Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.19.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22622	0.443
27DAP/17DAP	0.78137	0.332
39DAP/27DAP	1.30268	0.548
41DAP/39DAP	1.18245	0.416
42DAP/41DAP	1.64551	0.29
43DAP/42DAP	1.4278	0.546
47DAP/43DAP	1.61594	0.253
52DAP/47DAP	1.2581	0.451
57DAP/52DAP	0.96103	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.85937	0.008
17DAP/reference	1.47641	0.011
27DAP/reference	1.82268	0.007
39DAP/reference	1.08666	0.581
41DAP/reference	1.03008	0.963
42DAP/reference	1.05201	0.264
43DAP/reference	0.85521	0.024
47DAP/reference	0.85462	0.012
52DAP/reference	0.82201	0.044
57DAP/reference	0.96977	0.503

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00073	1
27DAP/17DAP	1.01932	0.957
39DAP/27DAP	1.66236	0.066
41DAP/39DAP	0.56101	0.013
42DAP/41DAP	2.81381	0.002
43DAP/42DAP	3.09829	0.014
47DAP/43DAP	0.99489	0.971
52DAP/47DAP	1.41897	0.315
57DAP/52DAP	1.21696	0.596
57DAP/7DAP	1.86718	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93602	0.361
17DAP/reference	0.92467	0.192
27DAP/reference	0.99443	0.656
39DAP/reference	0.98537	0.552
41DAP/reference	1.00745	0.741
42DAP/reference	1.034	0.889
43DAP/reference	0.9017	0.091
47DAP/reference	0.73705	0.04
52DAP/reference	0.81559	0.046
57DAP/reference	0.97211	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4044	0.238
17DAP/reference	1.85967	0.011
27DAP/reference	1.29809	0.126
39DAP/reference	0.79783	0.113
41DAP/reference	0.83779	0.01
42DAP/reference	1.05555	0.899
43DAP/reference	1.04944	1
47DAP/reference	0.8227	0.015
52DAP/reference	0.70052	0.004
57DAP/reference	0.77059	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93912	0.362
17DAP/reference	1.12549	0.538
27DAP/reference	0.89114	0.097
39DAP/reference	1.87903	0.342
41DAP/reference	1.00527	1
42DAP/reference	0.94696	0.287
43DAP/reference	0.8672	0.071
47DAP/reference	0.6288	0.004
52DAP/reference	0.84647	0.262
57DAP/reference	0.81006	0.036

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22488	0.966
26DAP/20DAP	0.95044	1
34DAP/26DAP	1.21313	0.819
51DAP/34DAP	1.67849	0.159
52DAP/51DAP	0.76422	1
53DAP/52DAP	3.99798	0.02
55DAP/53DAP	1.01789	1
57DAP/55DAP	0.60414	0.03
62DAP/57DAP	0.97925	1
68DAP/62DAP	1.38757	0.759
68DAP/14DAP	0.57297	0.375

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.06246	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.13115	0.058
Mature Green Tomato/Ripe Tomato	0.19227	0.016
Immature Eggplant/Mature Eggplant	0.35579	0.057
Ripe Pepper/Ripe Tomato	4.12387	1
Mature Eggplant/Ripe Tomato	4.3824	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8834	0.883
1-1-2/M82	1.41597	1
12-2/M82	1.18316
12-4/M82	0.60174	0.619
1-3/M82	1.06493	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.99016	1
3-2/M82	N/A	N/A
4-1-1/M82	1.68497	0.977
4-1/M82	1.44079	1
4-3-2/M82	1.09791
4-3/M82	1.72457	0.268
5-3/M82	0.88532	0.49
6-2/M82	N/A	N/A
6-3/M82	1.19341	1
7-1/M82	0.92025	1
7-2/M82	1.34309	0.324
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75136	0.243
IL2-6/WTpooled	1.12877
IL7-5/WTpooled	0.86929	1
IL7-3/WTpooled	1.31935
IL12-4/WTpooled	1.30863
IL1-4/WTpooled	0.78315	0.422
WT/WTpooled	1.02401

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.93252	0.75

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9586	0.734
DC3000/delta hrp 6h	1.16675	0.672
DC3000/delta hrp 12h	0.97722	1
DC3000/delta hrp 24h	0.86771	0.105

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.81001	0.059
DC3000 delta B/DC3000 delta AB	1.00724	0.738

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05402	1
Exp 36h	0.73893	0.456
Exp 60h	0.68324	0.251

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.00652	1
Var 0h	0.45055	1
Var 12h I row2-row1	0.92117	0.565
Var 12h NI row2-row1	1.23015	0.649
Var 36h I row2-row1	1.06865	0.908
Var 36h NI row2-row1	1.37016	0.253
Var 60h I row2-row1	0.88772	0.285
Var 60h NI row2-row1	1.30276	0.904
Time course 0hI-0hNI	1.00768	1
Time course 12hI-12hNI	0.92745	0.264
Time course 36hI-36hNI	0.84489	0.112
Time course 60hI-60hNI	0.27288	0.005

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.76751	0.309
transgenic ySAMdc/azygous control (breaker)	1.31682	1
transgenic ySAMdc/azygous control (red)	0.96686	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.68882	0.172

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.22705	0.237

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.40733	0.088
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.12416	1