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Androgen Receptor and FoxA1 Interaction Study Marko Laakso Biswajyoti Sahu Kristian Ovaska Olli A. J¨anne Sampsa Hautaniemi July 10, 2011 Abstract This Anduril analysis compares androgen receptor (AR) and FoxA1 binding sites in LNCaP-1F5 prostate cancer cells. Binding site data have been integrated with expression profiles obtained for the DHT stimulus. This document is generated automatically by Anduril (Engine 1.2.2). Contents 1 Expression analysis for AR 5 2 Summary of DEGs in AR 6 3 List of differentially expressed genes 6 3.1 Gene set: fcC fcOver..................................................6 3.2 Gene set: fcC fcUnder.................................................6 3.3 Gene set: fcA1 fcOver.................................................6 3.4 Gene set: fcA1 fcUnder................................................7 3.5 Gene set: fcE fcOver..................................................7 3.6 Gene set: fcE fcUnder.................................................8 4 Expression analysis for GR 9 5 Summary of DEGs in GR 9 6 List of differentially expressed genes 9 6.1 Gene set: fcsiCx fcOver................................................9 6.2 Gene set: fcsiCx fcUnder............................................... 10 6.3 Gene set: fcsiFx fcOver................................................ 10 6.4 Gene set: fcsiFx fcUnder................................................ 11 7 Gene set overlaps 14 8 Gene set comparison 17 9 Candidate report for Unique DEGs for AR 19 9.1 Moksiskaan candidate pathway............................................ 19 9.1.1 GO enrichment of the candidate pathway.................................. 22 9.2 Candidate genes.................................................... 27 9.2.1 GO enrichment of all candidates....................................... 35 10 Candidate report for Unique DEGs for AR with siFOXA1 36 10.1 Moksiskaan candidate pathway............................................ 36 10.1.1 GO enrichment of the candidate pathway.................................. 38 10.2 Candidate genes.................................................... 41 10.2.1 GO enrichment of all candidates....................................... 53 11 Candidate report for Common DEGs for AR and siFOXA1 56 11.1 Moksiskaan candidate pathway............................................ 56 11.1.1 GO enrichment of the candidate pathway.................................. 61 11.2 Candidate genes.................................................... 66 11.2.1 GO enrichment of all candidates....................................... 71 2 12 ChIP-seq peaks 73 12.1 AR DHT binding sites................................................. 74 12.2 FoxA1 binding sites.................................................. 76 12.3 AR binding sites (siFOXA1).............................................. 78 12.4 FoxA1 binding sites (siFOXA1)............................................ 81 12.5 AR and FoxA1 binding site overlaps......................................... 83 12.6 AR and FoxA1 binding site overlaps (up)...................................... 85 12.7 AR and FoxA1 binding site overlaps (down)..................................... 87 12.8 AR without FoxA1 binding site overlaps....................................... 89 12.9 AR without FoxA1 binding site overlaps (up).................................... 91 12.10AR without FoxA1 binding site overlaps (down).................................. 93 12.11FoxA1 without AR binding site overlaps....................................... 95 12.12FoxA1 without AR binding site overlaps (up).................................... 97 12.13FoxA1 without AR binding site overlaps (down).................................. 