package gem;
import gem.parser.HPRDParser;
import gem.parser.TREDParser;
import gem.parser.TabDelimitedFileParser;
import java.util.*;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.BufferedWriter;
import java.io.FileWriter;
/**
* @author Ozgun Babur
*/
public class TripletMaker
{
public static void main(String[] args) throws Throwable
{
prepare("AR");
// makeARTripesWithMod("AKR1C1", "AKR1C2", "AKR1C3", "AKR1C4", "CYB5A", "CYP11A1", "CYP11B1",
// "CYP11B2", "CYP17A1", "CYP19A1", "CYP21A2", "CYP3A4", "CYP3A43", "CYP3A5", "CYP3A7",
// "HSD17B1", "HSD17B10", "HSD17B11", "HSD17B12", "HSD17B13", "HSD17B14", "HSD17B2",
// "HSD17B3", "HSD17B4", "HSD17B6", "HSD17B7", "HSD17B8", "HSD3B1", "HSD3B2", "HSD3B7",
// "RDH5", "SHBG", "SRD5A1", "SRD5A2", "SRD5A3", "STAR", "UGT2B15", "UGT2B17", "UGT2B7");
// makeARTripesWithMod("NR3C1");
// prepareCompleteSetForAllTargets();
}
public static void make(String factor, Collection<String> moduls, Collection<String> targets,
String filename) throws Throwable
{
writeTrips(make(factor, moduls, targets), filename);
}
public static List<String> make(String factor, Collection<String> moduls,
Collection<String> targets) throws Throwable
{
assert factor != null;
Set<String> mods = new HashSet<String>();
Set<String> tars = new HashSet<String>();
Map<String,String> s2g = Triplet.getSymbolToGeneMap();
for (String t : targets)
{
assert t != null;
// if (!s2g.containsKey(t)) t = EntrezGeneParser.searchForOfficialName(t);
if (t == null) continue;
if (!moduls.contains(t))
tars.add(t);
}
for (String m : moduls)
{
// System.out.println("m = " + m);
assert m != null;
// if (!s2g.containsKey(m)) m = EntrezGeneParser.searchForOfficialName(m);
if (m != null)
if (!targets.contains(m))
mods.add(m);
else
System.out.println("both M and T = " + m);
}
mods.remove(factor);
tars.remove(factor);
System.out.println("mods = " + mods.size());
System.out.println("tars = " + tars.size());
List<String> trips = new ArrayList<String>();
for (String mod : mods)
{
if (s2g.get(mod) == null)
{
System.out.println("modulator " + mod + " has no gene ID");
continue;
}
for (String tar : tars)
{
if (s2g.get(tar) == null) continue;
if (!mod.equals(tar) && !mod.equals(factor) && !tar.equals(factor))
{
trips.add(s2g.get(mod) + "\t" + s2g.get(factor) + "\t" + s2g.get(tar));
}
}
}
return trips;
}
public static void writeTrips(List<String> trips, String filename) throws Throwable
{
BufferedWriter writer = new BufferedWriter(new FileWriter(filename));
writer.write("Modulator\tFactor\tTarget");
for (String trip : trips)
{
writer.write("\n" + trip);
}
writer.close();
}
public static Set<String> getInteractors(String symbol) throws Throwable
{
Set<String> set = new HashSet<String>();
BufferedReader reader = new BufferedReader(new FileReader("resource/HPRD.txt"));
for (String line = reader.readLine(); line != null; line = reader.readLine())
{
String[] tokens = line.split("\t");
if (tokens[0].equals(symbol) && !tokens[3].equals(symbol))
{
set.add(tokens[3]);
}
else if (tokens[3].equals(symbol) && !tokens[0].equals(symbol))
{
set.add(tokens[0]);
}
}
reader.close();
return set;
}
private static void prepare(String factorSym) throws Throwable
{
Set<String> set = new HashSet<String>();
set.add(factorSym);
Map<String,Set<String>> map = HPRDParser.readFor(set);
Set<String> interactors = map.get(factorSym);
// if (factorSym.equals("AR")) interactors.add("PARK7");
// if (factorSym.equals("ETV1")) interactors.add("KIT");
