Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.2.2.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13126	0.575
27DAP/17DAP	0.85909	0.611
39DAP/27DAP	1.02653	0.782
41DAP/39DAP	0.69664	0.104
42DAP/41DAP	1.13894	0.672
43DAP/42DAP	1.07127	1
47DAP/43DAP	1.25453	0.576
52DAP/47DAP	1.36732	0.451
57DAP/52DAP	1.32453	0.837

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00113	0.771
17DAP/reference	0.77176	0.017
27DAP/reference	0.99239	0.779
39DAP/reference	0.86262	0.114
41DAP/reference	0.72982	0.018
42DAP/reference	1.01741	0.812
43DAP/reference	0.9385	0.234
47DAP/reference	1.14456	0.032
52DAP/reference	1.25964	0.092
57DAP/reference	1.27533	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.38416	0.054
27DAP/17DAP	1.03481	0.943
39DAP/27DAP	1.14839	0.296
41DAP/39DAP	1.15759	0.719
42DAP/41DAP	1.01696	1
43DAP/42DAP	0.89836	0.06
47DAP/43DAP	1.08824	0.414
52DAP/47DAP	1.2565	0.424
57DAP/52DAP	1.38895	0.128
57DAP/7DAP	1.78855	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.61133	0.029
17DAP/reference	1.39995	0.03
27DAP/reference	1.07918	0.664
39DAP/reference	1.388	0.391
41DAP/reference	0.93687	0.298
42DAP/reference	1.00024	0.713
43DAP/reference	1.04352	0.802
47DAP/reference	0.96212	0.504
52DAP/reference	0.65036	0.072
57DAP/reference	1.09918	0.076

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91253	0.342
17DAP/reference	0.90805	0.26
27DAP/reference	0.9323	0.317
39DAP/reference	1.04508	1
41DAP/reference	1.16689	0.06
42DAP/reference	1.02038	0.879
43DAP/reference	0.72334	0.039
47DAP/reference	0.84987	0.021
52DAP/reference	0.86032	0.031
57DAP/reference	0.69158	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55059	0.043
17DAP/reference	1.15504	0.595
27DAP/reference	1.27186	0.057
39DAP/reference	1.13021	0.65
41DAP/reference	1.15777	0.139
42DAP/reference	1.19396	0.138
43DAP/reference	1.11162	0.326
47DAP/reference	0.93798	0.348
52DAP/reference	1.19162	0.341
57DAP/reference	1.69458	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.32487	0.075
26DAP/20DAP	0.73051	0.244
34DAP/26DAP	1.18927	1
51DAP/34DAP	1.15323	0.795
52DAP/51DAP	0.8709	1
53DAP/52DAP	1.27801	0.712
55DAP/53DAP	0.93258	0.675
57DAP/55DAP	0.82841	0.458
62DAP/57DAP	0.90428	0.466
68DAP/62DAP	1.35568	0.597
68DAP/14DAP	1.20101	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.46696	0.049

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80025	0.257
Mature Green Tomato/Ripe Tomato	1.12647	0.752
Immature Eggplant/Mature Eggplant	1.12809	0.348
Ripe Pepper/Ripe Tomato	0.5692	0.293
Mature Eggplant/Ripe Tomato	0.57664	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14098	0.536
1-1-2/M82	1.12398	1
12-2/M82	0.96549	1
12-4/M82	0.85641	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.72662	N/A
2-6/M82	1.26204	0.505
3-2/M82	0.89487	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.86366	N/A
4-3-2/M82	1.21066	N/A
4-3/M82	1.07499	1
5-3/M82	0.8456	1
6-2/M82	N/A	N/A
6-3/M82	0.68776	N/A
7-1/M82	0.57555	N/A
7-2/M82	1.23197	0.291
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95011	1
IL2-6/WTpooled	1.04075	1
IL7-5/WTpooled	0.71499	1
IL7-3/WTpooled	0.77938	0.418
IL12-4/WTpooled	1.17223	0.557
IL1-4/WTpooled	0.90157	0.562
WT/WTpooled	0.93144	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	1.19994	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93013	1
DC3000/delta hrp 6h	1.09606	1
DC3000/delta hrp 12h	1.00575	1
DC3000/delta hrp 24h	0.62316	0.053

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78831	0.232
DC3000 delta B/DC3000 delta AB	0.77188	0.1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0256	1
Exp 36h	0.87987	0.589
Exp 60h	0.83537	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03066	1
Var 0h	1.79982	0.936
Var 12h I row2-row1	0.8646	0.514
Var 12h NI row2-row1	0.95314	0.82
Var 36h I row2-row1	1.08686	1
Var 36h NI row2-row1	1.41401	0.482
Var 60h I row2-row1	1.40052	0.562
Var 60h NI row2-row1	1.10362	0.904
Time course 0hI-0hNI	0.91303	0.339
Time course 12hI-12hNI	0.94597	0.551
Time course 36hI-36hNI	0.81545	0.023
Time course 60hI-60hNI	0.19468	0.005

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)	1.06881	0.455
transgenic ySAMdc/azygous control (breaker)	0.79202	0.173
transgenic ySAMdc/azygous control (red)	0.97813	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.24558	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96278	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.7407	0.084
Manapal/WT (break)	1.96683	0.13
Manapal/WT (red)	1.75288	0.142