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Table 3 Performance for MEME searching for short linear motifs in a realistic motif discovery scenario

From: Profile-based short linear protein motif discovery

HPRDID Hubgene symbol Number of proteins (with motif) Complex name Motif name (from ELM) Regular expression from ELM database SLiMFinder with evolutionary weighting and RLC Masking Meme default MEME with evolutionary weighting RLC masking
150 GRB2 164 (146) Grb2 LIG_SH3 P.P - - -
   164 (103)   LIG_SH2_GRB2 Y.N Y.N[LMV] (3) NK[NEK]KNRY[KV][DN]I (2) KNRY[KPV][ND]ILP (1)
215 YWHAH 47 (13) 14-3-3 Eta LIG_14-3-3_1 R[SFYW].S.p [KR]S.S.P (1) - PKIHRSASEP (17)
350 CLTC 35 (15) Clathrin, heavy polypeptide LIG_Clathr_Clatbox_1 L[ILM].[ILMF][DE] LLDL (4) - LLDL[EDM][DS][FA]QP (18)
453 CCNA2 25 (23) Cyclin, A2 LIG_CYCLIN_1 [RK].L.{0,1}[FYLIVMP] - A[CK]R[RN]LFG (7) SA[CK]R[NR]LFG (8)
607 FNTA 10 (2) Farnessyltransferas e alpha subunit MOD_ASX_betaOH_EGF C[^DENQ][LIVM].$ - C[DT]IS (30) C[DT]IS (17)
627 IGTAS 15 (7) Intergin alpha 5 LIG_RGD RGD - KGDRGDA (25) RG[DQ] (34)
1456 PCNA 65 (13) Proliferating cell nuclear antigen LIG_PCNA Q.[ILM].[FHM][FHM] Q.[IL].FF (1) TL[YES]SFF (3) TL[YES]SFF (2)
1574 RB1 110 (28) Retinoblastoma 1 LIG_RB [LI].C.[DE] - - -
3288 PPARG 22 (15) Peroxisome proliferator AR LIG_NRBOX L.LL L.RLL (1) HKILHRLLQ (4) [LT][VS]HKLVQ[AL][IL] (1)
3334 DYNLL1 52 (5) Dynien light chain 1 LIG_Dynien_DLC8_1 [KR].TQT - [MV]S[CY][DS]K[ES]TQTP (95) KSTQT (10)
3786 NEDD4 28 (17) NEDD4 LIG_WW_1 PP.Y PP.Y (7) PPAY (83) PPPYSSI (2)
3833 TRAF6 22 (19) TRAF6 LIG_TRAF6 .P.E.[FYWHDE]. - - -
4015 CTBP1 26 (14) C-terminal binding protien LIG_CtBP P.[DEN]LVAST] D.P[IL]D (6) - P[LI]DLS (1)
4946 CCNA1 20 (20) Cyclin A1 LIG_CYCLIN_1 [RK].L.{0,1}[FYLIVMP] - A[CK]R[RN]LFG (3) A[CK]R[RN]LFG (1)
5462 GIPC1 26 (7) GIPC1 LIG_PDZ_1 .[ST].[VIL]$ S.V$ (1) - -
5639 YWHAG 206 (28) 14-3-3 gamma LIG_14-3-3_1 R[SFYW].S.P R.RS.S.S (1) SRSRSRS[KR]SR (51) [SK]SRSRS[RK]SR (30)
8968 EPS15 24 (10) Eps15 LIG_EH NPF TNPF (1) TNPF[LS](3) TNPF (1)
9045 UBE2I 87 (78) Ubiquitin conjugating enzyme E1 MOD_SUMO [VILAFP]K.[EDNGP] VK.E (2) M[KM]VKDEY (18) VEIVYE (7)
9347 GGA2 19 (2) GGA2 LIG_AP_GAE_1 [DE][DES].F.[DE] [LVIMFD] DDF.F.A (1) D[DL]FG[GDE]F (6) D[DL]FG[GDE]F (7)
9424 YAP1 15 (8) YES associated protein LIG_WW_1 PP.Y - [PL][PD]PPY (50) H[CT][TY][LP]PPPY (6)
  1. The HPRD dataset used, its name and the number of proteins in that dataset along with the ELM known to mediate some interactions with the protein hub are shown. The regular expression returned highest that matches the annotated ELM and its rank (in brackets) for SLiMFinder and MEME with and without RLC masking and evolutionary weighting are shown. No result is indicated with a dash. Niall Haslam 24 October 2012 09:19.