// if (factorSym.equals("MITF")) interactors.addAll(Arrays.asList("MAP2K1", "MAP2K2", "MAPK3", "RPS6KA1", "RPS6KA2", "RPS6KA3", "HIF1", "YWHAZ", "MAPK11"));
System.out.println("number of interacting proteins = " + interactors.size());
TabDelimitedFileParser parser =
new TabDelimitedFileParser("resource/factors/" + factorSym + "-select-small.txt");
Set<String> targets = parser.getColumnSet(0);
// parser = new TabDelimitedFileParser("resource/factors/" + factorSym + "_andr.txt");
// Set<String> confirmed = parser.getColumnSet(0);
// confirmed.removeAll(interactors);
interactors.removeAll(targets);
System.out.println("number of targets = " + targets.size());
make(factorSym, interactors, targets, "resource/factor-trips/" + factorSym + "-select.txt");
}
private static void prepareSmallGroup(String factorSym, String... mod) throws Throwable
{
Set<String> interactors = new HashSet<String>(Arrays.asList(mod));
interactors.add(factorSym);
System.out.println("number of interacting proteins = " + interactors.size());
TabDelimitedFileParser parser =
new TabDelimitedFileParser("resource/factors/" + factorSym + ".txt");
Set<String> targets = parser.getColumnSet(0);
System.out.println("number of targets = " + targets.size());
List<String> trips = new ArrayList<String>();
for (String fac : interactors)
{
trips.addAll(make(fac, interactors, targets));
}
writeTrips(trips, "resource/factor-trips/" + factorSym + "-group.txt");
}
private static void prepare(String factorSym, String modSym) throws Throwable
{
Set<String> interactors = new HashSet<String>();
interactors.add(modSym);
TabDelimitedFileParser parser =
new TabDelimitedFileParser("resource/factors/" + factorSym + ".txt");
Set<String> targets = parser.getColumnSet(0);
if (targets.contains(modSym)) System.out.println(modSym + " is also a target");
targets.removeAll(interactors);
System.out.println("number of targets = " + targets.size());
make(factorSym, interactors, targets, "resource/factor-trips/" + factorSym + "-by-" + modSym + ".txt");
}
private static void prepareAR() throws Throwable
{
Set<String> set = new HashSet<String>();
set.add("AR");
Map<String,Set<String>> map = HPRDParser.readFor(set);
Set<String> interactors = map.get("AR");
Set<String> targets = getARTargets_ChEA();
make("AR", interactors, targets, "resource/triplets_AR_hprd_ChEA.txt");
}
private static void prepareBRCA2() throws Throwable
{
String[] mods = new String[]{"C11orf30"};
String[] tars = new String[]{"FHIT", "ESR1"};
make("BRCA2", Arrays.asList(mods), Arrays.asList(tars), "resource/triplets_BRCA2.txt");
}
private static void prepareFOXM1() throws Throwable
{
Set<String> mods = getInteractors("FOXM1");
mods.addAll(Arrays.asList("MAP2K1", "CDKN2A", "RB1", "CCNE1", "SP1", "ONECUT1", "CREBBP",
"CCNB1", "CDK4", "CDK2", "GSK3A", "CHEK2"));
// Emek's search
mods.addAll(Arrays.asList("CREBBP", "MMP2", "CCND1", "LAMA4", "CDC25B", "CENPB", "XRCC1",
"EP300", "CCNB2", "TGFA", "PLK1", "NFATC3", "BIRC5", "ONECUT1", "SKP2", "CKS1B", "AURKB",
"GAS1", "FPR2", "CENPA", "CDKN2A", "CENPF", "NEK2", "ARR3", "BRCA2", "CCNB1", "CHEK2",
"ETV5", "F12", "CCNE1", "STAT3", "CDH1", "ESR1", "CDK2", "FOXO3"));
List<String> tars = Arrays.asList("CENPA", "ONECUT1", "HSPA1A", "CCNB2", "MYC", "NEK2",
"MMP2", "LAMA4", "ETV5", "CCND1", "NFATC3", "BRCA2", "TGFA", "GAS1", "XRCC1",
"CENPB","CCNB1", "CDC2", "SKP2", "FOS", "CENPF", "ESR1", "HIST1H2BA", "CDC25B", "AURKB",
"BIRC5", "PLK1", "HSPA4", "KDR", "CKS1B");
make("FOXM1", mods, tars, "resource/triplets_FOXM1.txt");
}
