Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.10.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07744	0.851
27DAP/17DAP	0.82006	0.661
39DAP/27DAP	1.03458	1
41DAP/39DAP	0.74465	0.157
42DAP/41DAP	1.13895	1
43DAP/42DAP	0.82925	0.576
47DAP/43DAP	1.98846	0.538
52DAP/47DAP	0.76602	0.461
57DAP/52DAP	0.81337	0.681

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94535	0.269
17DAP/reference	1.0101	0.843
27DAP/reference	0.95952	0.525
39DAP/reference	0.93264	0.206
41DAP/reference	0.97771	0.667
42DAP/reference	0.93409	0.225
43DAP/reference	0.94295	0.576
47DAP/reference	0.87379	0.005
52DAP/reference	0.99013	0.598
57DAP/reference	0.91015	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.99424	0.068
27DAP/17DAP	1.20498	0.306
39DAP/27DAP	1.04236	1
41DAP/39DAP	1.20024	0.427
42DAP/41DAP	1.06048	0.999
43DAP/42DAP	1.17697	0.147
47DAP/43DAP	0.99336	0.928
52DAP/47DAP	1.08822	0.766
57DAP/52DAP	1.62347	0.049
57DAP/7DAP	2.5858	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06008	0.776
17DAP/reference	0.95313	0.295
27DAP/reference	1.0561	0.664
39DAP/reference	1.17234	0.175
41DAP/reference	0.97359	0.489
42DAP/reference	1.19238	0.132
43DAP/reference	1.09499	0.603
47DAP/reference	1.02048	1
52DAP/reference	1.16498	0.183
57DAP/reference	1.27176	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96483	0.607
17DAP/reference	0.87701	0.287
27DAP/reference	0.99465	0.686
39DAP/reference	0.96964	0.442
41DAP/reference	0.90281	0.262
42DAP/reference	0.84894	0.121
43DAP/reference	1.03158	0.831
47DAP/reference	0.87799	0.137
52DAP/reference	1.07051	1
57DAP/reference	0.81941	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07745	1
17DAP/reference	0.99107	0.751
27DAP/reference	1.14004	0.271
39DAP/reference	1.03774	0.858
41DAP/reference	1.008	1
42DAP/reference	1.11178	0.333
43DAP/reference	0.99947	0.767
47DAP/reference	0.94013	0.371
52DAP/reference	1.10315	0.862
57DAP/reference	0.98701	0.643

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02747	1
26DAP/20DAP	1.52825	0.555
34DAP/26DAP	1.437	1
51DAP/34DAP	1.15666	0.759
52DAP/51DAP	1.12086	0.873
53DAP/52DAP	1.32349	0.398
55DAP/53DAP	1.34366	0.703
57DAP/55DAP	1.01386	0.891
62DAP/57DAP	1.08018	1
68DAP/62DAP	1.08754	1
68DAP/14DAP	1.11059	0.469

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03989	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83738
Mature Green Tomato/Ripe Tomato	1.08796
Immature Eggplant/Mature Eggplant	0.82582	0.067
Ripe Pepper/Ripe Tomato	0.74196	1
Mature Eggplant/Ripe Tomato	2.55101	0.26

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	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
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	N/A	N/A
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	0.98215	1
IL2-6/WTpooled	1.14328	0.584
IL7-5/WTpooled	1.48295	0.75
IL7-3/WTpooled	1.10745	1
IL12-4/WTpooled	0.94299	1
IL1-4/WTpooled	1.16091	1
WT/WTpooled	0.97417	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	0.71962

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99858	1
DC3000/delta hrp 6h	0.73081	0.95
DC3000/delta hrp 12h	0.95756
DC3000/delta hrp 24h	1.01366	1

Experiment: DC3000 effector mutants

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

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.74476	0.328
Exp 36h	1.2389	1
Exp 60h	0.72665	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07887	1
Var 0h	0.9962	1
Var 12h I row2-row1	5.03441	0.58
Var 12h NI row2-row1	1.03515	1
Var 36h I row2-row1	0.92587	0.575
Var 36h NI row2-row1	0.89171	0.706
Var 60h I row2-row1	0.96436	0.285
Var 60h NI row2-row1	0.7307	0.904
Time course 0hI-0hNI	0.92507	0.659
Time course 12hI-12hNI	0.93502	0.53
Time course 36hI-36hNI	0.8058	0.027
Time course 60hI-60hNI	2.02477	1

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)	1.15378	0.256
transgenic ySAMdc/azygous control (breaker)	0.72141	0.173
transgenic ySAMdc/azygous control (red)	0.94395	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.48207	0.023

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07183	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92481	1
Manapal/WT (break)	1.27277	0.381
Manapal/WT (red)	0.9751	0.863