Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.5.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67125	0.023
27DAP/17DAP	0.80699	0.424
39DAP/27DAP	1.24026	0.397
41DAP/39DAP	0.85852	0.459
42DAP/41DAP	1.06379	0.992
43DAP/42DAP	1.28428	0.417
47DAP/43DAP	0.75662	0.239
52DAP/47DAP	1.1851	0.671
57DAP/52DAP	1.08669	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.02964	0.006
17DAP/reference	1.25264	0.178
27DAP/reference	1.01303	0.923
39DAP/reference	1.04869	0.722
41DAP/reference	1.04309	0.451
42DAP/reference	1.06602	0.311
43DAP/reference	1.15924	0.028
47DAP/reference	1.05108	0.685
52DAP/reference	0.67223	0.027
57DAP/reference	0.90386	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81269	0.062
27DAP/17DAP	0.99111	0.943
39DAP/27DAP	0.86767	0.105
41DAP/39DAP	1.14764	0.565
42DAP/41DAP	1.02929	1
43DAP/42DAP	0.98687	0.854
47DAP/43DAP	0.87505	0.225
52DAP/47DAP	1.05899	0.799
57DAP/52DAP	1.05336	0.992
57DAP/7DAP	0.5545	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49452	0.037
17DAP/reference	1.0708	0.18
27DAP/reference	0.91656	0.051
39DAP/reference	0.9316	0.17
41DAP/reference	0.80857	0.033
42DAP/reference	0.78224	0.012
43DAP/reference	0.78003	0.016
47DAP/reference	1.00227	1
52DAP/reference	0.70826	0.011
57DAP/reference	0.75367	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.79658	0.038
17DAP/reference	1.87569	0.007
27DAP/reference	1.50831	0.016
39DAP/reference	1.05116	1
41DAP/reference	1.13592	0.215
42DAP/reference	1.09208	0.369
43DAP/reference	1.25261	0.09
47DAP/reference	1.16567	0.081
52DAP/reference	1.00779	0.713
57DAP/reference	0.93993	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27202	0.015
17DAP/reference	1.18382	0.145
27DAP/reference	0.82801	0.034
39DAP/reference	0.88065	0.083
41DAP/reference	0.89005	0.058
42DAP/reference	0.99062	0.816
43DAP/reference	0.96506	0.523
47DAP/reference	0.9286	0.296
52DAP/reference	0.96107	0.611
57DAP/reference	0.91439	0.283

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07372	1
26DAP/20DAP	1.12238	0.85
34DAP/26DAP	0.96514	0.936
51DAP/34DAP	1.01035	0.96
52DAP/51DAP	0.81683	1
53DAP/52DAP	0.96518	0.824
55DAP/53DAP	0.93804	0.686
57DAP/55DAP	1.4244	0.074
62DAP/57DAP	1.0908	0.902
68DAP/62DAP	0.89069	0.7
68DAP/14DAP	0.85929	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.31037	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.22736	0.063
Mature Green Tomato/Ripe Tomato	1.63319	0.015
Immature Eggplant/Mature Eggplant	0.66708	0.063
Ripe Pepper/Ripe Tomato	0.45236	0.224
Mature Eggplant/Ripe Tomato	0.88681	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.6323	0.503
1-1-2/M82	1.1228
12-2/M82	0.97274	1
12-4/M82	1.09904	1
1-3/M82	1.51051
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	1.07977	0.967
4-1-1/M82	0.83086
4-1/M82	1.28058	1
4-3-2/M82	1.11533	1
4-3/M82	N/A	N/A
5-3/M82	0.95693	1
6-2/M82	N/A	N/A
6-3/M82	1.02463	1
7-1/M82	1.05793	0.598
7-2/M82	1.04617
9-3-2/M82	1.00477	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84746	0.321
IL2-6/WTpooled	0.92732	1
IL7-5/WTpooled	0.86088	1
IL7-3/WTpooled	0.79826	0.298
IL12-4/WTpooled	0.75076	0.554
IL1-4/WTpooled	0.9319	0.834
WT/WTpooled	0.89586	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	1.00613	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0387	0.921
DC3000/delta hrp 6h	1.06811	1
DC3000/delta hrp 12h	0.7861	1
DC3000/delta hrp 24h	2.51902	0.271

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86991
DC3000 delta B/DC3000 delta AB	1.04184	0.579

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95127	1
Exp 36h	N/A	N/A
Exp 60h	0.98886	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03959	1
Var 0h	0.83052	1
Var 12h I row2-row1	1.04962	1
Var 12h NI row2-row1	1.00702	1
Var 36h I row2-row1	1.34607	1
Var 36h NI row2-row1	1.08281	1
Var 60h I row2-row1	1.11138	0.562
Var 60h NI row2-row1	1.15143	1
Time course 0hI-0hNI	1.04001	0.852
Time course 12hI-12hNI	0.98071	0.87
Time course 36hI-36hNI	0.78252	0.102
Time course 60hI-60hNI	0.49393	0.006

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)	1.00043	1
transgenic ySAMdc/azygous control (breaker)	0.70014	0.118
transgenic ySAMdc/azygous control (red)	0.95693	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03359	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68786	0.172
Manapal/WT (break)	0.76036	0.236
Manapal/WT (red)	0.95871	0.607