Table 1. Top 1% of depleting shRNAs in vitro and in vivo. We calculated the absolute values of fold-changes for all genes that depleted from input to end point. We mapped all genes to their human homologues for use with SAMNet. Fold-changes were calculated using DESeq2.
| Gene | Abs (f.c.) |
| In vivo | |
| ASRGL1 | 10.818 |
| FNDC5 | 10.233 |
| MRPL37 | 9.670 |
| ATP6V1C1 | 9.478 |
| DHX37 | 9.244 |
| NRG2 | 9.155 |
| ATP10B | 8.940 |
| HOXD3 | 8.765 |
| HDHD1 | 8.760 |
| PCBP4 | 8.744 |
| DHDDS | 8.633 |
| SERF1A | 8.474 |
| SLC29A2 | 8.390 |
| STK32B | 8.296 |
| POLQ | 8.241 |
| GTF3C5 | 8.164 |
| SPC24 | 8.140 |
| IPO11 | 8.102 |
| GMPS | 8.102 |
| UBE2H | 8.073 |
| ZNF416 | 8.025 |
| CASP14 | 8.014 |
| SCD | 8.000 |
| MAPRE3 | 7.898 |
| PLEKHA5 | 7.879 |
| SMARCD1 | 7.856 |
| DENND1C | 7.840 |
| TMEM156 | 7.821 |
| TMEM176A | 7.800 |
| LPPR5 | 7.751 |
| SRP72 | 7.704 |
| ATP6AP2 | 7.595 |
| FOXO6 | 7.588 |
| WISP3 | 7.564 |
| LCE3C | 7.562 |
| ZBTB4 | 7.512 |
| RCC1 | 7.512 |
| FXYD6 | 7.512 |
| UBE2L6 | 7.505 |
| SNTB1 | 7.498 |
| TIMD4 | 7.480 |
| DVL1 | 7.452 |
| COLEC12 | 7.440 |
| DHRS7C | 7.440 |
| CTSC | 7.435 |
| CECR5 | 7.425 |
| IQCH | 7.425 |
| MTRF1L | 7.366 |
| TGS1 | 7.337 |
| TIGD5 | 7.327 |
| SPATA13 | 7.306 |
| CPSF6 | 7.296 |
| NDUFS1 | 7.292 |
| ARMCX6 | 7.281 |
| OR13C4 | 7.275 |
| BCMO1 | 7.270 |
| SF3A1 | 7.268 |
| DIAPH3 | 7.266 |
| PGLYRP2 | 7.249 |
| ABHD12B | 7.242 |
| DRD1 | 7.241 |
| ODF2 | 7.238 |
| POGZ | 7.215 |
| TDRD7 | 7.206 |
| C9orf69 | 7.193 |
| ALKBH2 | 7.143 |
| GRHL3 | 7.119 |
| C17orf97 | 7.111 |
| SUZ12 | 7.111 |
| TMEM79 | 7.106 |
| LAG3 | 7.062 |
| IDH3A | 7.042 |
| C4orf32 | 7.039 |
| PNO1 | 7.018 |
| FUT10 | 7.005 |
| VCPIP1 | 6.990 |
| TFDP1 | 6.974 |
| RPL7 | 6.966 |
| RNF11 | 6.956 |
| SLC6A2 | 6.951 |
| YEATS2 | 6.932 |
| LAP3 | 6.928 |
| ADAMTS18 | 6.927 |
| TRIM33 | 6.916 |
| In vitro | |
| C10orf71 | 10.038 |
| KCNA5 | 9.965 |
| TMEM165 | 9.751 |
| C1orf85 | 9.671 |
| KLF3 | 9.633 |
| CEBPA | 9.333 |
| TPSG1 | 8.975 |
| ZNF367 | 8.826 |
| GTPBP10 | 8.774 |
| MFSD3 | 8.754 |
| GLB1L | 8.558 |
| DNTT | 8.498 |
| MYT1 | 8.285 |
| ANKS6 | 8.262 |
| KRT77 | 8.160 |
| NRARP | 8.103 |
| PPP3CB | 8.099 |
| MAD2L1 | 8.055 |
| CRNKL1 | 8.016 |
| ACTC1 | 8.016 |
| AHCYL1 | 8.016 |
| FCRL3 | 7.996 |
| SURF4 | 7.996 |
| RCOR2 | 7.962 |
| FCGR3A | 7.955 |
| ZNF616 | 7.913 |
| BAG5 | 7.902 |
| SASS6 | 7.803 |
| SMYD5 | 7.760 |
| TRIM59 | 7.745 |
| ZNF347 | 7.723 |
| NFAT5 | 7.721 |
| MATR3 | 7.649 |
| MED8 | 7.643 |
| CCT2 | 7.550 |
| RAB33A | 7.545 |
| MCPH1 | 7.440 |
| KCTD1 | 7.407 |
| POLR3GL | 7.380 |
| MPZL1 | 7.365 |
| INTS1 | 7.341 |
| DNMT3A | 7.334 |
| ARL9 | 7.304 |
| DOK2 | 7.285 |
| SYNJ2 | 7.285 |
| MBTPS2 | 7.228 |
| C4orf17 | 7.183 |
| NHLRC1 | 7.107 |
| ATXN3 | 7.090 |
| MID2 | 7.090 |
| CHM | 7.022 |
| MEIS1 | 6.997 |
| ZNF583 | 6.922 |
| LAT | 6.909 |
| ZNF217 | 6.908 |
| TPRKB | 6.893 |
| POLR2B | 6.881 |
| SPIRE1 | 6.849 |
| ENO3 | 6.826 |
| ZKSCAN2 | 6.722 |
| C1orf106 | 6.694 |
| REG1A | 6.675 |
| ZBTB24 | 6.667 |
| TTLL9 | 6.663 |
| ITGB1BP1 | 6.633 |
| IL5RA | 6.607 |
| SNTB2 | 6.598 |
| AKR1D1 | 6.560 |
| ZFYVE26 | 6.554 |
| MRPL13 | 6.484 |
| TDGF1 | 6.457 |
| LGALS7 | 6.428 |
| GCH1 | 6.378 |
| DSEL | 6.301 |
| EIF2S3 | 6.300 |
| S100A4 | 6.299 |
| MRO | 6.279 |
| HMGA2 | 6.157 |
| RASL10A | 6.154 |
| GIT2 | 6.148 |
| PPARG | 6.131 |
| SCLT1 | 6.104 |
| ASXL2 | 6.091 |
| TM7SF3 | 6.078 |
| NOS3 | 6.044 |
| BICD1 | 6.040 |
| NR3C1 | 6.035 |