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Supplementary Materials For Supplementary Materials for Identification of candidate biomarkers for Idiopathic Thrombocytopenic Purpura by Bioinformatics Analysis of Microarray Data Samira Gilanchi, Hakimeh Zali*, Mohammad Faranoush*, Mostafa Rezaei Tavirani, Keyvan Shahriary and Mahyar Daskareh To whom correspondence should be addressed. E-mail [email protected]; [email protected] Volume 19, issue 4 (autumn 2020) This PDF file includes: Tables S1 to S8 Table S1. Up-regulated DEGs that obtain from analysis from 7 newly diagnosed ITP than 6 chronic ITP samples. In table M means log2FC, T is T statistics, P-values evaluated based on Benjamini false discovery rate. Top genes are selected for more valuation with P-value < 0.05, and B is B statistic. Up-regulated genes M T P-Value B 1 FNBP4 1.089255 9.645201 0.0067318 6.692063 2 G2E3 0.993745 7.38905 0.0306136 4.269833 3 SAR1B 1.523974 7.35994 0.0306136 4.233735 4 PER3 1.297768 7.261088 0.0306136 4.11015 5 MSI2 1.60714 7.23665 0.0306136 4.079358 6 CASK 1.854101 7.07773 0.0324118 3.876782 7 TM2D1 1.510449 7.006354 0.0326833 3.784474 8 RPRD1A 1.155052 6.971092 0.0326833 3.738565 9 SLC39A6 1.032869 6.868857 0.033521 3.604313 10 CAMTA1 2.258868 6.855413 0.033521 3.586531 11 PTAR1 1.602835 6.828607 0.033521 3.550986 12 LOC101929734 1.620399 6.561583 0.039368 3.190433 13 ADNP2 1.084491 6.519255 0.0400375 3.132189 14 ZNF224 1.234505 6.365865 0.0400375 2.918603 15 TUBE1 0.990095 6.354317 0.0400375 2.902363 16 GIGYF2 0.741529 6.353043 0.0400375 2.900571 17 ABCA5 1.293839 6.341226 0.0400375 2.883927 18 FBXW7 1.205229 6.303732 0.0400375 2.830962 19 METTL8 1.073161 6.298249 0.0400375 2.823197 20 IL1RAP 1.257333 6.24383 0.0404726 2.74585 21 TNRC6A 0.894899 6.218077 0.0404726 2.709073 22 GSPT1 1.406084 6.210119 0.0404726 2.697685 23 FAM178A 1.428243 6.187739 0.0404726 2.665603 24 GFPT1 1.229498 6.155903 0.0404726 2.619821 25 BAZ1B 0.63851 6.098917 0.0416029 2.537444 26 IFNGR1 1.406398 6.044768 0.0435208 2.458658 27 TAOK1 1.135816 6.031329 0.0435546 2.439026 28 MIER3 1.470019 6.010599 0.0437901 2.408686 29 EML4 1.21403 5.992304 0.0437901 2.381849 30 SF1 2.419055 5.979368 0.0437901 2.36284 31 BBS2 0.900097 5.966395 0.0437901 2.343747 32 DYNC1LI2 0.94218 5.935166 0.0437901 2.29767 33 GPATCH11 0.768424 5.923691 0.0437901 2.280697 34 SCARB2 1.14523 5.922954 0.0437901 2.279606 35 PJA2 1.008988 5.910003 0.0439652 2.260422 36 RAB8B 1.803071 5.867977 0.0451902 2.197976 37 C2orf49 0.631136 5.839604 0.0451902 2.155649 38 CLIP1 1.182693 5.837234 0.0451902 2.152107 39 CAPN7 0.64129 5.816295 0.0451902 2.120774 40 TMED2 1.869119 5.805709 0.0451902 2.104904 41 TBC1D5 0.615565 5.779152 0.0451902 2.06501 42 ELL2 1.252154 5.731373 0.0451902 1.992939 43 ATF2 0.947451 5.711385 0.0451902 1.962674 44 GSPT1 0.873036 5.709465 0.0451902 1.959763 45 LINS 1.566022 5.699534 0.0451902 1.944699 46 SOCS5 1.382893 5.680112 0.0451902 1.915188 47 PAK2 0.922675 5.679562 0.0451902 1.914352 48 ERO1L 0.743072 5.664249 0.0451902 1.891038 49 ZNF382 1.33402 5.649846 0.0451902 1.869075 50 AKT3 1.097085 5.64984 0.0451902 1.869067 51 DNAJB14 1.2606 5.642786 0.0451902 1.858296 52 KIAA0430 0.830526 5.631546 0.0451902 1.841119 53 LOC283357 1.388744 