private static void prepareFOXP3() throws Throwable
{
Set<String> mods = new HashSet<String>(Arrays.asList(FOXP3_REGS));
mods.addAll(Arrays.asList(FOXP3_NON_TR_REGS));
Set<String> tars = new HashSet<String>(Arrays.asList(FOXP3_TARS));
tars.addAll(Arrays.asList(FOXP3_TARS_NATURE));
make("FOXP3", mods, tars, "resource/triplets_FOXP3.txt");
}
private static void prepareGlobal() throws Throwable
{
Map<String, String> s2g = Triplet.getSymbolToGeneMap();
List<String> trips = new ArrayList<String>();
Map<String, Set<String>> pairs = TREDParser.getTFPairs();
for (String fac : pairs.keySet())
{
Set<String> tars = pairs.get(fac);
if (!s2g.containsKey(fac)) continue;
Set<String> mods = getInteractors(fac);
trips.addAll(make(fac, mods, tars));
}
writeTrips(trips, "resource/triplets.txt");
}
private static void prepareCompleteSetForTarget() throws Throwable
{
String tar = "KLK3";
List<Triplet> trips = Triplet.readTrips("result/All_fdr0.05_var1.0.xls");
for (Triplet t : trips)
{
t.backFromURLToIDs();
}
trips = Triplet.selectTarget(trips, tar, true);
Set<String> mods = new HashSet<String>();
Set<String> facs = new HashSet<String>();
Set<String> tars = new HashSet<String>();
tars.add(tar);
for (Triplet t : trips)
{
if (Triplet.getGeneToSymbolMap().containsKey(t.modulator))
mods.add(Triplet.getGeneToSymbolMap().get(t.modulator));
if (Triplet.getGeneToSymbolMap().containsKey(t.factor))
facs.add(Triplet.getGeneToSymbolMap().get(t.factor));
}
mods.addAll(facs);
List<String> triplets = new ArrayList<String>();
for (String fac : facs)
{
triplets.addAll(make(fac, mods, tars));
}
writeTrips(triplets, "resource/tartrips/triplets_tar_" + tar + ".txt");
}
private static void prepareCompleteSetForAllTargets() throws Throwable
{
// List<Triplet> trips = Triplet.readTrips("result/All_fdr0.05_var1.0.xls");
List<Triplet> trips = Triplet.readTrips("result/Result_fdr0.05_var1.0.xls");
for (Triplet t : trips)
{
t.backFromURLToSymbol();
}
Map<String, Set<String>> mods = new HashMap<String, Set<String>>();
Map<String, Set<String>> facs = new HashMap<String, Set<String>>();
Set<String> tars = new HashSet<String>();
for (Triplet t : trips)
{
if (t.target == null || t.factor == null || t.modulator == null) continue;
if (!mods.containsKey(t.target))
{
mods.put(t.target, new HashSet<String>());
facs.put(t.target, new HashSet<String>());
}
mods.get(t.target).add(t.modulator);
facs.get(t.target).add(t.factor);
}
List<String> triplets = new ArrayList<String>();
for (String tar : mods.keySet())
{
mods.get(tar).addAll(facs.get(tar));
tars.clear();
tars.add(tar);
// for (String fac : facs.get(tar))
for (String fac : mods.get(tar))
{
triplets.addAll(make(fac, mods.get(tar), tars));
}
}
// writeTrips(triplets, "resource/tartrips/triplets_tar_all.txt");
writeTrips(triplets, "resource/tartrips/triplets_tar_mod-mod_all.txt");
}
private static void makeARTripesWithCandMod() throws Throwable
{
String mod = "TWIST1";
List<String> mods = Arrays.asList(mod);
writeTrips(make("AR", new HashSet<String>(mods), getARTargets()), "resource/" + mod +"-AR-trips.txt");
}
private static void makeARTripesWithMod(String... mod) throws Throwable
{
List<String> mods = Arrays.asList(mod);
Set<String> targets = getARTargets_ChEA();
targets.removeAll(mods);
writeTrips(make("AR", new HashSet<String>(mods), targets), "resource/" + "NR3C1" + "-AR-trips.txt");
}
private static Set<String> getARTargets_ChEA()
{
TabDelimitedFileParser parser = new TabDelimitedFileParser("resource/AR_tars.txt");