99 12.14AR and FoxA1 siFOXA1 binding site overlaps.................................... 101 12.15AR and FoxA1 siFOXA1 binding site overlaps (up)................................. 103 12.16AR and FoxA1 siFOXA1 binding site overlaps (down)............................... 105 12.17AR without FoxA1 siFOXA1 binding site overlaps................................. 107 12.18AR without FoxA1 siFOXA1 binding site overlaps (up).............................. 110 12.19AR without FoxA1 siFOXA1 binding site overlaps (down)............................. 112 12.20FoxA1 without AR siFOXA1 binding site overlaps................................. 114 12.21FoxA1 without AR siFOXA1 binding site overlaps (up).............................. 116 12.22FoxA1 without AR siFOXA1 binding site overlaps (down)............................. 118 12.23AR and AR siFOXA1 binding site overlaps..................................... 120 12.24AR and AR siFOXA1 binding site overlaps (up).................................. 122 12.25AR and AR siFOXA1 binding site overlaps (down)................................. 124 12.26AR without AR siFOXA1 binding site overlaps................................... 126 12.27AR without AR siFOXA1 binding site overlaps (up)................................ 128 12.28AR without AR siFOXA1 binding site overlaps (down)............................... 130 12.29AR siFOXA1 without AR binding site overlaps................................... 132 12.30AR siFOXA1 without AR binding site overlaps (up)................................ 135 12.31AR siFOXA1 without AR binding site overlaps (down)............................... 137 12.32FoxA1 and FoxA1 siFOXA1 binding site overlaps.................................. 139 12.33FoxA1 and FoxA1 siFOXA1 binding site overlaps (up)............................... 141 12.34FoxA1 and FoxA1 siFOXA1 binding site overlaps (down)............................. 143 12.35FoxA1 without FoxA1 siFOXA1 binding site overlaps................................ 145 12.36FoxA1 without FoxA1 siFOXA1 binding site overlaps (up)............................. 147 12.37FoxA1 without FoxA1 siFOXA1 binding site overlaps (down)........................... 149 12.38FoxA1 siFOXA1 without FoxA1 binding site overlaps................................ 151 12.39FoxA1 siFOXA1 without FoxA1 binding site overlaps (up)............................. 153 12.40FoxA1 siFOXA1 without FoxA1 binding site overlaps (down)........................... 155 3 12.41AR and FoxA1 binding site overlaps (stable).................................... 157 12.42AR without FoxA1 binding site overlaps (stable).................................. 159 12.43FoxA1 without AR binding site overlaps (stable).................................. 161 12.44AR and AR siFOXA1 binding site overlaps (stable)................................. 163 12.45AR without AR siFOXA1 binding site overlaps (stable).............................. 165 12.46AR siFOXA1 without AR binding site overlaps (stable).............................. 167 12.47FoxA1 and FoxA1 siFOXA1 binding site overlaps (stable)............................. 170 12.48FoxA1 without FoxA1 siFOXA1 binding site overlaps (stable)........................... 172 12.49FoxA1 siFOXA1 without FoxA1 binding site overlaps (stable)........................... 174 12.50AR and FoxA1 siFOXA1 binding site overlaps (stable)............................... 176 12.51AR without FoxA1 siFOXA1 binding site overlaps (stable)............................. 178 12.52FoxA1 without AR siFOXA1 binding site overlaps (stable)............................. 181 12.53GR DEX binding sites................................................. 183 12.54GR DEX binding sites (siFOXA1).......................................... 