Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.20.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83111	0.226
27DAP/17DAP	0.46945	0.029
39DAP/27DAP	1.1226	1
41DAP/39DAP	1.23034	0.224
42DAP/41DAP	0.99383	1
43DAP/42DAP	1.08705	1
47DAP/43DAP	1.01939	0.943
52DAP/47DAP	1.5688	0.667
57DAP/52DAP	1.23858	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70069	0.008
17DAP/reference	1.06675	0.201
27DAP/reference	0.94467	0.428
39DAP/reference	0.94939	0.513
41DAP/reference	0.96759	0.341
42DAP/reference	0.90774	0.054
43DAP/reference	0.95062	0.287
47DAP/reference	1.01174	1
52DAP/reference	1.00425	1
57DAP/reference	1.03025	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	N/A	N/A
27DAP/17DAP	0.80143	0.614
39DAP/27DAP	0.94897	0.898
41DAP/39DAP	0.84435	0.804
42DAP/41DAP	1.15092	0.961
43DAP/42DAP	0.81369	0.576
47DAP/43DAP	1.49221	0.906
52DAP/47DAP	0.67825
57DAP/52DAP	0.96571	0.828
57DAP/7DAP	0.68908	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37441	0.031
17DAP/reference	1.05079	0.244
27DAP/reference	0.90796	0.035
39DAP/reference	0.92623	0.126
41DAP/reference	0.9778	0.469
42DAP/reference	0.9667	0.355
43DAP/reference	0.83322	0.037
47DAP/reference	0.87942	0.128
52DAP/reference	0.78049	0.02
57DAP/reference	0.74442	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55559	0.035
17DAP/reference	1.14512	0.271
27DAP/reference	1.18571	0.066
39DAP/reference	1.05873	0.935
41DAP/reference	1.02919	1
42DAP/reference	1.00388	0.723
43DAP/reference	1.05207	0.522
47DAP/reference	1.00084	0.73
52DAP/reference	0.87528	0.013
57DAP/reference	0.99324	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34947	0.03
17DAP/reference	0.96147	0.433
27DAP/reference	0.72628	0.031
39DAP/reference	0.85257	0.035
41DAP/reference	0.87757	0.046
42DAP/reference	0.96392	0.552
43DAP/reference	0.81129	0.043
47DAP/reference	0.88126	0.069
52DAP/reference	0.89412	0.319
57DAP/reference	1.55559	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91805	0.89
26DAP/20DAP	0.56971
34DAP/26DAP	1.86944	0.819
51DAP/34DAP	1.01494	0.962
52DAP/51DAP	1.16721	0.904
53DAP/52DAP	1.18822	0.738
55DAP/53DAP	1.14332	0.126
57DAP/55DAP	1.06935	0.935
62DAP/57DAP	1.92571	0.303
68DAP/62DAP	1.01438	0.914
68DAP/14DAP	0.89661	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.55146

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.55739	0.129
Mature Green Tomato/Ripe Tomato	1.84303	0.022
Immature Eggplant/Mature Eggplant	0.69539	0.07
Ripe Pepper/Ripe Tomato	0.51604	0.224
Mature Eggplant/Ripe Tomato	1.3753	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9247	0.944
1-1-2/M82	1.01589	1
12-2/M82	1.15227	1
12-4/M82	0.97773	1
1-3/M82	1.0309	1
2-1-1/M82	0.97152	1
2-1/M82	1.30035	1
2-6/M82	1.10211	0.695
3-2/M82	0.92177
4-1-1/M82	0.87455
4-1/M82	1.30926
4-3-2/M82	N/A	N/A
4-3/M82	0.95641	1
5-3/M82	1.09127	1
6-2/M82	0.8168	0.481
6-3/M82	0.87943
7-1/M82	0.91441
7-2/M82	0.9494	0.796
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97931	0.321
IL2-6/WTpooled	1.16107	0.788
IL7-5/WTpooled	0.97047	1
IL7-3/WTpooled	1.25016	0.362
IL12-4/WTpooled	1.17634	0.553
IL1-4/WTpooled	0.97943	1
WT/WTpooled	0.99156	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06463	0.921
DC3000/delta hrp 6h	1.23429	0.978
DC3000/delta hrp 12h	1.03952	1
DC3000/delta hrp 24h	1.06708	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07212	1
Exp 36h	1.72556	0.693
Exp 60h	0.93272	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.36668	0.278
transgenic ySAMdc/azygous control (breaker)	0.69879	0.122
transgenic ySAMdc/azygous control (red)	0.95285	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05316	0.155

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.32988	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.52988	0.172
Manapal/WT (break)	0.69552	0.333
Manapal/WT (red)	0.46619	0.181