Set<String> targets = parser.getColumnSet("AR Targets");
return targets;
}
private static Set<String> getARTargets()
{
Set<String> tars = new HashSet<String>();
List<Triplet> trips = Triplet.readTrips("resource/AR-hprd-tredlit-trips.txt");
for (Triplet t : trips)
{
tars.add(Triplet.getGeneToSymbolMap().get(t.target));
}
return tars;
}
private static final String[] DDC_TARS = new String[]{"E2F7", "MICAL1", "MTA1", "SYTL2",
"ZNF277", "ZNF333", "ZNF488", "CYP26B1", "PLA2G2F", "TGM2", "YME1L1", "DRD3", "GABRE",
"MUC4", "OPCML", "UNC5C", "C2orf11", "PON2", "GPR15", "PTGDR", "CD109", "AGR2", "ARR3",
"C4orf17", "CADPS", "DEPDC4", "FLJ32810", "TMEPAI"};
private static final String[] FOXP3_REGS = new String[]{"AATF", "ABT1", "ASH2L", "BCLAF1",
"BRD7", "CARM1", "CBFB", "CBX1", "CBX4", "CEBPZ", "CHD1L", "CHD4", "CNOT2", "CNOT3",
"CNOT7", "DMAP1", "ELF1", "ERCC3", "FLI1", "FOXK1", "FOXO1", "FOXP1", "FOXP3", "FOXP4",
"EHMT2", "GATA3", "GATAD2A", "GTF2B", "GTF2E1", "GTF2H2", "GTF3C2", "GTF3C5", "HDAC1",
"HDAC2", "HLTF", "IKZF1", "IKZF4", "IRF3", "KDM1A", "KDM4A", "KRI1", "MED12", "MED15",
"MED17", "MED18", "MED19", "MED20", "MED21", "MED22", "MED24", "MED30", "MED31", "MYST1",
"MYST2", "NCOA5", "NFATC2", "NFKB1", "NKRF", "NMI", "NR2C2", "NR3C1", "PELP1", "PHF8",
"PIAS1", "POLR2A", "POLR2B", "PRPF6", "RAI14", "RCOR1", "RNF40", "RUNX1", "RUNX3", "SAP130",
"SAP18", "SAP30BP", "SIN3A", "SIRT7", "SLTM", "SMAD2", "SMAD4", "SMARCA4", "SMARCAL1",
"SMARCB1", "SMARCC1", "SMARCC2", "SMARCD2", "SMARCE1", "SNIP1", "SP2", "SSRP1", "STAT3",
"SUB1", "SUZ12", "TCF12", "TCF20", "TRERF1", "TP53", "YBX1", "YY1", "ZC3HAV1", "ZCCHC8",
"ZNF148", "ZNF346"};
private static final String[] FOXP3_NON_TR_REGS = new String[]{"SKIV2L", "SFRS2IP", "GLTSCR2",
"TBL3", "TDRD3", "EXOSC7", "GCN1L1", "FYB", "IK", "BAT2", "DHX36", "WDR33", "RAE1", "SRRT",
"BCL7A", "PAICS", "PPIL2", "SENP3", "UBE2S", "UFD1L", "CUL3", "WARS", "RPL35A", "DARS",
"EIF4G1", "EIF2C2", "ARHGEF6", "FTSJ3", "WDR3", "SRPK2", "STRAP", "THOC4", "PRPF4B",
"PLRG1", "SRRM1", "SART1", "ZCCHC8", "PRPF3", "THOC3", "DDX41", "WAC", "SLBP", "SNRNP70",
"STRBP", "PDCD4", "PARK7", "SNRPB2", "IGF2BP3", "EXOSC1", "DDX56", "NCBP2", "PUM2",
"EXOSC5", "RBM27", "CASC3", "CLP1", "ADAR", "GTPBP4", "KPNA3", "SEC23A", "AP3S1", "PDCD6IP",
"RANBP2", "COPB1", "SEC24C", "TNPO1", "YWHAG", "NUP155", "AP1B1", "CCT4", "VBP1", "CMAS",
"ABCF2", "DHX37", "KIF4A", "TRIM25", "MLLT10", "LIMS1", "LUC7L", "LPXN", "PHF8", "TES",
"ACSL4", "LAT", "PLEKHA2", "CLIC1", "ADD1", "CORO1A", "ADD3", "ARPC1B", "ARPC5", "RAI14",
"GSN", "CORO2B", "PPP2R5A", "VRK1", "ATM", "CHEK1", "CSK", "MARK2", "PRKAR2A", "MAP2K1",
"ABL1", "CDK6", "GSK3B", "GIT2", "MARK3", "PFKFB3", "RPS6KA3", "ORC2L", "TOP1", "RRM2",
"LIG1", "POLD1", "ORC3L", "MCM10", "RAD21", "RAD23B", "XPC", "MSH6", "PES1", "AATF",
"CD2AP", "KIF11", "PRC1", "CDC23", "TOP3B", "TERF2", "SKIV2L"};
private static final String[] FOXP3_TARS = new String[]{"ABT1", "ABTB2", "ADD3", "ADIPOQ",
"AGR2", "AKAP13", "AKR1D1", "AMPH", "ANKRD12", "ANKRD44", "AP4S1", "APH1A", "ARHGAP15",
"ARHGAP5", "ARHGEF10", "ARHGEF3", "ARID5B", "ARL4A", "ARL6", "ASXL2", "ATG16L1", "ATP2B1",
"ATP6V1A", "B3GNT2", "BACH2", "BCL11B", "BCL2", "BTBD10", "CADPS", "CAST", "CBLB", "CD28",
"CD44", "CD69", "CD84", "CDC2L6", "CDC42SE2", "CDK2", "CENPK", "CHD9", "CITED2", "CLEC2D",
"CMAH", "CNOT2", "CNOT6L", "COBLL1", "CPE", "CPM", "CPNE4", "CPOX", "CREM", "CTLA4",
"CUGBP2", "CXCR4", "DBF4", "DCTN6", "DENND5A", "DOCK10", "DPH5", "DUSP22", "ELF1", "ELK3",
