Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.6.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11698	0.977
27DAP/17DAP	1.39556	0.629
39DAP/27DAP	1.32709	0.719
41DAP/39DAP	1.59768	0.264
42DAP/41DAP	1.11351	0.938
43DAP/42DAP	0.91994	0.77
47DAP/43DAP	1.1795	0.618
52DAP/47DAP	1.30207	0.421
57DAP/52DAP	0.97424	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96441	0.476
17DAP/reference	0.99779	0.957
27DAP/reference	1.03559	0.709
39DAP/reference	1.0544	0.403
41DAP/reference	1.00229	1
42DAP/reference	0.92283	0.163
43DAP/reference	0.89114	0.155
47DAP/reference	1.0613	0.463
52DAP/reference	1.02239	1
57DAP/reference	1.21787	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92736	0.415
27DAP/17DAP	1.02385	0.968
39DAP/27DAP	0.96872	0.784
41DAP/39DAP	1.11216	0.849
42DAP/41DAP	0.92259	0.495
43DAP/42DAP	1.11612	0.324
47DAP/43DAP	0.96296	0.781
52DAP/47DAP	1.04108	0.892
57DAP/52DAP	0.88835	0.454
57DAP/7DAP	0.96042	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77014	0.138
17DAP/reference	0.77243	0.031
27DAP/reference	1.03335	0.664
39DAP/reference	0.86709	0.109
41DAP/reference	0.96182	0.431
42DAP/reference	0.89168	0.275
43DAP/reference	0.92757	0.066
47DAP/reference	1.04886	0.948
52DAP/reference	0.96426	0.523
57DAP/reference	0.88795	0.101

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91115	0.374
17DAP/reference	0.89457	0.134
27DAP/reference	0.75662	0.1
39DAP/reference	0.94531	0.37
41DAP/reference	0.98996	0.481
42DAP/reference	1.04593	0.81
43DAP/reference	1.21079	0.624
47DAP/reference	1.0582	0.343
52DAP/reference	0.96538	0.407
57DAP/reference	1.04709	0.98

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79635	0.037
17DAP/reference	0.9285	0.358
27DAP/reference	0.93841	0.416
39DAP/reference	6.26074	0.563
41DAP/reference	0.9248	0.264
42DAP/reference	0.9648	0.445
43DAP/reference	0.84769	0.206
47DAP/reference	1.11198	0.163
52DAP/reference	0.89361	0.342
57DAP/reference	1.02689	0.954

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1149	1
26DAP/20DAP	0.86604	1
34DAP/26DAP	1.17249	0.819
51DAP/34DAP	1.50211	0.627
52DAP/51DAP	0.94386	1
53DAP/52DAP	1.12288	0.58
55DAP/53DAP	1.04077	0.885
57DAP/55DAP	0.98777	0.902
62DAP/57DAP	0.85171	0.681
68DAP/62DAP	1.10866	0.7
68DAP/14DAP	1.25928	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83755	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.8112	0.347
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.71667
Mature Eggplant/Ripe Tomato	1.07358	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14204	0.742
1-1-2/M82	0.99883	1
12-2/M82	0.87672
12-4/M82	0.8563	0.358
1-3/M82	1.11893
2-1-1/M82	0.57473
2-1/M82	1.05493	1
2-6/M82	0.74148	1
3-2/M82	1.01271
4-1-1/M82	0.93856	1
4-1/M82	0.87478	1
4-3-2/M82	0.81703	0.37
4-3/M82	0.88167	0.72
5-3/M82	0.9611
6-2/M82	0.78845	0.481
6-3/M82	0.94991	1
7-1/M82	1.00317
7-2/M82	N/A	N/A
9-3-2/M82	0.86613	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.79285	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07174	1
IL12-4/WTpooled	1.09253	0.595
IL1-4/WTpooled	0.82559	0.457
WT/WTpooled	1.0425	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	1.04351	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10581	0.758
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.96988	1
DC3000/delta hrp 24h	1.27301	0.397

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0878	0.476
DC3000 delta B/DC3000 delta AB	1.0528	0.55

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	1.01017	1
Var 0h	1.22189	0.339
Var 12h I row2-row1	1.21426	0.613
Var 12h NI row2-row1	0.82317	0.494
Var 36h I row2-row1	0.76367	1
Var 36h NI row2-row1	1.15816	1
Var 60h I row2-row1	1.05729	1
Var 60h NI row2-row1	1.19322	0.904
Time course 0hI-0hNI	1.02929	0.867
Time course 12hI-12hNI	0.90579	0.747
Time course 36hI-36hNI	1.0494	0.28
Time course 60hI-60hNI	1.38955	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)	0.89195	0.246
transgenic ySAMdc/azygous control (breaker)	1.34593	0.178
transgenic ySAMdc/azygous control (red)	1.10934	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99533	0.609

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91502	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92695	1
Manapal/WT (break)	0.97204	1
Manapal/WT (red)	1.2206	0.222