Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18606	0.67
27DAP/17DAP	1.20923	0.793
39DAP/27DAP	1.11206	0.974
41DAP/39DAP	0.89336	0.602
42DAP/41DAP	1.26689	0.573
43DAP/42DAP	1.00126	0.937
47DAP/43DAP	1.14337	0.595
52DAP/47DAP	0.97939	0.865
57DAP/52DAP	1.20038	0.737

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8364	0.109
17DAP/reference	0.61472	0.009
27DAP/reference	0.71509	0.134
39DAP/reference	0.71938	0.018
41DAP/reference	0.72079	0.026
42DAP/reference	0.7071	0.002
43DAP/reference	0.88067	0.211
47DAP/reference	0.92652	0.148
52DAP/reference	0.93117	0.36
57DAP/reference	1.15072	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0306	0.91
27DAP/17DAP	1.01193	1
39DAP/27DAP	0.91614	0.371
41DAP/39DAP	0.97247	0.885
42DAP/41DAP	1.12391	0.687
43DAP/42DAP	0.92802	0.351
47DAP/43DAP	1.05288	0.485
52DAP/47DAP	1.03334	0.892
57DAP/52DAP	1.04838	0.726
57DAP/7DAP	1.072	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33423	0.368
17DAP/reference	1.96154	0.023
27DAP/reference	2.26855	0.007
39DAP/reference	1.89899	0.005
41DAP/reference	1.99573	0.072
42DAP/reference	N/A	N/A
43DAP/reference	4.00377
47DAP/reference	1.40935	1
52DAP/reference	2.48272	0.007
57DAP/reference	3.78559	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68972	0.034
17DAP/reference	0.61875	0.004
27DAP/reference	0.82825	0.051
39DAP/reference	0.7701	0.037
41DAP/reference	0.87361	0.108
42DAP/reference	0.83862	0.035
43DAP/reference	0.71854	0.005
47DAP/reference	0.79597	0.015
52DAP/reference	0.78305	0.031
57DAP/reference	0.63298	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47626	0.433
17DAP/reference	1.45889	0.631
27DAP/reference	2.84054	0.078
39DAP/reference	2.43436	0.163
41DAP/reference	2.6371	0.027
42DAP/reference	1.50323	0.481
43DAP/reference	1.97289	0.121
47DAP/reference	0.59979	0.004
52DAP/reference	0.40663
57DAP/reference	1.87109	0.16

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8821	0.807
26DAP/20DAP	0.89004	0.512
34DAP/26DAP	1.13101	0.819
51DAP/34DAP	0.99685	0.924
52DAP/51DAP	1.23011	0.163
53DAP/52DAP	1.02936	0.901
55DAP/53DAP	1.13049	0.399
57DAP/55DAP	1.03927	0.975
62DAP/57DAP	1.07931	0.133
68DAP/62DAP	0.90538	0.609
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69541	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.00332	0.898
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

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	N/A	N/A
12-4/M82	1.40493
1-3/M82	N/A	N/A
2-1-1/M82	N/A	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	1.05647
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.08375
7-2/M82	N/A	N/A
9-3-2/M82	0.87022	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.22757	0.277
IL2-6/WTpooled	1.06001	0.584
IL7-5/WTpooled	1.02351	0.75
IL7-3/WTpooled	1.15995	1
IL12-4/WTpooled	0.98867	1
IL1-4/WTpooled	1.02415	1
WT/WTpooled	0.97527	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	0.86655	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.08238	1
DC3000/delta hrp 12h	1.11262	1
DC3000/delta hrp 24h	6.62445	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.89768	0.196
DC3000 delta B/DC3000 delta AB	0.83341	0.035

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01124	1
Var 0h	0.95769	1
Var 12h I row2-row1	0.87791	0.418
Var 12h NI row2-row1	1.16296	0.649
Var 36h I row2-row1	0.8671	0.805
Var 36h NI row2-row1	1.26646	0.482
Var 60h I row2-row1	0.9985	1
Var 60h NI row2-row1	1.0934	0.904
Time course 0hI-0hNI	1.01064	1
Time course 12hI-12hNI	0.90982	0.098
Time course 36hI-36hNI	0.82115	0.05
Time course 60hI-60hNI	0.32147	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)	1.12297	0.212
transgenic ySAMdc/azygous control (breaker)	1.55848	1
transgenic ySAMdc/azygous control (red)	0.79926	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94314	0.444

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.62919	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.5369	0.14
Manapal/WT (break)	1.04889	1
Manapal/WT (red)	0.85855	0.728