"ERRFI1", "ESD", "ETNK1", "ETS1", "EVI5", "EXOC6B", "EXT1", "F2RL1", "FEM1C", "FLI1",
"FOXP1", "FRMD4B", "GALNT4", "GATA3", "GBP1", "GBP4", "GDI2", "GFI1", "GLCCI1", "GPD2",
"GPHN", "GPLD1", "GPR18", "GPR183", "HBP1", "HBS1L", "HERPUD2", "HIF1A", "HIVEP2", "IBTK",
"ICOS", "IDS", "IFNAR2", "IFNGR1", "IFT57", "IL2RA", "IL7R", "INPP4B", "IRF4", "IRF6",
"ITGA6", "JAK1", "JARID2", "JMJD1C", "KIF3B", "KLF3", "KLF6", "L3MBTL3", "LATS2", "LEF1",
"LNX2", "LPAR6", "LRCH1", "LRIG1", "LRRC8C", "LTA4H", "MALT1", "MAN1A2", "MAP3K1", "MAP3K5",
"MAP3K8", "MBNL1", "MDFIC", "MTFR1", "MUTED", "MYO9A", "MYST4", "NAT12", "NCK2", "NCOA3",
"NEK7", "NFKBIZ", "NIPBL", "NR3C1", "NR4A2", "NRIP1", "NRP1", "NT5E", "NUDCD3", "NUP153",
"P2RY10", "P4HA1", "PAK1IP1", "PARL", "PCTK2", "PDE3B", "PDE4B", "PELI1", "PHTF2", "PIK3R1",
"PIP4K2A", "PPP2R5C", "PPP3CC", "PRDM1", "PRKCH", "PRSS2", "PSMA1", "PTGER2", "PTGER3",
"PTK2B", "PTPRC", "PVT1", "RAB8B", "RABGAP1L", "RAPGEF6", "RCBTB2", "RFX3", "RGS1", "RHOH",
"RNF125", "ROD1", "RPL5", "RRAS2", "SAMHD1", "SAMSN1", "SATB1", "SCML4", "SDCBP", "SESN1",
"SGIP1", "SGMS1", "SLA", "SLAMF1", "SLAMF6", "SLC35B3", "SLC37A3", "SMC5", "SNX14", "SNX9",
"SOCS2", "SRI", "ST8SIA1", "STARD6", "STAT4", "STAT5B", "STK10", "STRN3", "SYNE2", "TASP1",
"TBC1D15", "TBC1D4", "TBC1D5", "TCF12", "TGFBR2", "TLR1", "TMEM64", "TNFAIP3", "TNFSF11",
"TOP1", "TOP2B", "TOX", "TPP2", "TRAT1", "TRIM34", "TRIO", "TUBB2C", "TUBE1", "UBAC2",
"UTRN", "VPS54", "VRK2", "WBP4", "WDR37", "WIPF1", "WNK1", "ZBED3", "ZBTB20", "ZBTB25",
"ZC3HAV1", "ZFAND6", "ZFP36L2", "ZKSCAN3", "ZNRF1"};
private static final String[] FOXP3_TARS_NATURE = new String[]{"MTG1", "ABT1", "HIST1H4B",
"PRDX6", "EPC2", "NXN", "MDM2", "MAP4K1", "CLIP1", "CREB3L3", "TGIF1", "EPM2AIP1",
"LDLRAP1", "NAT9", "CD84", "MED24", "NME1", "TRDMT1", "RASGRP4", "CCL1", "MAP4K4", "PPEF2",
"CATSPER2", "DTL", "UCP2", "BLCAP", "SLC25A12", "STAT3", "REL", "PET112L", "RDM1", "ATP10D",
"KISS1R", "MAP2K2", "IRF4", "MRPS33", "TJP1", "DUSP16", "DNAJB4", "SEMA4A", "DDIT4", "CBX3",
"HRSP12", "COPG", "H3F3B", "POLD4", "6-Mar", "ABCA7", "NRD1", "HIST1H4J", "RHEB", "GOLPH3",
"MMP9", "TIAL1", "ARPC1B", "ANTXR2", "P2RY10", "AHCYL1", "STXBP4", "CBX7", "NUP62", "BIRC3",
"MBD4", "HIST1H3I", "DDB1", "ARL4C", "PRPS1", "UBAP2L", "GIMAP5", "TIPARP", "CXCR6", "RGS1",
"NPAS4", "R3HDM1", "RNF38", "CDK4", "ADH1A", "TEC", "PNKP", "SLC22A4", "PECAM1", "DSCR3",
"EIF2AK3", "ST8SIA4", "AQP11", "NDUFS6", "CD3G", "CNPY2", "CYLD", "RBM7", "WBP2", "DCK",
"SCNM1", "SNAPC3", "PTGER1", "HIST1H3E", "CRYBA4", "NUP210", "MINK1", "RGS5", "MAP3K1",
"ATP2A1", "CPT1A", "CSF1", "HIST1H2AE", "CDC27", "HIST1H3A", "NPAT", "PDCD1", "PAQR7",
"CAD", "WBSCR27", "TRPA1", "TRPC4AP", "TAZ", "NKX2-6", "LRRC8C", "PMVK", "FAF1", "IFNK",
"BRE", "SLC17A5", "P2RY14", "EVI2A", "TAX1BP1", "PIGL", "GSR", "EIF4EBP2", "IL17RA",
"VPS11", "CYP1A1", "CTSD", "ITK", "MED1", "QPCTL", "LSM5", "GSTT2", "XPO7", "CD274",
"HSPBAP1", "KDM6A", "ORC5L", "PPP4R1", "HMGB1", "ZBTB37", "ACTR3", "TSC22D4", "PHTF2",
"TTC5", "TBL1X", "VPS72", "GLB1", "GOLPH3L", "HNRNPU", "JAK2", "LRP10", "PSMA3", "HIST1H1D",
"AGGF1", "RBM47", "GGT1", "LRP2BP", "HELZ", "PPIE", "ARMC6", "LEPROTL1", "RIOK2", "TOMM34",
"RPUSD2", "NMI", "MRPL36", "CSNK1G2", "CBX1", "SLC23A2", "LDB1", "ARHGDIB", "SIX6", "UBR1",
"UBXN4", "POU2AF1", "HERC3", "PON2", "GBP2", "LIPC", "FAH", "LIX1", "SIRT1", "GMFB",
"ATPIF1", "SESN1", "DNTT", "ATP6V1D", "UBE3B", "LRRC25", "STOML1", "KCNA3", "MAF1",