5.614235 0.0451902 1.814622 54 ABL2 0.970876 5.611618 0.0451902 1.810612 55 EIF4E3 1.490178 5.581755 0.0461011 1.764772 56 FBXO38 1.473477 5.563832 0.0461011 1.737189 57 BUB3 0.846439 5.559647 0.0461011 1.730741 58 FOXN3 0.729011 5.551631 0.0461011 1.718382 59 FYCO1 0.685791 5.550846 0.0461011 1.71717 60 RCOR3 1.111475 5.540362 0.0461011 1.700989 61 CELF2 0.950587 5.514707 0.0461011 1.661313 62 LOC286161 0.874993 5.496367 0.0461011 1.632884 63 MID2 2.498842 5.487535 0.0461011 1.619173 64 VIM 1.077912 5.478964 0.0461011 1.605856 65 FKBP5 1.340329 5.462894 0.0461011 1.580853 66 DDI2 0.802653 5.447908 0.0461011 1.557498 67 FAM102B 1.604417 5.441605 0.0461011 1.547664 68 SSR1 0.671231 5.41403 0.0464563 1.504564 69 USP33 1.082804 5.413965 0.0464563 1.504464 70 LOC441155 1.320178 5.407527 0.0465531 1.494382 71 EBLN3 0.865344 5.399293 0.0465531 1.48148 72 TAOK1 1.238425 5.394765 0.0465619 1.47438 73 FEM1C 1.176922 5.381844 0.0468877 1.454102 74 PHLPP2 0.842615 5.377182 0.0468877 1.446778 75 KATNBL1 1.066378 5.369693 0.0468877 1.435007 76 RYK 1.038018 5.369199 0.0468877 1.434229 77 PCF11 0.923752 5.346921 0.0480425 1.399155 78 ZNF652 0.702938 5.320464 0.049098 1.357397 Table S2. Down-regulated DEGs that obtain from analysis from 7 newly diagnosed ITP and 6 chronic ITP samples. In table M means log2FC, T is T statistics, P-values evaluated based on Benjamini false discovery rate. Top genes are selected for more valuation with P-value < 0.05, and B is B statistics Down- regulated genes M t P-Value B 1 ANPEP -0.735878826 -9.534773023 0.006731833 6.589335938 2 CHST2 -1.88015076 -8.319640697 0.017919754 5.355538925 3 DTX1 -1.749320818 -8.249838309 0.017919754 5.278554231 4 HDAC1 -0.774621454 -7.334693025 0.030613591 4.202317954 5 RNF123 -1.692692914 -7.289549357 0.030613591 4.145891021 6 AIF1 -1.004697039 -6.753471759 0.035415994 3.450729146 7 ATG7 -1.053550632 -6.721844599 0.035415994 3.408247991 8 FTH1P5 -0.626809793 -6.652339759 0.037015382 3.314307169 9 LOC100134317 -1.193919711 -6.629978435 0.037015382 3.283913481 10 SETMAR -0.837673399 -6.372754087 0.04003745 2.928280907 11 ACRC -0.923974318 -6.328993446 0.04003745 2.866672611 12 ZNF324 -1.293234841 -6.299714425 0.04003745 2.82527201 13 LOC100130093 -1.091433807 -6.237114887 0.04047256 2.736270886 14 DAGLB -1.12014016 -6.1993276 0.04047256 2.682226349 15 DUSP22 -0.69810855 -6.143905623 0.04047256 2.60252354 16 DAP -1.15484218 -6.110946593 0.041602909 2.554878573 17 KPNA2 -0.757591152 -5.96667344 0.043790091 2.34415709 18 TOPORS-AS1 -1.026182831 -5.927690522 0.043790091 2.286615563 19 SMIM12 -1.164931094 -5.8345256 0.045190183 2.148057695 20 ARRB1 -1.855926621 -5.831570925 0.045190183 2.143639442 21 TBC1D9B -1.003040692 -5.79978503 0.045190183 2.096015561 22 FARSA -1.089148521 -5.760964566 0.045190183 2.037621166 23 TUFM -0.737102234 -5.746319758 0.045190183 2.015526331 24 PPM1G -0.809004205 -5.698111162 0.045190183 1.942538785 25 MAU2 -0.725621444 -5.688755813 0.045190183 1.928329651 26 CYB561A3 -1.291094781 -5.68285354 0.045190183 1.919357586 27 MRPL45 -0.600284876 -5.671898012 0.045190183 1.902688575 28 TEX264 -0.96019039 -5.654495545 0.045190183 1.876169124 29 GRK5 -0.896145434 -5.654157813 0.045190183 1.875653956 30 COPRS -0.973549797 -5.52372126 0.046101091 1.675266232 31 MFNG -0.666183832 -5.49299702 0.046101091 1.627653526 32 HIST1H2BK -1.427762269 -5.488703475 0.046101091 1.620987469 33 TOPORS-AS1 -0.748894367 -5.486521934 0.046101091 1.617599291 34 TEX264 -0.971091862 -5.482213726 0.046101091 1.610905853 35 AIF1 -1.159172706 -5.481899391 0.046101091 1.610417367 36 PLA2G6 -0.971440161 -5.473211953 0.046101091 1.59691037 37 TBC1D13 -0.988326082 -5.471430671 0.046101091 1.59413934 38 COMMD9 -0.765036844 -5.469800785 0.046101091 1.59160337 39 RHOG -1.37279767 -5.467830565 0.046101091 1.588537282 40 TOX2 -1.727269695 -5.464495332 0.046101091 1.583345479 41 EIF4E2 -1.052136382 -5.460569655 0.046101091 1.577232208 42 MEN1 -1.034120822 -5.454648946 0.046101091 1.568007362 43 LASP1 -0.831433786 -5.446247014 0.046101091 1.554906698 44 TMEM214 -1.042821964 -5.429086581 0.046456312 1.528113287 45 UBE2R2 -0.859762728 -5.421047185 0.046456312 1.515544335 46 HDAC7 -0.861652419 -5.400374922 0.046553106 1.48317619 47 B4GALT7 -0.873618293 -5.3516994 0.047991908 1.406684887 48 PUSL1 -1.015661172 -5.339559454 0.048314234 1.387547283 49 ABHD16A -0.708618318 -5.32449758 0.049097958 1.363770168 50 CDIP1 -0.860815247 -5.318151293 0.049097958 1.353740696 51 UBAP2 -0.735560264 -5.31243509 0.049244602 1.344701393 52 TUBA1A -0.85617395 -5.305815959 0.04947288 1.334227626 53 UQCR11 -0.712583116 -5.30149897 0.049503945 1.327392822 Table S3. Gene ontology enrichment based on biological process term for up-regulated DEGs. They were selected with P-value < 0.05 as the significant biological process. Enrichment Score is related the type of analysis in DAVID database with selecting "functional annotation clustering" for analysis of gene lists. Category Term P-Value Genes Annotation Cluster 1 Enrichment Score: 1.6089173346492356 DYNC1LI2, RAB8B, TAOK1, VIM, EML4, ATF2, BBS2, GO:1902589 single-organism organelle organization 0.005313 FBXW7, CLIP1, TUBE1, FYCO1, USP33, ABL2, BUB3 GO:0000226 microtubule cytoskeleton organization 0.020728 BBS2, DYNC1LI2, CLIP1, TUBE1, USP33, EML4 BBS2, DYNC1LI2, CLIP1, TUBE1, FYCO1, USP33, GO:0007017 microtubule-based process 0.026109 EML4 Annotation Cluster 2 Enrichment Score: 1.5454786370206883 GO:0010506 regulation of autophagy 0.003125 FBXW7, TBC1D5, ABL2, FYCO1, USP33, MID2 GO:0010508 positive regulation of autophagy 0.03688 TBC1D5, FYCO1, MID2 Annotation Cluster 3 Enrichment Score: 1.1276637957883262 GO:0000075 cell cycle checkpoint 0.010137 TAOK1, GIGYF2, BUB3, FOXN3, ATF2 FBXW7, GSPT1, TAOK1, KIAA0430, CLIP1, TUBE1, GO:0022402 cell cycle process 0.010174 GIGYF2, USP33, BUB3, FOXN3, EML4, ATF2 GO:0000077 DNA damage checkpoint 0.017372 TAOK1, GIGYF2, FOXN3, ATF2 TAOK1, KIAA0430, FOXN3, EML4, ATF2, FBXW7, GO:0007049 cell cycle 0.017944 GSPT1, PAK2, CLIP1, TUBE1, USP33, GIGYF2, BUB3 GO:0031570 DNA integrity checkpoint 0.020624 TAOK1, GIGYF2, FOXN3, ATF2 GO:0007093 mitotic cell cycle checkpoint 0.020967 GIGYF2, BUB3, FOXN3, ATF2 GO:0045930 negative regulation of mitotic cell cycle 0.047204 GIGYF2, BUB3, FOXN3, ATF2 Annotation Cluster 4 Enrichment Score: 1.0524732568167308 DYNC1LI2, VIM, KIAA0430, ATF2, ABCA5, SSR1, FBXW7, TMED2, PAK2, IL1RAP, TBC1D5, TUBE1, SCARB2,
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