Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

Mason, Mary E; Koch, Jennifer L; Krasowski, Marek; Loo, Judy

doi:10.1186/1477-5956-11-2

Proteome Science

Table 3 Significant effects, means, and expression ratio for protein spots with significant beech bark disease (BBD) effect

From: Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

Spot		BBD q-value ^a	STAND ^b	INT ^c	mean_H ^d	sd_H ^d	mean_D ^d	sd_D ^d	Ratio of means ^e	Direction in healthy
11		0.0470	NS	SIG	26,174	65,030	72,775	87,910	2.7804	down
13		0.0328	SIG	SIG	94,894	219,401	59,736	143,489	1.5886	up
19		0.0000^f	SIG	SIG	8,004	5,915	62,232	97,523	7.7749	down
103	*	0.0199	NS	NS	55,653	177,669	296,935	581,023	5.3354	down
108		0.0004	SIG	SIG	258,261	376,114	111,723	168,407	2.3116	up
109	*	0.0023	NS	NS	617,595	986,852	153,958	248,739	4.0114	up
110		0.0001	SIG	SIG	39,356	97,166	220,462	387,308	5.6017	down
210		0.0004	NS	SIG	757,282	605,616	285,096	446,196	2.6562	up
303		0.0002	SIG	SIG	173,237	616,608	633,878	976,099	3.6590	down
306		0.0022	NS	SIG	8,004	5,915	149,834	274,377	18.7195	down
307		0.0275	SIG	NS	759,264	688,274	302,438	516,028	2.5105	up
408		0.0000^f	SIG	SIG	258,525	539,218	856,239	1,833,144	3.3120	down
410		0.0041	SIG	NS	26,580	63,389	118,326	141,769	4.4517	down
411		0.0295	SIG	NS	165,226	431,575	708,030	1,274,849	4.2852	down
412		0.0054	SIG	SIG	447,495	1,004,238	310,856	722,114	1.4396	up
505	*	0.0470	NS	NS	925,741	886,816	477,691	544,289	1.9379	up
601	*	0.0318	NS	NS	333,862	424,610	725,308	843,336	2.1725	down
602		0.0000^f	SIG	SIG	365,242	873,890	1,394,639	1,721,661	3.8184	down
603		0.0076	SIG	NS	1,533,077	1,657,207	1,053,773	1,360,574	1.4548	up
606		0.0216	SIG	SIG	43,523	126,690	8,417	8,283	5.1708	up
610		0.0001	SIG	SIG	146,957	447,440	8,417	8,283	17.4593	up
704		0.0000^f	SIG	SIG	68,064	212,603	899,841	2,069,461	13.2205	down
804	*	0.0013	NS	NS	8,004	5,915	148,985	250,618	18.6134	down
1004	*	0.0023	NS	NS	8,004	5,915	175,554	294,631	21.9328	down
1005		0.0012	SIG	SIG	83,946	197,401	354,800	440,759	4.2265	down
1109		0.0000^f	SIG	SIG	83,319	265,430	503,759	1,143,792	6.0462	up
1303		0.0012	SIG	SIG	364,487	1,135,686	155,251	282,766	2.3477	up
1309	*	0.0043	NS	NS	297,936	428,232	70,605	95,878	4.2197	up
1401	*	0.0075	NS	NS	1,381,518	1,428,751	573,957	882,187	2.4070	up
1402	*	0.0168	NS	NS	1,221,781	1,194,937	2,454,219	2,386,797	2.0087	down
1405		0.0219	SIG	NS	536,821	589,544	164,445	364,867	3.2644	up
1704		0.0076	NS	SIG	107,476	344,505	651,980	1,109,723	6.0663	down
2101	*	0.0238	NS	NS	1,068,400	1,220,098	824,152	883,156	1.2964	up
2107		0.0158	SIG	SIG	65,274	230,953	293,355	519,761	4.4942	down
2312	*	0.0284	NS	NS	350,710	704,649	8,417	8,283	41.6664	up
2506	*	0.0469	NS	NS	1,897,806	1,096,881	2,497,681	1,221,943	1.3161	down
2507	*	0.0012	NS	NS	417,660	599,615	1,048,242	1,050,906	2.5098	down
2611		0.0498	SIG	SIG	1,535,001	1,783,491	2,205,570	2,796,718	1.4369	down
2614		0.0000^f	SIG	SIG	8,004	5,915	285,838	432,421	35.7112	down
2615		0.0008	SIG	SIG	62,288	208,601	431,929	1,018,078	6.9344	down
2801		0.0000^f	SIG	SIG	8,004	5,915	869,550	1,285,546	108.6371	down
2803		0.0010	SIG	SIG	712,668	1,115,376	580,029	825,345	1.2287	up
