Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.1.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1722	0.725
27DAP/17DAP	1.16788	0.847
39DAP/27DAP	1.17896	0.876
41DAP/39DAP	1.15345	0.511
42DAP/41DAP	1.4656	0.578
43DAP/42DAP	0.84884	0.7
47DAP/43DAP	0.90134	0.625
52DAP/47DAP	1.08312	0.964
57DAP/52DAP	1.28895	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15981	0.121
17DAP/reference	1.04126	0.294
27DAP/reference	1.03428	0.75
39DAP/reference	1.09235	0.051
41DAP/reference	1.02269	0.808
42DAP/reference	1.07363	0.026
43DAP/reference	1.12469	0.033
47DAP/reference	1.15619	0.035
52DAP/reference	1.114	0.027
57DAP/reference	1.11208	0.141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11609	0.144
27DAP/17DAP	0.96254	0.878
39DAP/27DAP	1.1654	0.182
41DAP/39DAP	1.03468	0.849
42DAP/41DAP	1.01168	0.934
43DAP/42DAP	0.97963	0.854
47DAP/43DAP	0.98217	0.911
52DAP/47DAP	0.96365	0.876
57DAP/52DAP	0.91408	0.348
57DAP/7DAP	1.08997

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95039	0.361
17DAP/reference	0.77403	0.015
27DAP/reference	0.88537	0.033
39DAP/reference	0.95047	0.307
41DAP/reference	0.76432	0.036
42DAP/reference	0.82291	0.031
43DAP/reference	0.81472	0.025
47DAP/reference	0.96656	0.671
52DAP/reference	0.78969	0.035
57DAP/reference	0.89164	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12911	0.175
17DAP/reference	1.22977	0.03
27DAP/reference	1.16667	0.174
39DAP/reference	1.19965	0.346
41DAP/reference	1.05462	1
42DAP/reference	1.12291	0.267
43DAP/reference	1.38883	0.01
47DAP/reference	1.06298	0.159
52DAP/reference	1.13821	0.208
57DAP/reference	1.34468	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86963	0.169
17DAP/reference	1.02475	0.934
27DAP/reference	0.66516	0.036
39DAP/reference	0.73515	0.012
41DAP/reference	0.89058	0.264
42DAP/reference	1.00276	1
43DAP/reference	0.88847	0.237
47DAP/reference	1.13294	0.044
52DAP/reference	0.89056	0.334
57DAP/reference	1.53861	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95532	1
26DAP/20DAP	0.93041	1
34DAP/26DAP	1.04424	1
51DAP/34DAP	1.28714	0.082
52DAP/51DAP	0.85001	1
53DAP/52DAP	1.28754	0.068
55DAP/53DAP	1.12758	0.247
57DAP/55DAP	0.88597	0.464
62DAP/57DAP	0.66613	0.01
68DAP/62DAP	0.86465	0.7
68DAP/14DAP	0.95911	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93846	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.44381	0.081
Mature Green Tomato/Ripe Tomato	1.01716	0.774
Immature Eggplant/Mature Eggplant	0.86625	0.082
Ripe Pepper/Ripe Tomato	2.682	0.258
Mature Eggplant/Ripe Tomato	0.79035	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07085
1-1-2/M82	1.13674	1
12-2/M82	1.0258	1
12-4/M82	0.90901	0.619
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	1.03386	0.695
3-2/M82	0.92463	0.188
4-1-1/M82	1.05064
4-1/M82	1.0935
4-3-2/M82	1.01715	1
4-3/M82	1.45181	0.268
5-3/M82	0.93307	1
6-2/M82	0.99126
6-3/M82	N/A	N/A
7-1/M82	1.05259
7-2/M82	1.0898	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94997	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.47535	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.86757	1
IL1-4/WTpooled	0.89263	0.834
WT/WTpooled	0.95057

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	0.91743	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06745	0.921
DC3000/delta hrp 6h	1.02044	1
DC3000/delta hrp 12h	1.10302	1
DC3000/delta hrp 24h	1.01317	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65373	0.068
DC3000 delta B/DC3000 delta AB	0.99886	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04839	1
Exp 36h	1.08486	1
Exp 60h	1.2339	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94089	1
Var 0h	1.16544	0.98
Var 12h I row2-row1	2.0713	0.544
Var 12h NI row2-row1	0.86592	0.494
Var 36h I row2-row1	1.02072	1
Var 36h NI row2-row1	1.11877	1
Var 60h I row2-row1	0.97309	0.952
Var 60h NI row2-row1	1.07258	0.904
Time course 0hI-0hNI	0.95404	0.711
Time course 12hI-12hNI	0.98053	0.847
Time course 36hI-36hNI	1.0136	0.975
Time course 60hI-60hNI	0.8251	0.026

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)	0.98482	0.789
transgenic ySAMdc/azygous control (breaker)	1.14414	0.248
transgenic ySAMdc/azygous control (red)	0.92069	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08298	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89941	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91091	1
Manapal/WT (break)	1.13393	1
Manapal/WT (red)	1.15635	0.413