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. 2015 Oct 27;7(11):3097–3114. doi: 10.1093/gbe/evv207

Table 3.

List of Stem Cell Regulating Genes with Significant MK Test, Which Detects Recurrent Positive Selection, before and after False Discovery Rate Correction

FBgn Name Gene Name DoSMAF MK Test P Values MK Test FDR P Values Literature Annotated Functiona GO Annotated Molecular Functionb
Both stem cell
    FBgn0004391 shtd 0.308 1.48 E-12 4.49 E-10 GSCMAINT; CELLEF; NSCSR; Cell cycle activity Mitotic anaphase-promoting complex activity
    FBgn0053123 CG33123 0.195 4.65 E-06 0.000269 NSCSR; ribosome associated process Leucine-tRNA ligase activity
    FBgn0020306 dom 0.15 5.82 E-06 0.000321 GSCMAINT; Transcription and chromatin remodeling Helicase activity
    FBgn0030241 feo 0.259 0.00042 0.0105 GSCMAINT; GSCEF Microtubule binding
    FBgn0015664 Dref 0.178 0.00377 0.055 GSCMAINT; Transcription and chromatin remodeling Sequence-specific DNA binding transcription factor activity
    FBgn0030500 Ndc80 0.176 0.0159 0.147 GSCDIFF; Kinetochore/Spindle —
    FBgn0002183 dre4 0.0906 0.0192 0.167 Transcription and chromatin remodeling DNA binding
    FBgn0085436 Not1 0.135 0.0212 0.174 GSCMAINT; Transcription and chromatin remodeling Protein binding
    FBgn0029672 CG2875 0.187 0.0296 0.223 — —
    FBgn0260789 mxc 0.131 0.032 0.227 GSCMAINT; CELLEF; Transcription and chromatin remodeling DNA binding
    FBgn0024227 ial 0.136 0.0381 0.254 GSCEF; NSCCG Protein serine/threonine kinase activity
    FBgn0027783 SMC2 0.106 0.0386 0.254 GSCMAINT; GSCEF DNA binding
    FBgn0032728 Tango6 −0.304 0.0415 0.263 CELLEF —
    FBgn0053554 Nipped-A 0.154 0.0483 0.291 GSCMAINT; Transcription and chromatin remodeling Protein kinase activity
Germline stem cell
    FBgn0011230 poe 0.133 5.36 E-11 1.09 E-08 GSCEF Calmodulin binding
    FBgn0032006 Pvr 0.295 7.58 E-11 1.32 E-08 — Protein tyrosine kinase activity
    FBgn0021761 Nup154 0.341 3.09 E-09 3.13 E-07 GSCDIFF; Nuclear pore Structural constituent of nuclear pore
    FBgn0028982 Spt6 0.288 3.48 E-09 3.26 E-07 GSCMAINT; CELLEF; Transcription and chromatin remodeling Chromatin binding
    FBgn0021796 Tor 0.165 2.57 E-06 0.000161 GSCMAINT; CELLEF Protein kinase activity
    FBgn0262647 Nup160 0.27 8.28 E-06 0.00042 GSCMAINT; CELLEF; Nuclear pore Protein binding
    FBgn0261854 aPKC 0.447 1.35 E-05 0.000632 GSCMAINT; CELLEF Protein kinase C activity
    FBgn0261954 east 0.32 1.95 E-05 0.000877 GSCMAINT —
    FBgn0001624 dlg1 0.354 5.46 E-05 0.00189 — Guanylate kinase activity
    FBgn0261797 Dhc64C 0.0475 5.67 E-05 0.00191 GSCDIFF; Kinetochore/Spindle ATPase activity, coupled
    FBgn0082582 tmod 0.531 0.00015 0.00443 — Actin binding
    FBgn0027537 Nup93-1 0.356 0.0002 0.00566 — Structural constituent of nuclear pore
    FBgn0033762 ZnT49B 0.264 0.00025 0.00673 GSCMAINT Cation transmembrane transporter activity
    FBgn0040273 Spt5 0.143 0.00095 0.0206 CELLEF; Transcription and chromatin remodeling —
    FBgn0031119 CG1812 0.277 0.00286 0.0484 GSCMAINT Actin binding
    FBgn0038805 TFAM 0.361 0.00298 0.0493 GSCMAINT; Mitochondrial function Sequence-specific DNA binding transcription factor activity
    FBgn0260936 scny 0.243 0.00314 0.0509 GSCMAINT; CELLEF; Transcription and chromatin remodeling Ubiquitin-specific protease activity
    FBgn0039680 Cap-D2 0.125 0.0032 0.0512 — —
    FBgn0031344 CG7420 0.283 0.00414 0.0576 GSCMAINT; CELLEF —
    FBgn0010382 CycE 0.237 0.00414 0.0576 GSCMAINT; GSCEF Cyclin-dependent protein ser/thr kinase regulator activity
    FBgn0050020 CG30020 0.223 0.00452 0.0604 GSCMAINT; Transcription and chromatin remodeling Nucleic acid binding
    FBgn0267350 PI4KIIIalpha 0.0671 0.00604 0.073 — 1-phosphatidylinositol 4-kinase activity
    FBgn0000158 bam 0.373 0.00729 0.0821 GSCDIFF; Translation Translation repressor activity
    FBgn0011802 Gem3 0.131 0.00735 0.0821 GSCMAINT; CELLEF; Splicing RNA helicase activity