"PPP1R13B", "DHFR", "EIF4E3", "SFRS1", "ZEB1", "HSPA13", "TNFRSF19", "KDELC2", "FOXJ3",
"ZFAND6", "ARIH2", "SLC35B4", "UBA3", "ATP5L", "ORMDL1", "GCNT3", "PGAM1", "LIF", "NFIA",
"CISH", "MTHFD2", "CAMK2G", "COPS7B", "DLEC1", "HIST1H2BJ", "RPLP1", "PDCD2", "SERTAD3",
"WDR44", "LRRC41", "GCK", "CDKN1B", "CLIC1", "TNFRSF1B", "ASPH", "KCTD2", "JARID2",
"CHORDC1", "BBS4", "AP4B1", "GNG2", "HSD17B10", "USP4", "ASH1L", "GPR146", "CTSS",
"HIST1H1T", "BRCA1", "CTDSPL2", "ZC3HAV1", "GABPB1", "SYT3", "TBK1", "NDUFC1", "ARID1A",
"TIMM22", "SRP19", "HIBADH", "HSPH1", "HNRNPF", "MAPKAPK3", "MAT2B", "CWF19L2", "KLF6",
"CDC40", "USP8", "COMMD3", "AIPL1", "PSMC2", "DNMBP", "SLC16A6", "ANXA9", "ARID3B", "FEM1B",
"PRPF18", "ATG9B", "SERF2", "MOXD2", "NUP43", "HIST1H2BN", "PHF6", "ANAPC11", "SLC17A6",
"BSPRY", "GPD2", "NT5E", "CXCR5", "LRRC6", "EEA1", "IDH1", "ITIH5", "PRKAR1A", "ACAD8",
"RDX", "TBCE", "NSUN6", "STAT6", "MSH3", "LY96", "SYF2", "RAD1", "GLYAT", "BRIX1",
"HIST2H3B", "KCNAB3", "HIST1H2BG", "PANX1", "SART3", "GIMAP1", "ITCH", "LYSMD3", "RPL29",
"OSBPL8", "TSHZ1", "MAGEB3", "RBL1", "SLC11A2", "NUDT4", "UBE2N", "AP2A2", "RFX3", "PIAS4",
"PPAT", "STX7", "RHOG", "PAICS", "6-Sep", "RPS26", "PIK3CD", "FYCO1", "USP10", "GNA13",
"PCNXL3", "SRP54", "HIST1H4F", "RAB8B", "PMS2", "DIXDC1", "TFB2M", "CCNI", "SESTD1",
"BNIP2", "SGSH", "LSM10", "TERF1", "MNT", "SEC11A", "ATM", "EGLN1", "PIM1", "JMJD6",
"RAB19", "ITGB3BP", "HIST1H4C", "HECTD2", "SPA17", "DHRS3", "HSF4", "CAT", "CBLN3", "NR1D1",
"PDE6D", "TLE3", "DHRS9", "RAG1", "PML", "FYB", "PRDX1", "PSD4", "KIF15", "PCTK2", "WASF1",
"ZBTB1", "CPA3", "FGD6", "HMMR", "ITGAV", "PRCC", "KIF11", "ITM2B", "TPM4", "EML4",
"MAD1L1", "MED16", "APAF1", "CROT", "DNAJB12", "CENPK", "MRPS28", "HOOK2", "TTC16",
"HIST1H2BF", "NRBP1", "FKBP1A", "GPX2", "RBM6", "ARL15", "TESK2", "ETS1", "HIST1H4K",
"GIMAP4", "NSMCE1", "FZD7", "TOM1L2", "SLC20A1", "APBB1IP", "NCOR1", "ADIPOQ", "MCM10",
"HIST1H3H", "LASS2", "REST", "SLC22A5", "NDUFB3", "PJA1", "DDX24", "RNF128", "NAP1L4",
"ADM", "SUPV3L1", "STX1A", "DDB2", "ARL10", "ING3", "HIVEP1", "RPS29", "NRIP1", "SIPA1L1",
"FZR1", "ATF7IP", "TOLLIP", "NR1H3", "TMC6", "TP53", "BACH1", "PLDN", "CD2", "WDR34",
"UQCRH", "GPR18", "USP6NL", "EMP3", "SLC25A15", "PRTN3", "RCL1", "CRTAM", "SNAPC4", "TMPO",
"SCARB2", "GRB2", "NDFIP1", "PLEKHG6", "UNC5A", "TMED5", "KDM5C", "STC2", "ZNF280B", "CSK",
"NUPL1", "PPP2R5C", "ITGB7", "PGK1", "SERINC1", "DARS2", "ZER1", "PIGK", "INPP1", "PTGER4",
"SLC5A6", "TCEB3", "PDIA3", "CLK1", "ME2", "F12", "POP5", "CCND2", "SLFN5", "ANKRD22",
"IGSF8", "SLC3A2", "PTPN2", "CTSC", "CD28", "SLC37A3", "RTN4IP1", "PAPLN", "CSNK1A1",
"HIST1H2AH", "SIL1", "CENPI", "ARL11", "DNAJC8", "ELANE", "ARF6", "IL10RA", "ZFP36L1",
"SMYD3", "SMAD7", "VAMP4", "PPT1", "SETDB1", "DIRC2", "PCMT1", "DYRK1A", "WAC", "EVI2B",
"SNAI3", "DDX42", "RIOK1", "HIST1H3D", "PLEKHB1", "GPR22", "TCF4", "PIP5K1B", "DUSP10",
"WEE1", "JUNB", "SDF2", "SCFD2", "RANBP2", "MTFMT", "NFATC3", "TMPRSS4", "TCTA",
"HIST1H2BM", "PRPF8", "HIST1H1B", "NARG1L", "NFAT5", "RNF121", "DARS", "MEF2A", "USP48",
"GFPT1", "ARHGAP11A", "ZFAND5", "KIF23", "ST13", "ANKMY2", "ZKSCAN5", "PSMB5", "LRRC42",
"VTCN1", "ABHD8", "GLO1", "RIPK1", "BASP1", "PPIL5", "MAPRE2", "RABGAP1L", "HBP1", "AKT1S1",
"SMAD3", "HIAT1", "ALG9", "TSNAXIP1", "SESN2", "GTF2A2", "DNAJA2", "TBRG1", "ABCB8", "POT1",
"NPTN", "FBXO46", "FTH1", "CCR3", "DCLRE1A", "BRMS1L", "TXNIP", "IL2", "PMPCA", "CMTM7",
"FBXO9", "DGKA", "SCP2", "PPP2R1A", "STK11IP", "APEX2", "ZPBP2", "POFUT1", "ASCC1",
