Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.19.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89191	0.395
27DAP/17DAP	1.09038	0.872
39DAP/27DAP	1.09121	1
41DAP/39DAP	0.90059	0.593
42DAP/41DAP	0.89034	1
43DAP/42DAP	1.03094	0.937
47DAP/43DAP	0.90934	0.667
52DAP/47DAP	0.89158	0.675
57DAP/52DAP	1.25184	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81769	0.14
17DAP/reference	0.81652	0.017
27DAP/reference	0.95408	0.567
39DAP/reference	0.67217	0.078
41DAP/reference	0.71626	0.009
42DAP/reference	0.7755	0.01
43DAP/reference	1.03661
47DAP/reference	0.84078	0.003
52DAP/reference	1.34549	0.069
57DAP/reference	0.85475

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19181	0.278
27DAP/17DAP	1.01305	0.943
39DAP/27DAP	0.88266	0.338
41DAP/39DAP	1.0146	1
42DAP/41DAP	1.02069	1
43DAP/42DAP	1.06172	0.746
47DAP/43DAP	1.04158	0.906
52DAP/47DAP	1.40658	0.268
57DAP/52DAP	1.27527	0.217
57DAP/7DAP	0.94651	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01797	1
17DAP/reference	0.91845	0.192
27DAP/reference	0.91056	0.2
39DAP/reference	0.97691	0.474
41DAP/reference	0.99864	0.709
42DAP/reference	1.16697	0.405
43DAP/reference	0.90182	0.368
47DAP/reference	1.08007	0.404
52DAP/reference	1.10796	0.599
57DAP/reference	1.10527	0.851

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79136	0.01
17DAP/reference	0.84655	0.134
27DAP/reference	1.06746	0.726
39DAP/reference	1.21058	0.272
41DAP/reference	1.1335	0.548
42DAP/reference	1.14815	0.115
43DAP/reference	0.76447	0.034
47DAP/reference	0.92986	0.221
52DAP/reference	1.07877	0.498
57DAP/reference	0.79305	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98693	0.653
17DAP/reference	0.86063	0.3
27DAP/reference	1.12468	0.271
39DAP/reference	1.02574	1
41DAP/reference	1.12879	0.222
42DAP/reference	1.36805	0.134
43DAP/reference	1.56573	0.008
47DAP/reference	1.00037	0.708
52DAP/reference	1.36133	0.443
57DAP/reference	1.74533	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08653	1
26DAP/20DAP	1.12786	1
34DAP/26DAP	1.09985	0.819
51DAP/34DAP	1.29245	0.137
52DAP/51DAP	1.28953	0.225
53DAP/52DAP	0.90189	0.329
55DAP/53DAP	0.93423	0.648
57DAP/55DAP	0.89356	0.56
62DAP/57DAP	0.98229	0.994
68DAP/62DAP	1.87981	0.126
68DAP/14DAP	2.15343	0.067

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.58674	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.97493	0.783
Mature Green Tomato/Ripe Tomato	0.63248	0.024
Immature Eggplant/Mature Eggplant	0.76907
Ripe Pepper/Ripe Tomato	1.16834	1
Mature Eggplant/Ripe Tomato	0.76113

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.99999
12-2/M82	N/A	N/A
12-4/M82	0.88087	0.282
1-3/M82	1.32742
2-1-1/M82	0.56336
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	1.0009	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.00232
7-2/M82	1.3794
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05075	0.365
IL2-6/WTpooled	1.11883	0.46
IL7-5/WTpooled	1.02552	1
IL7-3/WTpooled	1.10611	0.362
IL12-4/WTpooled	0.92311	0.581
IL1-4/WTpooled	1.10964	0.426
WT/WTpooled	1.01805	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	0.944	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02289	1
DC3000/delta hrp 6h	0.8523	0.95
DC3000/delta hrp 12h	1.05036	1
DC3000/delta hrp 24h	1.25696	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96633	0.803
DC3000 delta B/DC3000 delta AB	0.97905	0.873

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10283	1
Exp 36h	0.8921	0.879
Exp 60h	1.02681	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06505	1
Var 0h	0.90512	1
Var 12h I row2-row1	0.99197	1
Var 12h NI row2-row1	1.08687	0.34
Var 36h I row2-row1	0.82361	1
Var 36h NI row2-row1	1.06726	1
Var 60h I row2-row1	0.85177	0.439
Var 60h NI row2-row1	0.89376	0.977
Time course 0hI-0hNI	0.91954	0.397
Time course 12hI-12hNI	0.98899	0.953
Time course 36hI-36hNI	0.96207	0.476
Time course 60hI-60hNI	0.78111	0.047

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)	0.87193	0.309
transgenic ySAMdc/azygous control (breaker)	1.21456	0.248
transgenic ySAMdc/azygous control (red)	1.01501	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97952	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84718	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.0087	1