Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.5.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15989	0.904
27DAP/17DAP	0.89477	0.763
39DAP/27DAP	1.00683	0.769
41DAP/39DAP	1.21784	0.921
42DAP/41DAP	1.08778	0.983
43DAP/42DAP	0.95382	0.877
47DAP/43DAP	0.80101	0.402
52DAP/47DAP	1.01043	0.95
57DAP/52DAP	1.22583	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60214	0.03
17DAP/reference	0.56853	0.007
27DAP/reference	0.70586	0.027
39DAP/reference	0.71027	0.044
41DAP/reference	0.60144	0.01
42DAP/reference	0.71428	0.003
43DAP/reference	0.68481	0.014
47DAP/reference	0.7654	0.013
52DAP/reference	0.73646	0.047
57DAP/reference	0.86631	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87778	0.388
27DAP/17DAP	1.17238	0.465
39DAP/27DAP	0.91691	0.462
41DAP/39DAP	0.8898	0.729
42DAP/41DAP	1.06055	0.879
43DAP/42DAP	0.89405	0.431
47DAP/43DAP	1.24028	0.805
52DAP/47DAP	1.10471	0.718
57DAP/52DAP	1.35511	0.251
57DAP/7DAP	0.77329

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78231	0.078
17DAP/reference	0.8146	0.072
27DAP/reference	0.92631	0.248
39DAP/reference	0.86749	0.073
41DAP/reference	0.66243	0.016
42DAP/reference	0.85438	0.117
43DAP/reference	0.72971	0.026
47DAP/reference	0.66847	0.044
52DAP/reference	0.83922	0.083
57DAP/reference	0.85718	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75268	0.046
17DAP/reference	0.63433	0.005
27DAP/reference	0.73442	0.014
39DAP/reference	0.61264	0.015
41DAP/reference	0.79388	0.1
42DAP/reference	0.67488	0.013
43DAP/reference	0.75407	0.051
47DAP/reference	0.67889	0.012
52DAP/reference	0.70239	0.005
57DAP/reference	0.57564	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76732	0.061
17DAP/reference	0.88148	0.407
27DAP/reference	0.7356	0.062
39DAP/reference	0.82236	0.163
41DAP/reference	0.89001	0.132
42DAP/reference	0.88427	0.108
43DAP/reference	0.82242	0.102
47DAP/reference	0.54214	0.009
52DAP/reference	1.34304	0.759
57DAP/reference	0.94342	0.402

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.58338	0.915
26DAP/20DAP	0.7871	1
34DAP/26DAP	1.00404	1
51DAP/34DAP	0.86627
52DAP/51DAP	1.48636	0.121
53DAP/52DAP	0.75702	0.186
55DAP/53DAP	1.67533	0.157
57DAP/55DAP	1.53357	0.584
62DAP/57DAP	0.93506	0.871
68DAP/62DAP	0.96276	0.863
68DAP/14DAP	1.1612	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98487	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.50464	0.185
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

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	0.98477
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	1.3387
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	1.3491
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.91592
IL12-4/WTpooled	0.68947
IL1-4/WTpooled	0.99978	1
WT/WTpooled	0.60969

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	0.94966	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97957	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.84062	1
DC3000/delta hrp 24h	2.28561	0.029

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.40686	0.053
DC3000 delta B/DC3000 delta AB	1.32675	0.282

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0523	1
Var 0h	0.80182	1
Var 12h I row2-row1	0.89704	0.467
Var 12h NI row2-row1	1.14624	0.281
Var 36h I row2-row1	0.90075	0.291
Var 36h NI row2-row1	0.85774	0.522
Var 60h I row2-row1	0.9463	0.285
Var 60h NI row2-row1	1.21731	0.904
Time course 0hI-0hNI	0.96615	0.861
Time course 12hI-12hNI	1.06257	0.672
Time course 36hI-36hNI	1.14132	0.028
Time course 60hI-60hNI	0.9952	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)	1.2431	0.921
transgenic ySAMdc/azygous control (breaker)	1.22647	1
transgenic ySAMdc/azygous control (red)	1.37415	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97208	0.186

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.54297	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.44956	1
Manapal/WT (red)	1.15618	1