Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.10.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9831	0.83
27DAP/17DAP	1.10483	0.92
39DAP/27DAP	1.14692	0.643
41DAP/39DAP	1.02314	0.982
42DAP/41DAP	1.09444	0.882
43DAP/42DAP	0.74801	0.346
47DAP/43DAP	0.93363	0.705
52DAP/47DAP	1.14861	0.945
57DAP/52DAP	0.99085	0.974

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9812	0.562
17DAP/reference	1.05635	0.092
27DAP/reference	0.9791	0.497
39DAP/reference	1.01378	0.545
41DAP/reference	1.09649	0.019
42DAP/reference	0.90533	0.024
43DAP/reference	1.04171	0.382
47DAP/reference	0.96557	0.207
52DAP/reference	0.91106	0.073
57DAP/reference	1.03568	0.643

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85413	0.228
27DAP/17DAP	1.02763	1
39DAP/27DAP	1.14425	0.373
41DAP/39DAP	0.94584	0.861
42DAP/41DAP	1.0777	0.783
43DAP/42DAP	1.15882	0.056
47DAP/43DAP	1.12201	0.286
52DAP/47DAP	0.92181	0.572
57DAP/52DAP	1.37927	0.091
57DAP/7DAP	0.82622	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98993	0.682
17DAP/reference	1.2456	0.162
27DAP/reference	1.06879	0.974
39DAP/reference	1.46491	0.149
41DAP/reference	1.62143	0.057
42DAP/reference	1.36391	0.046
43DAP/reference	1.49414	0.022
47DAP/reference	1.04306	0.996
52DAP/reference	1.12524	0.684
57DAP/reference	1.30697	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00375	0.97
17DAP/reference	1.0763	0.278
27DAP/reference	0.96583	0.407
39DAP/reference	0.97651	0.416
41DAP/reference	0.88725	0.063
42DAP/reference	0.93218	0.135
43DAP/reference	0.95354	0.414
47DAP/reference	0.91009	0.028
52DAP/reference	1.0673	0.471
57DAP/reference	1.11049	0.127

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07255	0.939
17DAP/reference	1.06046	1
27DAP/reference	1.62548	0.03
39DAP/reference	1.46524	0.084
41DAP/reference	1.25703	0.174
42DAP/reference	1.06178	0.923
43DAP/reference	1.02931	0.91
47DAP/reference	0.89076	0.041
52DAP/reference	1.19854	0.233
57DAP/reference	0.85775	0.199

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98072	1
26DAP/20DAP	1.90529	0.137
34DAP/26DAP	1.03044	1
51DAP/34DAP	1.17447	0.496
52DAP/51DAP	1.03908	0.888
53DAP/52DAP	1.55345	0.144
55DAP/53DAP	1.04293
57DAP/55DAP	1.18277	0.854
62DAP/57DAP	0.87964	0.466
68DAP/62DAP	1.11126	0.808
68DAP/14DAP	1.10578	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7034	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.92143	0.539
Mature Green Tomato/Ripe Tomato	1.38086	0.948
Immature Eggplant/Mature Eggplant	1.4519	0.053
Ripe Pepper/Ripe Tomato	0.76872	0.293
Mature Eggplant/Ripe Tomato	0.91019	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04378	1
1-1-2/M82	0.96191	1
12-2/M82	1.05224	1
12-4/M82	1.3204
1-3/M82	0.94892	1
2-1-1/M82	1.18316	0.689
2-1/M82	1.05197	1
2-6/M82	1.12156	0.505
3-2/M82	0.87398
4-1-1/M82	0.94566	1
4-1/M82	1.04247
4-3-2/M82	0.8808
4-3/M82	0.80711	0.611
5-3/M82	0.96906	1
6-2/M82	0.89898	1
6-3/M82	1.05326	1
7-1/M82	1.04392	1
7-2/M82	0.999	1
9-3-2/M82	1.02897

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.40559
IL2-6/WTpooled	1.07722	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13901	1
IL12-4/WTpooled	0.91645	0.71
IL1-4/WTpooled	1.14106	0.426
WT/WTpooled	0.91016	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	0.87889	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98097	1
DC3000/delta hrp 6h	0.88775	0.95
DC3000/delta hrp 12h	1.14779	1
DC3000/delta hrp 24h	1.05263	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.45091	0.25
DC3000 delta B/DC3000 delta AB	1.08721	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01923	1
Exp 36h	1.36848	0.489
Exp 60h	1.37225	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94778	1
Var 0h	0.96069	1
Var 12h I row2-row1	1.18286	0.544
Var 12h NI row2-row1	1.2111	1
Var 36h I row2-row1	0.79211	0.805
Var 36h NI row2-row1	0.85806	0.61
Var 60h I row2-row1	0.81504	0.374
Var 60h NI row2-row1	1.0592	0.904
Time course 0hI-0hNI	1.07364	0.852
Time course 12hI-12hNI	1.08981	0.517
Time course 36hI-36hNI	1.37612	0.005
Time course 60hI-60hNI	1.96377	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)	1.09369	0.278
transgenic ySAMdc/azygous control (breaker)	1.08086	0.248
transgenic ySAMdc/azygous control (red)	1.07424	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95543	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.70743	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88932	1
Manapal/WT (break)	0.90907	1
Manapal/WT (red)	0.8525	0.216