Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.7.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.5438	0.148
27DAP/17DAP	1.04743	0.92
39DAP/27DAP	0.81031	0.495
41DAP/39DAP	0.82802	0.381
42DAP/41DAP	0.9025	1
43DAP/42DAP	0.88714	0.799
47DAP/43DAP	0.93796	0.773
52DAP/47DAP	1.05061	0.902
57DAP/52DAP	1.26991	0.685

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00235	0.824
17DAP/reference	0.97677	0.63
27DAP/reference	1.03961	0.58
39DAP/reference	0.98862	0.816
41DAP/reference	0.96575	0.542
42DAP/reference	1.09863	0.03
43DAP/reference	0.93971	0.448
47DAP/reference	1.12769	0.039
52DAP/reference	1.25914	0.186
57DAP/reference	1.16965	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.87705	0.037
27DAP/17DAP	0.87307	0.648
39DAP/27DAP	0.60468	0.034
41DAP/39DAP	1.13789	0.336
42DAP/41DAP	0.8706	0.17
43DAP/42DAP	0.72066	0.06
47DAP/43DAP	0.80028	0.053
52DAP/47DAP	1.18602	0.57
57DAP/52DAP	1.19112	0.382
57DAP/7DAP	0.60287	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00222	0.758
17DAP/reference	1.15371	0.399
27DAP/reference	1.21667	0.371
39DAP/reference	1.03767	0.538
41DAP/reference	0.89334	0.122
42DAP/reference	0.88687	0.111
43DAP/reference	0.81422	0.02
47DAP/reference	0.86944	0.101
52DAP/reference	0.90249	0.097
57DAP/reference	0.93698	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9522	0.564
17DAP/reference	1.08143	0.628
27DAP/reference	1.20693	0.097
39DAP/reference	1.15992	0.155
41DAP/reference	1.09344	0.688
42DAP/reference	1.08044	0.61
43DAP/reference	1.16858	0.479
47DAP/reference	0.93602	0.201
52DAP/reference	1.16802	0.194
57DAP/reference	0.97121	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21525	0.035
17DAP/reference	1.4371	0.139
27DAP/reference	1.43399	0.016
39DAP/reference	1.33731	0.011
41DAP/reference	1.05238	0.734
42DAP/reference	1.20517	0.15
43DAP/reference	1.23613	0.116
47DAP/reference	1.21534	0.017
52DAP/reference	0.94285	0.464
57DAP/reference	1.56505	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01053	1
26DAP/20DAP	0.94178	0.512
34DAP/26DAP	1.29772	0.819
51DAP/34DAP	0.62936	0.067
52DAP/51DAP	1.43732	0.048
53DAP/52DAP	0.80993	0.071
55DAP/53DAP	1.13397	0.341
57DAP/55DAP	0.75412	0.259
62DAP/57DAP	0.86045	0.681
68DAP/62DAP	0.90773	0.769
68DAP/14DAP	1.09337	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.59667	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.90415	0.058
Mature Green Tomato/Ripe Tomato	6.88803	0.015
Immature Eggplant/Mature Eggplant	0.89345
Ripe Pepper/Ripe Tomato	1.2098
Mature Eggplant/Ripe Tomato	0.70918	1

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	1.00657
1-3/M82	N/A	N/A
2-1-1/M82	1.36378
2-1/M82	N/A	N/A
2-6/M82	1.55034
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	1.20728
4-3/M82	N/A	N/A
5-3/M82	0.94599
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	0.88599	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9309	1
DC3000/delta hrp 6h	1.16659	1
DC3000/delta hrp 12h	1.388	1
DC3000/delta hrp 24h	0.63556	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.74768	0.023
DC3000 delta B/DC3000 delta AB	0.82311	0.067

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04776	1
Exp 36h	1.03409	1
Exp 60h	0.95318	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99264	1
Var 0h	1.07357	1
Var 12h I row2-row1	0.8849	0.467
Var 12h NI row2-row1	1.00255	1
Var 36h I row2-row1	0.91919	0.438
Var 36h NI row2-row1	1.2628	0.276
Var 60h I row2-row1	0.98908	1
Var 60h NI row2-row1	1.16666	0.904
Time course 0hI-0hNI	0.98278	0.955
Time course 12hI-12hNI	1.03822	0.698
Time course 36hI-36hNI	0.9961	0.708
Time course 60hI-60hNI	0.1855	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)	1.26194	0.482
transgenic ySAMdc/azygous control (breaker)	4.29981	0.172
transgenic ySAMdc/azygous control (red)	1.08273	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9336	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.3962	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.36673	0.083
Manapal/WT (break)	7.08527	0.126
Manapal/WT (red)	10.2711	0.15