2806		0.0001	SIG	SIG	443,822	1,084,784	129,571	442,770	3.4253	up
3201	*	0.0016	NS	NS	1,336,983	1,205,431	794,583	908,778	1.6826	up
3305		0.0000^f	SIG	SIG	89,683	248,936	303,148	448,565	3.3802	down
3306		0.0078	SIG	SIG	116,998	272,340	59,537	124,166	1.9651	up
3404		0.0082	SIG	NS	4,068,995	2,823,334	3,452,364	2,764,490	1.1786	up
3406		0.0000^f	SIG	SIG	44,870	125,570	462,745	547,706	10.3130	down
3412		0.0177	NS	SIG	322,035	683,636	130,942	334,190	2.4594	up
3502		0.0188	SIG	NS	442,850	650,679	786,812	1,011,948	1.7767	down
3607	*	0.0105	NS	NS	2,247,225	2,722,559	1,430,733	2,093,163	1.5707	up
3702	*	0.0001	NS	NS	633,076	1,243,273	3,792,473	3,730,678	5.9905	down
3708	*	0.0096	NS	NS	633,632	796,621	407,271	620,398	1.5558	up
3802		0.0015	SIG	SIG	8,004	5,915	111,820	262,030	13.9703	down
3905	*	0.0039	NS	NS	8,004	5,915	137,656	242,371	17.1980	down
4106		0.0066	SIG	SIG	105,844	212,452	397,149	845,289	3.7522	down
4201		0.0010	NS	SIG	8,004	5,915	254,207	454,577	31.7593	down
4305		0.0000^f	SIG	SIG	46,506	128,075	470,932	768,247	10.1263	down
4706	*	0.0481	NS	NS	2,739,148	3,047,552	917,692	1,062,566	2.9848	up
4802		0.0000^f	SIG	SIG	48,748	143,131	408,963	769,834	8.3894	down
4906	*	0.0302	NS	NS	873,770	1,402,616	628,704	1,038,074	1.3898	up
5301		0.0202	SIG	SIG	450,470	363,776	399,574	418,863	1.1274	up
5303	*	0.0062	NS	NS	3,456,984	1,373,851	5,360,468	2,202,726	1.5506	down
5505	*	0.0009	NS	NS	604,226	742,627	2,522,891	2,358,561	4.1754	down
5601	*	0.0063	NS	NS	456,028	681,368	1,497,166	1,370,793	3.2831	down
5605		0.0000^f	SIG	SIG	124,350	177,741	8,004	5,915	15.5356	up
5606		0.0000^f	SIG	SIG	110,019	153,695	8,004	5,915	13.7452	up
5703	*	0.0297	NS	NS	3,051,574	5,434,263	478,287	1,621,642	6.3802	up
5802	*	0.0011	NS	NS	1,190,828	915,352	508,682	528,700	2.3410	up
5908		0.0010	SIG	SIG	161,910	387,868	8,004	5,915	20.2282	up
5909		0.0012	SIG	SIG	8,417	8,283	143,259	352,729	17.0200	down
6208		0.0297	SIG	SIG	186,317	276,277	80,227	222,514	2.3224	up
6303		0.0328	NS	SIG	253,951	331,973	397,930	349,663	1.5670	down
6304		0.0018	NS	SIG	2,888,828	3,401,904	820,317	1,445,597	3.5216	up
6306	*	0.0099	NS	NS	1,800,296	1,365,419	2,730,178	2,859,788	1.5165	down
6501	*	0.0318	NS	NS	1,468,936	1,183,570	604,825	1,255,327	2.4287	up
6707	*	0.0193	NS	NS	11,970,218	12,515,695	6,247,307	6,508,633	1.9161	up
6709	*	0.0238	NS	NS	8,974,280	5,564,143	5,289,975	6,857,853	1.6965	up
6710	*	0.0238	NS	NS	1,400,824	2,287,877	404,306	569,323	3.4648	up
6807		0.0070	SIG	SIG	118,758	291,241	8,004	5,915	14.8370	up
6808		0.0009	SIG	SIG	1,174,714	1,224,320	239,503	580,829	4.9048	up
6809		0.0002	SIG	SIG	376,863	587,605	95,365	213,349	3.9518	up
7009		0.0004	SIG	SIG	175,933	391,166	265,335	410,728	1.5082	down
7106		0.0000^f	SIG	SIG	962,980	1,282,010	39,820	101,833	24.1835	up
7107	*	0.0009	NS	NS	387,387	501,608	50,505	130,300	7.6703	up
7110	*	0.0245	NS	NS	84,648	139,984	256,705	307,196	3.0326	down
7111		0.0000^f	SIG	SIG	658,929	1,249,222	148,370	341,871	4.4411	up
7112		0.0022	NS	SIG	73,598	133,128	8,004	5,915	9.1949	up
7203		0.0261	SIG	NS	1,311,783	732,419	927,380	799,253	1.4145	up
7207		0.0186	SIG	NS	60,957	126,879	21,092	40,907	2.8901	up
