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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.