"NUP153", "SMC1A", "HIST2H2BE", "NXT2", "SLC9A9", "NDOR1", "LPXN", "ATP6V0A1", "PDK1",
"DNASE1", "ERCC1", "PDCD6IP", "ARCN1", "ARHGAP12", "SRXN1", "CD53", "HIST1H2AD", "RASA3",
"MICAL1", "ARL6IP6", "ZDHHC9", "FRAT2", "CHD1", "SDCCAG3", "H2AFY", "ARMC8", "PSMC3",
"9-Mar", "LRRC8D", "IL9", "AP4M1", "DHX38", "CD3E", "CEPT1", "P2RX4", "PCGF2", "VEZF1",
"CNOT6L", "UBE2H", "LY9", "LIN28", "UBE2D3", "DAP3", "CAMK1D", "TRAIP", "SP6", "HSPA4",
"ALDH3A2", "ATP5H", "B4GALT1", "SLC25A19", "ID2", "EIF4ENIF1", "APLP2", "FIP1L1", "ADORA2A",
"GGNBP2", "MBTPS2", "LIPH", "PKN3", "EIF3K", "SAMSN1", "POLG2", "DAPP1", "SCML4", "INTS12",
"RIBC1", "RBPJ", "TGFBR2", "WDR6", "PLLP", "TMEM53", "SH2B3", "DET1", "MDM1", "MKNK1",
"GTPBP1", "PMS1", "ICAM2", "LCP2", "CITED2", "HNRNPA1", "STX12", "HIST2H2AB", "SCMH1",
"OSBPL9", "TMEM19", "ANGPTL4", "FOXO3", "ARID5B", "NIPA1", "GLT8D2", "ECT2", "TRPV2",
"GPR65", "METAP1", "DNAJB6", "TOP2B", "GPR82", "MLH1", "RWDD1", "TGFB1", "NSFL1C", "PLXNC1",
"AQP9", "UBE2B", "ADD1", "GPR35", "PCSK1", "HSP90B1", "SLC41A1", "RTN3", "XPO1", "TMEM49",
"BCL10", "MDH1", "ARHGAP1", "NFKB1", "IRF2", "TNFRSF9", "MUTED", "ETV3", "FKBP1B",
"FGFR1OP2", "WBP11", "PABPC1", "FGF7", "SLC26A11", "SACM1L", "USP36", "HIST1H4D", "MDM4",
"IER3", "SNX12", "SLC35D1", "SKIL", "PTTG1", "PPWD1", "ECE1", "VPS45", "HOOK3", "ZDHHC17",
"GRAP2", "LAS1L", "CLTC", "DOHH", "MSGN1", "DCLRE1B", "PSMD5", "GPR171", "RBM5", "RAB18",
"RBKS", "CABP1", "EGR2", "KIF3A", "PAPD4", "EIF4E", "LYPLA2", "MRPS31", "FASLG", "SLC39A1",
"YTHDF3", "SPAG9", "FGR", "MEFV", "CAB39", "MNS1", "FGD3", "CYSLTR1", "CHD1L", "HIST1H2BE",
"SUMO2", "DUT", "POLR3B", "SUPT6H", "EDEM1", "TAF8", "DSG2", "PPP1CB", "GRM6", "EPS15",
"STX16", "UBB", "EAF1", "KDM5B", "ALG8", "SPRED2", "MGEA5", "ARL4D", "TBC1D15", "INSIG1",
"MOBKL2A", "HIST1H3G", "CGREF1", "ELAC1", "FCGR3B", "HADHB", "GRK6", "MYLPF", "BCAR1",
"SDCBP", "CDC2L6", "POLR2A", "KIF5B", "PES1", "USF1", "ZFP1", "NCOA3", "RLBP1", "ACP2",
"MRPL45", "PPIL3", "TMEM50A", "HIST1H2AB", "TRAF3IP2", "UBE2R2", "IRF8", "ATF5", "EFTUD1",
"ROCK2", "RNF170", "HSPA9A", "ORM1", "TOPBP1", "SRRM2", "EIF2C2", "BMI1", "WASF2", "SPATA6",
"ZAP70", "SMPD2", "HIST3H2BB", "MAPK6", "RGS3", "TRPC2", "ZADH2", "SHMT2", "HIST1H2AG",
"PTPRC", "PIK3CG", "FNTB", "CCR8", "PRPF40A", "CCNG2", "LSM3", "SERPINB7", "WDR31", "GGPS1",
"ARSB", "CSRNP1", "ABHD1", "CAP1", "PTGIR", "HIST1H3C", "IL9R", "S100A6", "XCL1", "ELOVL5",
"MPP2", "TNFRSF18", "FOSL2", "USP21", "PCBP1", "WIBG", "HIST2H2BB", "LRRC27", "RABAC1",
"KPNA3", "AOX1", "HIST1H2BL", "PRRG4", "SLC23A3", "NUDCD2", "MEIG1", "TEX19", "FCGR3A",
"POU3F3", "MYO1E", "POLN", "TMC8", "FGL2", "EXTL2", "DBR1", "ACSL4", "HNRPDL", "PFKM",
"PRUNE", "LNPEP", "EIF3H", "ATXN1", "TGOLN2", "EXOSC4", "PTPN22", "SYTL1", "EEF2", "E2F2",
"PYGL", "FBXL3", "SHC1", "SYNJ2", "NFATC2", "MADD", "CPNE7", "TBL1XR1", "LST1", "RCHY1",
"METTL5", "GLIPR1", "CRYAB", "HMG20A", "CAMK2D", "RGS2", "PKM2", "CMTM6", "FRG1", "SUPT7L",
"POLR3C", "HIST1H2AC", "CCR4", "NARG1", "CTDSP1", "LRRC10", "NBR1", "TOR1AIP1", "CDKN2D",
"CENPC1", "ITGA9", "CLEC12A", "XRCC4", "SEPHS1", "CD226", "TTK", "CX3CR1", "NCF1", "ELL3",
"CCND3", "MBP", "TRAPPC2", "BZW2", "ASF1A", "ARL6IP5", "IFIT2", "APH1A", "ADAM10", "NCKAP1",
"CDK9", "TAT", "GTF2B", "IFT122", "MYL4", "SLC30A7", "PDE7B", "ZMPSTE24", "SSNA1", "CPD",
"H2AFZ", "MINA", "SRPK2", "CASC5", "TEX261", "ZRANB3", "CPSF2", "NDUFS4", "SYNRG", "MSH5",
"THUMPD3", "LBR", "DPYSL2", "NEK7", "POLDIP2", "TPST2", "NUMA1", "KIFC1", "TMOD3", "DAPK3",