7303		0.0052	SIG	SIG	246,921	602,207	615,797	1,105,070	2.4939	down
7408	*	0.0126	NS	NS	3,049,802	2,337,843	1,336,825	1,182,165	2.2814	up
7510		0.0098	SIG	SIG	305,493	558,423	397,578	1,073,627	1.3014	down
7602	*	0.0412	NS	NS	7,296,723	7,488,294	3,609,984	5,505,222	2.0213	up
7609		0.0016	SIG	SIG	381,570	946,188	8,004	5,915	47.6713	up
7803	*	0.0238	NS	NS	716,697	474,399	341,082	391,607	2.1012	up
7808	*	0.0075	NS	NS	704,023	626,350	305,591	487,526	2.3038	up
7809	*	0.0267	NS	NS	582,174	1,475,329	8,004	5,915	72.7338	up
7810	*	0.0297	NS	NS	442,246	1,119,936	8,004	5,915	55.2519	up
8002	*	0.0082	NS	NS	175,231	300,741	22,986	74,010	7.6235	up
8104	*	0.0188	NS	NS	1,096,503	874,012	394,837	541,448	2.7771	up
8202		0.0230	SIG	NS	29,407	58,674	56,069	97,123	1.9066	down
8303	*	0.0311	NS	NS	1,850,424	1,058,481	1,293,017	1,164,851	1.4311	up
8309	*	0.0008	NS	NS	340,383	449,968	902,563	716,532	2.6516	down
8311		0.0318	SIG	NS	85,387	133,171	26,149	58,170	3.2654	up
8312	*	0.0498	NS	NS	306,017	504,921	549,086	736,070	1.7943	down
8503	*	0.0193	NS	NS	587,330	907,526	123,323	558,974	4.7626	up
8506	*	0.0010	NS	NS	1,709,206	2,026,022	334,292	701,018	5.1129	up
8508	*	0.0158	NS	NS	1,395,005	1,198,636	633,833	820,628	2.2009	up
8512	*	0.0012	SIG	NS	8,417	8,283	1,173,776	1,657,190	139.4515	down
8604		0.0267	SIG	SIG	2,262,933	3,169,913	1,147,023	2,200,353	1.9729	up
8607		0.0020	SIG	NS	1,865,790	3,095,124	369,996	861,448	5.0427	up
8708	*	0.0076	NS	NS	177,743	461,377	632,706	1,403,084	3.5597	down
8801	*	0.0316	NS	NS	751,522	573,471	517,615	499,829	1.4519	up
8802	*	0.0034	NS	NS	511,552	398,150	269,962	349,834	1.8949	up
9302	*	0.0238	NS	NS	710,525	848,447	1,268,492	1,442,080	1.7853	down
9305		0.0085	SIG	SIG	301,789	462,883	368,200	614,918	1.2201	down
9401		0.0192	SIG	NS	717,956	641,915	419,853	410,107	1.7100	up
9402		0.0096	SIG	SIG	63,499	152,855	120,990	362,645	1.9054	down
9802		0.0021	SIG	SIG	112,023	263,531	8,004	5,915	13.9956	up

An asterisk to the right of the spot number indicates a spot with significant BBD effect and non-significant STAND and STANDxBBD interaction effect, and are the primary targets for biomarker development.
^aBBD effect with q-value <0.05. q-value controls the False Discovery rate, and q<0.05 allows for no more than 26 false positives in the 425 spots tested.
^bSTAND effect with p<0.0001 (Bonferroni adjusted critical value).
^cSTANDxBBD interaction effect with p<0.0001 (Bonferroni adjusted critical value).
^dGaussian image spot intensity after normalization expressed in counts. Mean is the mean over the three technical replicates per tree for all trees in that disease condition. SD is standard deviation.
^eRatio is ratio of larger mean over smaller mean.
Mean = Gaussian image spot intensity after normalization expressed in counts. Mean is the mean over the three technical replicates for all trees in that disease condition.
SD = standard deviation.
^fQ-values displayed as 0.0000 are positive values <0.0001. See additional table 1 for actual q-values.

Back to article page

ISSN: 1477-5956

Contact us

General enquiries: journalsubmissions@springernature.com