Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.3.2.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99584	0.801
27DAP/17DAP	0.90007	0.782
39DAP/27DAP	0.76485	0.447
41DAP/39DAP	1.23745	0.575
42DAP/41DAP	1.07855	1
43DAP/42DAP	1.04879	1
47DAP/43DAP	1.08955	0.481
52DAP/47DAP	0.75283	0.442
57DAP/52DAP	0.97593	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02138	0.735
17DAP/reference	1.08168	0.412
27DAP/reference	1.07264	0.271
39DAP/reference	1.04792	0.186
41DAP/reference	1.03494	0.667
42DAP/reference	0.95881	0.211
43DAP/reference	1.19075	0.495
47DAP/reference	0.9954	0.636
52DAP/reference	0.88131	0.177
57DAP/reference	1.00725	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03529	0.899
27DAP/17DAP	0.84893	0.312
39DAP/27DAP	0.56108	0.035
41DAP/39DAP	1.17422	0.674
42DAP/41DAP	0.88186	0.368
43DAP/42DAP	0.89255	0.351
47DAP/43DAP	0.90902	0.666
52DAP/47DAP	0.96744	0.93
57DAP/52DAP	1.5204	0.411
57DAP/7DAP	1.00587	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54577	0.069
17DAP/reference	1.43885	0.011
27DAP/reference	1.20845	0.088
39DAP/reference	1.19036	0.096
41DAP/reference	1.23517	0.077
42DAP/reference	1.35377	0.174
43DAP/reference	0.92364	0.166
47DAP/reference	1.05385	0.7
52DAP/reference	1.0958	0.352
57DAP/reference	1.1908	0.147

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02034	0.605
17DAP/reference	0.96344	0.239
27DAP/reference	0.96989	0.393
39DAP/reference	0.95201	0.339
41DAP/reference	0.91782	0.148
42DAP/reference	0.88521	0.032
43DAP/reference	0.94625	0.352
47DAP/reference	0.99734	0.73
52DAP/reference	0.97765	0.38
57DAP/reference	1.05438	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3062	0.064
17DAP/reference	1.07039	0.638
27DAP/reference	1.01947	0.749
39DAP/reference	1.11316	0.203
41DAP/reference	0.99382	0.754
42DAP/reference	1.04199	0.907
43DAP/reference	0.95514	0.432
47DAP/reference	0.9721	0.421
52DAP/reference	1.12767	0.398
57DAP/reference	0.89904	0.131

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04904	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.28747	0.819
51DAP/34DAP	1.22699	0.068
52DAP/51DAP	1.08758	0.965
53DAP/52DAP	0.99342	0.97
55DAP/53DAP	1.25484	0.22
57DAP/55DAP	23.2121	0.728
62DAP/57DAP	0.93065	0.871
68DAP/62DAP	0.96597	0.834
68DAP/14DAP	1.16613	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73359	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71925	0.194
Mature Green Tomato/Ripe Tomato	2.30331	0.03
Immature Eggplant/Mature Eggplant	0.99608	1
Ripe Pepper/Ripe Tomato	5.12138	1
Mature Eggplant/Ripe Tomato	2.82674	0.26

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	1.03755	N/A
12-4/M82	1.10294	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.81828	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	0.70604	N/A
6-2/M82	0.83253	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	N/A	N/A
IL2-6/WTpooled	0.62538	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12893	1
IL12-4/WTpooled	1.01701	0.839
IL1-4/WTpooled	0.91557	N/A
WT/WTpooled	1.03251	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	0.81044	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03415	0.921
DC3000/delta hrp 6h	1.01414	0.95
DC3000/delta hrp 12h	1.09573	1
DC3000/delta hrp 24h	1.7519	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86495	0.513
DC3000 delta B/DC3000 delta AB	0.55459	0.043

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91921	1
Exp 36h	0.87413	0.699
Exp 60h	0.76964	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9772	1
Var 0h	1.14915	0.98
Var 12h I row2-row1	0.8817	0.565
Var 12h NI row2-row1	1.1891	0.649
Var 36h I row2-row1	0.93066	1
Var 36h NI row2-row1	1.12305	1
Var 60h I row2-row1	1.04186	N/A
Var 60h NI row2-row1	1.06544	1
Time course 0hI-0hNI	0.94577	0.643
Time course 12hI-12hNI	0.90251	0.108
Time course 36hI-36hNI	0.83174	0.082
Time course 60hI-60hNI	0.4453	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)	0.96348	0.529
transgenic ySAMdc/azygous control (breaker)	1.34314	0.248
transgenic ySAMdc/azygous control (red)	1.19523	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01333	0.656

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.7028	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.54731	0.14
Manapal/WT (break)	1.42022	0.123
Manapal/WT (red)	1.51737	0.222