Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.3.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84393	0.303
27DAP/17DAP	0.86596	0.67
39DAP/27DAP	0.77093	0.361
41DAP/39DAP	1.08196	1
42DAP/41DAP	1.59326	0.863
43DAP/42DAP	0.95293	0.864
47DAP/43DAP	1.18557	0.68
52DAP/47DAP	1.13475	0.758
57DAP/52DAP	1.26702	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12798	0.162
17DAP/reference	0.84837	0.278
27DAP/reference	0.90014	0.05
39DAP/reference	0.82382	0.06
41DAP/reference	0.98486	0.814
42DAP/reference	0.9576	0.233
43DAP/reference	0.50419	0.429
47DAP/reference	0.77061	0.002
52DAP/reference	0.76576	0.019
57DAP/reference	0.46133	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93227	0.454
27DAP/17DAP	1.01465	0.96
39DAP/27DAP	0.97766	0.87
41DAP/39DAP	1.06142	0.887
42DAP/41DAP	1.00269	0.884
43DAP/42DAP	1.06881	0.446
47DAP/43DAP	0.97222	0.796
52DAP/47DAP	1.01769	0.933
57DAP/52DAP	1.03113	0.856
57DAP/7DAP	1.00867	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04447	0.776
17DAP/reference	0.92171	0.253
27DAP/reference	1.02373	1
39DAP/reference	0.93757	0.264
41DAP/reference	0.99061	0.589
42DAP/reference	0.84933	0.07
43DAP/reference	1.00778	0.764
47DAP/reference	0.99146	0.671
52DAP/reference	0.91999	0.106
57DAP/reference	0.90198	0.086

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19378	0.069
17DAP/reference	1.09193	0.094
27DAP/reference	1.2089	0.136
39DAP/reference	1.2295	0.164
41DAP/reference	1.18899	0.099
42DAP/reference	1.04572	1
43DAP/reference	0.93126	0.344
47DAP/reference	1.0724	0.603
52DAP/reference	1.06669	0.471
57DAP/reference	1.12682	0.398

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07643	0.408
17DAP/reference	0.96126	0.624
27DAP/reference	0.99529	0.727
39DAP/reference	0.95473	0.43
41DAP/reference	1.1057	0.296
42DAP/reference	1.13036	0.356
43DAP/reference	1.02373	1
47DAP/reference	1.06474	0.655
52DAP/reference	1.12694	0.457
57DAP/reference	1.89664	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94487	1
26DAP/20DAP	0.86481	0.317
34DAP/26DAP	1.05729	1
51DAP/34DAP	0.94743	0.571
52DAP/51DAP	0.94922	0.151
53DAP/52DAP	0.89417	0.417
55DAP/53DAP	0.98432	0.838
57DAP/55DAP	0.95714	0.799
62DAP/57DAP	1.38053	0.833
68DAP/62DAP	1.27476	0.132
68DAP/14DAP	1.07953	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97114	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.846	0.017
Immature Eggplant/Mature Eggplant	1.95141
Ripe Pepper/Ripe Tomato	0.21864	0.293
Mature Eggplant/Ripe Tomato	0.60101	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.02066	1
12-2/M82	1.19735
12-4/M82	0.8498	0.259
1-3/M82	1.95133
2-1-1/M82	0.93864
2-1/M82	N/A	N/A
2-6/M82	1.31219
3-2/M82	1.2916
4-1-1/M82	N/A	N/A
4-1/M82	0.23442
4-3-2/M82	0.99177
4-3/M82	1.28621	0.268
5-3/M82	0.84967
6-2/M82	1.27531
6-3/M82	1.27028
7-1/M82	0.95857	1
7-2/M82	1.03357
9-3-2/M82	0.9165	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71243	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.14484	0.792
IL7-3/WTpooled	2.11039
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.97582	1
WT/WTpooled	N/A	N/A

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	0.90564	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07987	0.823
DC3000/delta hrp 6h	1.01529	1
DC3000/delta hrp 12h	1.14976	1
DC3000/delta hrp 24h	0.94103	0.618

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10857	0.25
DC3000 delta B/DC3000 delta AB	1.0611	0.565

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98565	1
Exp 36h	1.07024	0.693
Exp 60h	0.76655	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98004	1
Var 0h	1.04771	0.98
Var 12h I row2-row1	0.97902	0.948
Var 12h NI row2-row1	0.8677	0.494
Var 36h I row2-row1	0.98119	1
Var 36h NI row2-row1	1.09016	1
Var 60h I row2-row1	1.80192	1
Var 60h NI row2-row1	1.32107	0.904
Time course 0hI-0hNI	1.03872	0.852
Time course 12hI-12hNI	0.97684	0.806
Time course 36hI-36hNI	0.91847	0.129
Time course 60hI-60hNI	0.78324	0.009

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)	1.37622	0.331
transgenic ySAMdc/azygous control (breaker)	0.92944	0.49
transgenic ySAMdc/azygous control (red)	0.99036	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09005	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66074	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07908	1
Manapal/WT (break)	1.15374	1
Manapal/WT (red)	0.95462	0.607