"HIST3H2A", "DNAJC2", "POU2F3", "ARHGEF6", "CHMP4B", "CD72", "COBLL1", "TUBA8", "EMR4P",
"RNF11", "PSEN1", "SERTAD1", "MR1", "SFRS3", "YLPM1", "CDYL2", "CHEK1", "PPP3CA", "ELP3",
"RAB2A", "SSBP4", "PKN2", "MAP3K7IP2", "GATA3", "GNGT2", "CD3D", "MAP3K11", "PRMT5",
"COX11", "HIST1H4H", "FOLR4", "LCTL", "XPA", "IMP3", "FBRS", "MRPL48", "DHX33", "CREB1",
"CREB3L4", "MRPL34", "TNPO1", "AMPH", "MAD2L1BP", "HP1BP3", "ANXA7", "ZBTB5", "SLC25A37",
"TUBG1", "HIST2H2AC", "KBTBD3", "MTRF1L", "HNRNPL", "GMDS", "ARL5B", "RAD52", "OCIAD2",
"MYST4", "FOSB", "UBE2G2", "RAMP1", "CNOT2", "SLC2A8", "BAT2", "RCC2", "MCM7", "GABARAP",
"POLE4", "YES1", "MBNL1", "CNTF", "HIST1H2BH", "ATP1A2", "NQO2", "TMEM30A", "KPNB1", "BLM",
"MLLT3", "OGT", "GYPC", "C1GALT1", "ST3GAL4", "GIMAP6", "KCNJ2", "MCM3", "HIST1H4A",
"HIST4H4", "IL2RA", "HNRNPUL1", "SLC26A8", "C3", "WDR59", "TRADD", "PXMP4", "DAP", "DUSP6",
"KDM5A", "FLOT1", "THOC4", "PSMD8", "WFS1", "EIF2S1", "ZNF280D", "ZNF205", "CABC1", "ACTG1",
"PPP4C", "WBP1", "WSB2", "SLC6A4", "KAT2B", "SLC36A1", "RANBP10", "PTPRJ", "RHOB",
"PPP2R5A", "KCTD10", "DEGS2", "CMPK1", "MOBKL1B", "ARL4A", "APBA2", "NIF3L1", "MTMR1",
"WNT2B", "MCL1", "SYPL1", "ELAVL1", "LYSMD1", "ELL", "C2orf65", "DCLRE1C", "SENP1",
"TRIM33", "XBP1", "DNAJB14", "DDX39", "NDUFV2", "RPS3A", "ABHD2", "CCRN4L", "HIST1H1E",
"HIST1H2AI", "TES", "SLC25A24", "ABCB6", "HIST1H3B", "ARG2", "SPATA5L1", "NRP1", "CCDC18",
"UVRAG", "CGRRF1", "PSMB3", "LETMD1", "NASP", "PPP5C", "COG3", "PTK2", "PIKFYVE", "CXCL10",
"TRAF3IP3", "HIST1H3F", "STK10", "FCRLA", "SMAP2", "FBXW10", "TBC1D17", "PLG", "LAPTM5",
"LGALS8", "PITPNB", "DMPK", "ZNF35", "CLEC2D", "WBP5", "HCLS1", "IER3", "MYC", "SLC22A3",
"HERC1", "ARHGEF12", "OSTF1", "FYN", "MAP3K5", "RNMT", "TNFSF4", "S100A5", "CYTIP", "GAS5",
"DMWD", "SMARCC1", "EMP1", "RAGE", "KRR1", "TSC22D3", "ELF1", "PAIP2", "ANAPC5", "GGTA1",
"ITGAL", "UBE2V1", "PNRC2", "PSMD4", "AASDHPPT", "ACTR2", "WDR26", "SEC14L1", "NEDD9",
"SLC4A1AP", "P4HA3", "CUL3", "ERN1", "CD48", "MPG", "CTGF", "CDK5RAP3", "CCPG1", "SGPP1",
"ARIH1", "PPP2R2A", "EYA2", "PRAF2", "FBL", "ROD1", "ARHGAP10", "USP3", "TRAPPC5", "BIN3",
"FYTTD1", "HERC4", "NGLY1", "ASB3", "NPC1", "ECH1", "TPP2", "GOT2", "THY1", "ETF1", "KDM2B",
"AURKB", "RAP1A", "CD47", "GADD45B", "KIF2C", "TNFSF14", "JUB", "CTSE", "CDC2L1", "AK2",
"POLD3", "ZPBP", "F2RL2", "PLCD1", "CGA", "SYTL2", "SLC2A1", "FLI1", "TRAT1", "MAP2K6",
"AVPI1", "ARID5A", "NF2", "RHOA", "FARS2", "EDARADD", "WDR45", "HCST", "NFE2L2", "SLC39A3",
"UBL3", "DNASE1L1", "SURF4", "ENTPD5", "YWHAZ", "LMAN2", "TRIM44", "HIST1H2BK", "SIAE",
"LTB", "PER1", "ERCC3", "MIB1", "NHLRC2", "FUBP1", "CDKL3", "TRIM17", "TBC1D10B", "PSMC1",
"MTRF1", "C16orf70", "AMICA1", "BRCA1", "CHIC2", "SEPHS2", "NRGN", "SPACA4", "STK4", "HHAT",
"EID1", "CTPS", "ARF2", "SGK1", "NANP", "ACAT1", "SDCCAG1", "ZWINT", "EIF5", "PRPSAP1",
"HADHA", "SRPK1", "LRRC48", "GARS", "CCR1", "CRYGS", "HSPA4L", "TOR1AIP2", "GPAA1", "MYNN",
"TXNL4B", "GRAP", "UFC1", "PARK7", "RBL2", "FHL2", "MAP3K14", "ZC3H12D", "TRAPPC1", "DLX1",
"SLC39A10", "RGS14", "H3F3A", "DNAJC1", "RPS6KA5", "GTPBP2", "ICK", "CENPA", "MTO1",
"EWSR1", "CSTB", "GJA1", "CAGE1", "SH2D3C", "FSCN2", "PICALM", "NUF2", "EFCAB2", "MRPL33",
"CD276", "UBE2D1", "OPLAH", "TRIM8", "PLIN2", "DOK2", "MANBA", "NUP35", "SERPINA11", "MSH6",
"LRMP", "NUDT5", "SSBP3", "OAZ1", "HIST1H4I", "PLEKHF1", "RHBDF1", "ST6GALNAC1", "MOV10",
"METRNL", "ARHGAP15", "CELA1", "RPS6KA3", "GDI2", "KCNN4"};
}