Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.13.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8116	0.29
27DAP/17DAP	0.78759	0.478
39DAP/27DAP	0.93885	0.641
41DAP/39DAP	1.19572	0.494
42DAP/41DAP	0.97989	1
43DAP/42DAP	0.92691	0.776
47DAP/43DAP	0.97992	0.864
52DAP/47DAP	1.31993	0.52
57DAP/52DAP	0.99651	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88646	0.025
17DAP/reference	0.97171	0.393
27DAP/reference	0.99509	0.797
39DAP/reference	0.94808	0.228
41DAP/reference	0.97601	0.667
42DAP/reference	0.91842	0.023
43DAP/reference	1.00899	0.899
47DAP/reference	0.90618	0.005
52DAP/reference	0.9194	0.135
57DAP/reference	0.95765	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8901	0.099
27DAP/17DAP	1.01182	0.976
39DAP/27DAP	1.03834	0.659
41DAP/39DAP	1.01116	1
42DAP/41DAP	1.00002	0.887
43DAP/42DAP	1.01646	0.83
47DAP/43DAP	1.07679	0.837
52DAP/47DAP	1.02316	0.933
57DAP/52DAP	1.11158	0.539
57DAP/7DAP	1.17264	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98943	0.55
17DAP/reference	0.91896	0.056
27DAP/reference	0.94028	0.025
39DAP/reference	0.89984	0.013
41DAP/reference	0.91898	0.019
42DAP/reference	0.8766	0.01
43DAP/reference	0.9359	0.252
47DAP/reference	0.96181	0.079
52DAP/reference	0.90822	0.066
57DAP/reference	0.89009	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02922	0.642
17DAP/reference	1.01663	0.904
27DAP/reference	0.94847	0.257
39DAP/reference	0.93866	0.129
41DAP/reference	1.08115	0.814
42DAP/reference	0.9637	0.355
43DAP/reference	1.06737	0.356
47DAP/reference	0.98947	0.543
52DAP/reference	0.94924	0.101
57DAP/reference	0.987	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96492	0.214
17DAP/reference	0.98337	0.696
27DAP/reference	0.90907	0.05
39DAP/reference	0.918	0.083
41DAP/reference	0.93062	0.264
42DAP/reference	0.91508	0.134
43DAP/reference	0.90858	0.071
47DAP/reference	0.98674	0.558
52DAP/reference	0.86933	0.167
57DAP/reference	0.93756	0.171

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98419	1
26DAP/20DAP	0.90151	1
34DAP/26DAP	0.95177	0.874
51DAP/34DAP	0.92137	0.579
52DAP/51DAP	1.03532	0.77
53DAP/52DAP	0.96624	0.817
55DAP/53DAP	1.05336	1
57DAP/55DAP	1.05669	0.915
62DAP/57DAP	1.45445	0.158
68DAP/62DAP	1.01524	0.984
68DAP/14DAP	0.82192	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93441	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94382	0.673
Mature Green Tomato/Ripe Tomato	0.65651	0.119
Immature Eggplant/Mature Eggplant	2.97897	0.05
Ripe Pepper/Ripe Tomato	0.52096	0.224
Mature Eggplant/Ripe Tomato	0.71536	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93196	0.944
1-1-2/M82	0.91618	1
12-2/M82	1.13111	0.61
12-4/M82	0.8822	1
1-3/M82	0.93688	1
2-1-1/M82	0.94081
2-1/M82	N/A	N/A
2-6/M82	0.9588	1
3-2/M82	N/A	N/A
4-1-1/M82	0.93766	1
4-1/M82	1.2593
4-3-2/M82	0.89576	1
4-3/M82	N/A	N/A
5-3/M82	0.91637	1
6-2/M82	1.02314
6-3/M82	0.90577	0.715
7-1/M82	1.20302
7-2/M82	1.15817	0.385
9-3-2/M82	0.79322	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.03793	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03815	1
IL12-4/WTpooled	0.79722	0.581
IL1-4/WTpooled	0.91193	0.834
WT/WTpooled	1.06353	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	1.30089	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03806	0.921
DC3000/delta hrp 6h	1.06202	1
DC3000/delta hrp 12h	1.05575	1
DC3000/delta hrp 24h	1.06556	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21129	0.25
DC3000 delta B/DC3000 delta AB	1.17877	0.212

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91186	1
Exp 36h	1.26898	0.489
Exp 60h	1.26115	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95065	1
Var 0h	1.04369	0.98
Var 12h I row2-row1	1.23915	0.296
Var 12h NI row2-row1	0.85417	0.82
Var 36h I row2-row1	0.84513	0.805
Var 36h NI row2-row1	0.83904	0.743
Var 60h I row2-row1	1.28054	0.562
Var 60h NI row2-row1	1.12043	0.904
Time course 0hI-0hNI	1.04627	0.852
Time course 12hI-12hNI	1.06739	0.633
Time course 36hI-36hNI	0.9746	0.418
Time course 60hI-60hNI	1.22537	0.019

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)	1.30926	0.287
transgenic ySAMdc/azygous control (breaker)	0.45886	0.139
transgenic ySAMdc/azygous control (red)	1.11888	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00551	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04734	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73387	1
Manapal/WT (break)	0.83703	1
Manapal/WT (red)	0.51778	0.181