    FBgn0039016 Dcr-1 0.0957 0.00825 0.0887 Translation Double-stranded RNA binding
    FBgn0025815 Mcm6 0.13 0.0083 0.0887 GSCMAINT; GSCEF; DNA replication Chromatin binding
    FBgn0015245 Hsp60 0.183 0.0114 0.114 — Unfolded protein binding
    FBgn0002174 l(2)tid 0.208 0.01294 0.124 GSCMAINT; Transcription and chromatin remodeling Patched binding
    FBgn0004856 Bx42 0.22 0.01781 0.158 GSCEF Protein binding
    FBgn0024177 zpg 0.2 0.02133 0.174 GSCMAINT; CELLEF Gap junction channel activity
    FBgn0053526 PNUTS 0.155 0.02655 0.208 GSCMAINT Protein phosphatase regulator activity
    FBgn0027055 CSN3 −0.857 0.02722 0.211 GSCEF —
    FBgn0041164 armi 0.172 0.02817 0.215 — DNA helicase activity
    FBgn0052113 CG32113 0.0534 0.03186 0.227 GSCMAINT —
    FBgn0039120 Nup98-96 0.0951 0.0359 0.242 Nuclear pore Protein binding
    FBgn0003277 RpII215 0.0825 0.0385 0.254 GSCMAINT; CELLEF DNA-directed RNA polymerase activity
    FBgn0025455 CycT 0.217 0.04489 0.274 GSCEF; Transcription and chromatin remodeling Protein kinase binding
    FBgn0033846 mip120 0.142 0.04827 0.291 Transcription and chromatin remodeling DNA binding
    FBgn0029113 Uba2 −0.18 0.04833 0.291 GSCMAINT; GSCEF Ubiquitin activating enzyme activity
    FBgn0261938 mtRNApol 0.107 0.0491 0.294 GSCEF; Mitochondrial function DNA-directed RNA polymerase activity
Neural stem cell
    FBgn0001612 Grip91 0.443 2.75 E-11 6.70 E-09 — Microtubule binding
    FBgn0005630 lola 0.502 1.43 E-10 2.17 E-08 NSCDIFF Protein binding
    FBgn0030384 CG2577 0.354 2.29 E-05 0.00096 — Protein serine/threonine kinase activity
    FBgn0263257 Cngl 0.218 2.21 E-05 0.00096 — Intracellular cyclic nucleotide activated cation channel activity
    FBgn0061200 Nup153 0.282 2.58 E-05 0.00104 — Zinc ion binding
    FBgn0250847 CG14034 0.387 3.39 E-05 0.00133 — Phospholipase activity
    FBgn0264962 Inr-a 0.23 8.60 E-05 0.00275 — RNA binding
    FBgn0041147 ida 0.196 0.00049 0.0116 NSCSR; Cell cycle activity Mitotic anaphase-promoting complex activity
    FBgn0001222 Hsf 0.263 0.00157 0.0314 — DNA binding
    FBgn0037379 CG10979 −0.451 0.00333 0.0516 — Metal ion binding
    FBgn0032683 kon 0.113 0.00416 0.0576 — Protein binding
    FBgn0030706 CG8909 0.0659 0.00673 0.078 — Low-density lipoprotein receptor activity
    FBgn0040477 cid 0.405 0.00751 0.0831 — DNA binding
    FBgn0003044 Pcl 0.188 0.00797 0.0867 — Protein binding
    FBgn0031886 Nuf2 0.236 0.0108 0.109 — —
    FBgn0036248 ssp 0.281 0.0118 0.117 — Beta-catenin binding
    FBgn0259876 Cap-G 0.18 0.0141 0.134 — —
    FBgn0030951 CG6873 0.378 0.0205 0.171 — Actin binding
    FBgn0035026 Fcp1 −0.242 0.0265 0.208 — CTD phosphatase activity
    FBgn0053100 4EHP 0.423 0.0307 0.226 — Translation initiation factor activity
    FBgn0039475 CG6277 0.219 0.0322 0.228 — Phosphatidylcholine 1-acylhydrolase activity
    FBgn0039788 Rpt6R 0.138 0.0329 0.231 — ATPase activity
    FBgn0036643 Syx8 −0.702 0.0346 0.241 — SNAP receptor activity
    FBgn0250732 gfzf 0.287 0.0395 0.256 — Glutathione transferase activity
    FBgn0011704 RnrS −0.229 0.0445 0.274 — Ribonucleoside-diphosphate reductase activity

Note.— CELLEF, germline general cell essential factor; GSCEF, germline stem cell-specific essential factor; NSCCG, neural stem cell regulation of cell growth; NSCSR, neural stem cell self-renewal; DoSMAF, DoS statistics calculated after excluding minor allele frequencies of 5%; MK-test FDR P values, MK-test P values after FDR corrections; Note that these were analyzed from all stem cell regulating gene list identified from both Neumüller et al. (2011) and Yan et al. (2014) regardless of whether it was assigned a control gene or not from this study. Significant MK test P values after FDR correction are bolded.

aFunctional annotation based on the study of Neumüller et al. (2011) and Yan et al. (2014).

bFunctional annotation based on GO categorization on Flybase.