Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82201	0.522
27DAP/17DAP	1.10737	0.868
39DAP/27DAP	0.94548	0.67
41DAP/39DAP	0.78953	0.325
42DAP/41DAP	0.88228	1
43DAP/42DAP	0.92242	0.822
47DAP/43DAP	0.93666	0.663
52DAP/47DAP	1.86754	0.384
57DAP/52DAP	1.16803	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88661	0.188
17DAP/reference	0.91128	0.129
27DAP/reference	0.91931	0.257
39DAP/reference	0.973	0.638
41DAP/reference	0.92255	0.201
42DAP/reference	0.90302	0.012
43DAP/reference	0.97836	0.653
47DAP/reference	0.95161	0.224
52DAP/reference	1.08603	0.524
57DAP/reference	1.08726	0.037

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27762	0.414
27DAP/17DAP	0.9902	0.943
39DAP/27DAP	0.87405	0.311
41DAP/39DAP	1.1773	0.439
42DAP/41DAP	0.85401	0.088
43DAP/42DAP	0.99192	0.991
47DAP/43DAP	1.15848	0.359
52DAP/47DAP	1.03915	0.851
57DAP/52DAP	1.30404	0.155
57DAP/7DAP	1.12656	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80976	0.067
17DAP/reference	1.01192	0.693
27DAP/reference	1.1296	0.301
39DAP/reference	0.99463	0.64
41DAP/reference	1.12584	0.045
42DAP/reference	0.88045	0.077
43DAP/reference	0.99553	0.665
47DAP/reference	0.93873	0.504
52DAP/reference	0.99651	0.621
57DAP/reference	1.05302	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82582	0.062
17DAP/reference	0.85094	0.035
27DAP/reference	0.98744	0.598
39DAP/reference	1.035	1
41DAP/reference	1.098	0.427
42DAP/reference	1.00302	1
43DAP/reference	1.20244	0.343
47DAP/reference	1.12333	0.301
52DAP/reference	1.00619	1
57DAP/reference	1.06062	0.654

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9644	0.526
17DAP/reference	1.10493	0.45
27DAP/reference	1.35609	0.029
39DAP/reference	1.13522	0.189
41DAP/reference	1.22608	0.174
42DAP/reference	1.41305	0.014
43DAP/reference	1.11391	0.375
47DAP/reference	0.94059	0.259
52DAP/reference	1.01774	0.979
57DAP/reference	1.2136	0.094

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22215	0.966
26DAP/20DAP	0.96212	1
34DAP/26DAP	1.02036	1
51DAP/34DAP	0.90098	0.563
52DAP/51DAP	1.02671	1
53DAP/52DAP	0.96933	0.844
55DAP/53DAP	1.03387	1
57DAP/55DAP	1.11634	0.986
62DAP/57DAP	1.07574	1
68DAP/62DAP	1.09263	0.944
68DAP/14DAP	1.20331	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05561	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.20138	0.076
Mature Green Tomato/Ripe Tomato	0.56106	0.107
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	5.69312	1
Mature Eggplant/Ripe Tomato	0.72541

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.55448
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93871	0.243
IL2-6/WTpooled	0.91352	0.358
IL7-5/WTpooled	1.43834	0.792
IL7-3/WTpooled	1.0778	1
IL12-4/WTpooled	1.03935	1
IL1-4/WTpooled	1.07143	1
WT/WTpooled	0.97959	1

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	0.97368	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96581	1
DC3000/delta hrp 6h	0.89511	0.95
DC3000/delta hrp 12h	0.97202	1
DC3000/delta hrp 24h	1.03941	0.988

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56364	0.025
DC3000 delta B/DC3000 delta AB	0.56449	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.27313	1
Exp 36h	1.80248	0.409
Exp 60h	2.07385	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99552	1
Var 0h	2.46113	0.98
Var 12h I row2-row1	0.80306	0.363
Var 12h NI row2-row1	1.02368	1
Var 36h I row2-row1	0.97163	1
Var 36h NI row2-row1	0.95259	0.791
Var 60h I row2-row1	0.76905	0.306
Var 60h NI row2-row1	0.99455	1
Time course 0hI-0hNI	1.06696	0.833
Time course 12hI-12hNI	0.99562	1
Time course 36hI-36hNI	1.04111	0.513
Time course 60hI-60hNI	0.64047	0.008

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)	0.99089	0.862
transgenic ySAMdc/azygous control (breaker)	1.27785	0.248
transgenic ySAMdc/azygous control (red)	0.80478	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98952	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40824	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.39464	0.14
Manapal/WT (break)	1.14995	0.381
Manapal/WT (red)	1.12751	1