Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.18.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8973	0.395
27DAP/17DAP	1.02355	0.975
39DAP/27DAP	0.72901	0.293
41DAP/39DAP	1.28033	0.338
42DAP/41DAP	1.63433	0.709
43DAP/42DAP	0.98814	0.925
47DAP/43DAP	1.00508	0.913
52DAP/47DAP	0.94114	0.754
57DAP/52DAP	1.60862	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07874	0.334
17DAP/reference	0.8605	0.091
27DAP/reference	0.97137	0.654
39DAP/reference	0.83297	0.056
41DAP/reference	0.89565	0.341
42DAP/reference	0.99312	0.501
43DAP/reference	0.95415	0.346
47DAP/reference	1.04493	0.84
52DAP/reference	1.183	0.524
57DAP/reference	1.249	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08886	0.91
27DAP/17DAP	1.03797	0.912
39DAP/27DAP	0.99111	0.953
41DAP/39DAP	1.19277	0.79
42DAP/41DAP	0.92381	0.451
43DAP/42DAP	0.98612	0.801
47DAP/43DAP	1.02974	0.92
52DAP/47DAP	1.08609	0.703
57DAP/52DAP	0.94154	0.626
57DAP/7DAP	0.86539	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90347	0.296
17DAP/reference	0.92898	0.447
27DAP/reference	0.91347	0.402
39DAP/reference	1.16392	0.056
41DAP/reference	1.02568	0.723
42DAP/reference	1.10353	0.686
43DAP/reference	0.99207	0.608
47DAP/reference	1.25957	0.136
52DAP/reference	1.23425	0.171
57DAP/reference	0.95275	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86706	0.06
17DAP/reference	0.9198	0.07
27DAP/reference	1.08496	0.48
39DAP/reference	1.07338	0.412
41DAP/reference	1.09175	0.241
42DAP/reference	1.02558	1
43DAP/reference	0.77952	0.066
47DAP/reference	0.93936	0.221
52DAP/reference	0.9927	0.619
57DAP/reference	0.77453	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06551	1
17DAP/reference	0.96151	0.647
27DAP/reference	1.04948	0.51
39DAP/reference	1.09852	0.254
41DAP/reference	1.11056	0.754
42DAP/reference	1.18466	0.333
43DAP/reference	1.38817	0.026
47DAP/reference	1.04193	0.934
52DAP/reference	1.63555	0.053
57DAP/reference	1.66481	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10926	0.966
26DAP/20DAP	1.28106	0.197
34DAP/26DAP	0.90638	0.783
51DAP/34DAP	1.07364	0.962
52DAP/51DAP	0.91887	1
53DAP/52DAP	0.90635	0.604
55DAP/53DAP	1.21051	0.511
57DAP/55DAP	1.28566	0.779
62DAP/57DAP	1.07595	1
68DAP/62DAP	1.68763	0.052
68DAP/14DAP	2.55018	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.03226	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.17751	1
Mature Green Tomato/Ripe Tomato	0.68298	0.072
Immature Eggplant/Mature Eggplant	0.90744	0.144
Ripe Pepper/Ripe Tomato	1.09126	1
Mature Eggplant/Ripe Tomato	1.06007	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85225	0.605
1-1-2/M82	0.90549	1
12-2/M82	0.88728	0.955
12-4/M82	0.89466	1
1-3/M82	1.92395	0.248
2-1-1/M82	0.9847	0.92
2-1/M82	0.81141	0.345
2-6/M82	0.88048	0.501
3-2/M82	1.00997
4-1-1/M82	0.96259	1
4-1/M82	0.81141	0.525
4-3-2/M82	0.85298	1
4-3/M82	1.23971	1
5-3/M82	1.08778	1
6-2/M82	1.03418	1
6-3/M82	1.10117	1
7-1/M82	0.54577	1
7-2/M82	1.19532	0.385
9-3-2/M82	1.06922

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94266	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95645	1
IL12-4/WTpooled	1.18616	0.557
IL1-4/WTpooled	0.82538	0.444
WT/WTpooled	1.05218	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	1.12449	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05281	0.921
DC3000/delta hrp 6h	0.99155	0.95
DC3000/delta hrp 12h	1.06324	1
DC3000/delta hrp 24h	1.30746	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.25282	0.046
DC3000 delta B/DC3000 delta AB	1.36275	0.166

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93489	1
Exp 36h	0.90751	0.623
Exp 60h	1.00814	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00397	1
Var 0h	1.88553	0.782
Var 12h I row2-row1	0.93408	0.627
Var 12h NI row2-row1	1.07459	1
Var 36h I row2-row1	1.23525	0.41
Var 36h NI row2-row1	0.88066	0.272
Var 60h I row2-row1	0.93039	0.285
Var 60h NI row2-row1	1.03814	1
Time course 0hI-0hNI	1.12046	0.852
Time course 12hI-12hNI	0.97465	0.841
Time course 36hI-36hNI	1.09717	0.316
Time course 60hI-60hNI	1.99248	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)	0.9002	0.428
transgenic ySAMdc/azygous control (breaker)	0.74685	0.131
transgenic ySAMdc/azygous control (red)	1.03365	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.49939	0.044

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85492	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98505	1
Manapal/WT (break)	1.0502	1
Manapal/WT (red)	0.84201	0.181