989 UGT2B7_33032 54.3141 54.3141 15.595 15.595 186.641 186.641 54.3141 15.595 186.641 0 0 Hill,1(1) 4.802038669586182 4.802038669586182 4.802038669586182 4.802038669586182 0.0 4.802038669586182 54.3141 54.3141 15.595 15.595 186.641 186.641 UP 1.0 0.0 0.0 309596 vars2 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0 29142 vnn1 1 1 1 1 1 1 0 0 0 12 1 2766 0.99568 1.0 1.0 0.0 0 0 0 0 0