Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79804	0.232
27DAP/17DAP	1.11732	1
39DAP/27DAP	0.97118	0.7
41DAP/39DAP	1.11982	0.54
42DAP/41DAP	1.05606	0.978
43DAP/42DAP	0.85045	0.801
47DAP/43DAP	1.73841	0.309
52DAP/47DAP	1.33077	0.538
57DAP/52DAP	1.12939	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89734	0.118
17DAP/reference	1.00599	1
27DAP/reference	0.96249	0.552
39DAP/reference	0.87282	0.114
41DAP/reference	0.94288	0.434
42DAP/reference	0.95348	0.182
43DAP/reference	0.98534	0.763
47DAP/reference	0.96985	0.322
52DAP/reference	0.9751	0.438
57DAP/reference	1.07897	0.28

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33454	0.431
27DAP/17DAP	1.05927	0.9
39DAP/27DAP	1.06859	0.751
41DAP/39DAP	0.91123	0.645
42DAP/41DAP	1.07397	0.916
43DAP/42DAP	1.14267	0.134
47DAP/43DAP	0.93841	0.554
52DAP/47DAP	1.05344	0.868
57DAP/52DAP	0.97922	0.768
57DAP/7DAP	1.90883	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9703	0.326
17DAP/reference	1.0645	0.477
27DAP/reference	1.02351	0.974
39DAP/reference	1.2086	0.066
41DAP/reference	1.18296	0.046
42DAP/reference	1.21365	0.059
43DAP/reference	1.00382	1
47DAP/reference	1.05816	0.776
52DAP/reference	1.21093	0.02
57DAP/reference	1.15347	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87547	0.19
17DAP/reference	0.8436	0.072
27DAP/reference	0.81419	0.024
39DAP/reference	1.01649	1
41DAP/reference	0.95326	0.256
42DAP/reference	0.9126	0.089
43DAP/reference	0.92472	0.352
47DAP/reference	0.80381	0.012
52DAP/reference	0.94419	0.187
57DAP/reference	0.8216	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06548	0.903
17DAP/reference	1.07753	0.824
27DAP/reference	0.87249	0.184
39DAP/reference	1.31453	0.163
41DAP/reference	0.95932	0.512
42DAP/reference	1.12473	0.279
43DAP/reference	1.29537	0.259
47DAP/reference	0.88654	0.125
52DAP/reference	0.95967	0.637
57DAP/reference	1.09222	0.25

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21577	0.966
26DAP/20DAP	0.99609	1
34DAP/26DAP	0.95813	0.848
51DAP/34DAP	1.32455	0.241
52DAP/51DAP	0.96329	1
53DAP/52DAP	1.08443	0.678
55DAP/53DAP	1.16745	0.656
57DAP/55DAP	1.09407	0.818
62DAP/57DAP	1.37232
68DAP/62DAP	1.18931	0.422
68DAP/14DAP	1.45326

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09579	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93195
Mature Green Tomato/Ripe Tomato	0.73242	0.042
Immature Eggplant/Mature Eggplant	1.52592	0.063
Ripe Pepper/Ripe Tomato	0.60532	0.224
Mature Eggplant/Ripe Tomato	1.42287

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96117	0.961
1-1-2/M82	0.33946	1
12-2/M82	0.74553	0.955
12-4/M82	0.99368	1
1-3/M82	0.653
2-1-1/M82	0.72744	0.683
2-1/M82	N/A	N/A
2-6/M82	0.7134	1
3-2/M82	0.96607	1
4-1-1/M82	0.48429
4-1/M82	1.26569	0.326
4-3-2/M82	0.71785
4-3/M82	0.42317	0.551
5-3/M82	0.91908	1
6-2/M82	0.61123
6-3/M82	1.12183	1
7-1/M82	0.85281
7-2/M82	0.87283	0.57
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99823
IL2-6/WTpooled	1.1495	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.90707
IL12-4/WTpooled	0.91357
IL1-4/WTpooled	0.92491	0.562
WT/WTpooled	0.99666	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	0.97518	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98578	1
DC3000/delta hrp 6h	1.06049	0.95
DC3000/delta hrp 12h	1.00988	1
DC3000/delta hrp 24h	1.22963	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.8998
DC3000 delta B/DC3000 delta AB	1.03643

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7762	1
Exp 36h	N/A	N/A
Exp 60h	0.83327	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02039	1
Var 0h	0.57903	0.936
Var 12h I row2-row1	0.9805	0.856
Var 12h NI row2-row1	0.93277	0.488
Var 36h I row2-row1	1.09012	1
Var 36h NI row2-row1	0.84866	0.584
Var 60h I row2-row1	1.05632	1
Var 60h NI row2-row1	1.01925	1
Time course 0hI-0hNI	0.97638	0.911
Time course 12hI-12hNI	1.09629	0.774
Time course 36hI-36hNI	1.03409	0.58
Time course 60hI-60hNI	0.69737	0.011

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)	1.09496	0.863
transgenic ySAMdc/azygous control (breaker)	0.95775	1
transgenic ySAMdc/azygous control (red)	1.0651	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05901	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19784	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88747	1
Manapal/WT (break)	1.05977	1
Manapal/WT (red)	1.02871	1