185 12.55GR and GR siFOXA1 binding site overlaps..................................... 188 12.56GR without GR siFOXA1 binding site overlaps................................... 190 12.57GR siFOXA1 without GR binding site overlaps................................... 192 12.58AR and FOXA1 overlaps unique for AR parental.................................. 195 13 AR versus AR siFOXA1 197 14 Expression comparision 199 14.1 Box plots........................................................ 200 15 System configuration 213 4 1 Expression analysis for AR Group Definition Description ce median(ce1, ce2) AR controls for FoxA1 study cd median(cd1, cd2) AR cases (DHT) for FoxA1 study a1e median(a1e1, a1e2) siFOXA1 controls a1d median(a1d1, a1d2) siFOXA1 cases fcC ratio(cd/ce) AR DHT samples divided by their controls fcA1 ratio(a1d/a1e) siFOXA1 DHT samples divided by their controls fcE ratio(ce/a1e) siFOXA1 samples divided by the parental cells Table 1: Sample groups a1d1 a1d2 a1d (median) a1e2 fcA1 (ratio) a1e1 a1e (median) fcE (ratio) ce (median) ce1 fcC (ratio) ce2 cd1 cd (median) cd2 5 2 Summary of DEGs in AR Gene set Size fcC fcOver 195 fcC fcUnder 106 fcA1 fcOver 242 fcA1 fcUnder 175 fcE fcOver 188 fcE fcUnder 199 3 List of differentially expressed genes Overexpressed genes are sorted with the most overexpressed first and underexpressed genes with the most underexpressed first. Genes go by the column first and then by row. 3.1 Gene set: fcC fcOver Number of genes: 195 PHGR1 C1orf116 LPAR3 ATAD2 PYGB HSD17B11 RP11-546D6.2 SMPD2 FKBP5 SPDEF HES1 PPFIBP2 PAQR4 AC068353.1 CAMKK2 PTGER4 PGC DBI KLK3 JAG1 ACAD8 AL121833.1 MKLN1 MRPS18A SLC45A3 MBOAT2 NBL1 ELOVL2 HIVEP1 GDF15 VWF HMG20B S100P STK39 CEBPD BRP44 APP WDYHV1 CEBPG TNS3 NCAPD3 EXTL2 CNTNAP2 SLC2A12 SHROOM3 MTOR VIPR1 BMPR1B SAT1 PECI TMPRSS2 RP11-312J18.5 DHCR24 CTD-2048F20.1 CORO1B TACC2 MICAL1 TUBA3D TBC1D4 KLK2 HEBP2 ZBTB24 STRA13 TIPARP TSKU ZMIZ1 CTD-2653M23.1 DNAJB9 ABHD3 SGK1 CBLL1 MERTK PMEPA1 KRT8 MLPH PFKFB2 KIF22 TEX2 GLRX SETBP1 ST6GALNAC1 TRPM8 C9orf152 PRKCH MAPK6 REPS2 C15orf23 SEMA4A ALDH1A3 TM4SF1 ISG20 SMS CRIP2 AC020915.4 UGT2B28 SEPP1 CLDN8 RP11-529H2.2 HOMER2 CENPN HERC5 ATP1A1 RAB3IP UBE2G1 SORD NFKBIA FAM43A
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  • Supplementary Table S1. Correlation Between the Mutant P53-Interacting Partners and PTTG3P, PTTG1 and PTTG2, Based on Data from Starbase V3.0 Database

    Supplementary Table S1. Correlation Between the Mutant P53-Interacting Partners and PTTG3P, PTTG1 and PTTG2, Based on Data from Starbase V3.0 Database

    Supplementary Table S1. Correlation between the mutant p53-interacting partners and PTTG3P, PTTG1 and PTTG2, based on data from StarBase v3.0 database. PTTG3P PTTG1 PTTG2 Gene ID Coefficient-R p-value Coefficient-R p-value Coefficient-R p-value NF-YA ENSG00000001167 −0.077 8.59e-2 −0.210 2.09e-6 −0.122 6.23e-3 NF-YB ENSG00000120837 0.176 7.12e-5 0.227 2.82e-7 0.094 3.59e-2 NF-YC ENSG00000066136 0.124 5.45e-3 0.124 5.40e-3 0.051 2.51e-1 Sp1 ENSG00000185591 −0.014 7.50e-1 −0.201 5.82e-6 −0.072 1.07e-1 Ets-1 ENSG00000134954 −0.096 3.14e-2 −0.257 4.83e-9 0.034 4.46e-1 VDR ENSG00000111424 −0.091 4.10e-2 −0.216 1.03e-6 0.014 7.48e-1 SREBP-2 ENSG00000198911 −0.064 1.53e-1 −0.147 9.27e-4 −0.073 1.01e-1 TopBP1 ENSG00000163781 0.067 1.36e-1 0.051 2.57e-1 −0.020 6.57e-1 Pin1 ENSG00000127445 0.250 1.40e-8 0.571 9.56e-45 0.187 2.52e-5 MRE11 ENSG00000020922 0.063 1.56e-1 −0.007 8.81e-1 −0.024 5.93e-1 PML ENSG00000140464 0.072 1.05e-1 0.217 9.36e-7 0.166 1.85e-4 p63 ENSG00000073282 −0.120 7.04e-3 −0.283 1.08e-10 −0.198 7.71e-6 p73 ENSG00000078900 0.104 2.03e-2 0.258 4.67e-9 0.097 3.02e-2 Supplementary Table S2.