Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.6.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98953	0.83
27DAP/17DAP	1.04081	1
39DAP/27DAP	1.03361	0.749
41DAP/39DAP	1.22048	0.459
42DAP/41DAP	1.29717	0.477
43DAP/42DAP	1.30398	0.755
47DAP/43DAP	1.20683	0.825
52DAP/47DAP	0.96203	0.861
57DAP/52DAP	0.97005	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88533	0.217
17DAP/reference	0.94216	0.368
27DAP/reference	0.95572	0.538
39DAP/reference	0.92709	0.315
41DAP/reference	0.96154	0.667
42DAP/reference	0.87737	0.095
43DAP/reference	1.12757	0.053
47DAP/reference	0.93006	0.174
52DAP/reference	1.12972	0.256
57DAP/reference	1.12233	0.392

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94874	0.484
27DAP/17DAP	0.96728	0.878
39DAP/27DAP	1.11628	0.388
41DAP/39DAP	0.98285	0.997
42DAP/41DAP	0.94426	0.617
43DAP/42DAP	1.09365	0.446
47DAP/43DAP	0.97602	0.87
52DAP/47DAP	1.03733	0.868
57DAP/52DAP	1.00061	0.902
57DAP/7DAP	1.06596	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24714	0.054
17DAP/reference	0.97226	0.447
27DAP/reference	1.17411	0.551
39DAP/reference	1.17444	0.222
41DAP/reference	0.87564	0.122
42DAP/reference	0.95795	0.371
43DAP/reference	1.0376	0.746
47DAP/reference	1.00014	1
52DAP/reference	0.97945	0.523
57DAP/reference	0.986	0.53

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80288	0.019
17DAP/reference	0.79616	0.176
27DAP/reference	0.97002	0.554
39DAP/reference	0.99205	0.569
41DAP/reference	1.01519	1
42DAP/reference	0.92334	0.355
43DAP/reference	0.78895	0.02
47DAP/reference	0.88095	0.09
52DAP/reference	1.22551	0.012
57DAP/reference	0.98401	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73111	0.057
17DAP/reference	0.88033	0.308
27DAP/reference	1.13979	0.447
39DAP/reference	1.0972	0.353
41DAP/reference	1.08406	0.714
42DAP/reference	1.10404	0.979
43DAP/reference	1.10716	0.935
47DAP/reference	1.06317	0.76
52DAP/reference	0.89396	0.319
57DAP/reference	0.9195	0.326

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09538	1
26DAP/20DAP	0.86817	0.317
34DAP/26DAP	0.99133	0.98
51DAP/34DAP	0.96835	0.747
52DAP/51DAP	1.06063	0.565
53DAP/52DAP	1.00015	0.97
55DAP/53DAP	0.97591	0.775
57DAP/55DAP	1.33112	0.682
62DAP/57DAP	2.14476
68DAP/62DAP	1.07714	0.931
68DAP/14DAP	1.01165	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88974	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	6.12232	0.363
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.90563	1
Mature Eggplant/Ripe Tomato	2.22589	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95733	0.961
1-1-2/M82	1.01901	1
12-2/M82	N/A	N/A
12-4/M82	0.71988	0.33
1-3/M82	N/A	N/A
2-1-1/M82	0.94704
2-1/M82	N/A	N/A
2-6/M82	0.86618	1
3-2/M82	1.23155
4-1-1/M82	0.92888
4-1/M82	0.62553
4-3-2/M82	N/A	N/A
4-3/M82	1.04767	1
5-3/M82	1.21949	0.436
6-2/M82	N/A	N/A
6-3/M82	0.98014	1
7-1/M82	N/A	N/A
7-2/M82	1.11682	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.60528
IL2-6/WTpooled	1.20434	0.46
IL7-5/WTpooled	0.73934	1
IL7-3/WTpooled	1.12912	1
IL12-4/WTpooled	1.22057	0.52
IL1-4/WTpooled	1.00073	1
WT/WTpooled	0.9524	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	1.46865	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94528	1
DC3000/delta hrp 6h	1.40855	1
DC3000/delta hrp 12h	0.95963	1
DC3000/delta hrp 24h	0.65057	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9127	0.841
DC3000 delta B/DC3000 delta AB	1.08232	0.524

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.46451	0.693
Exp 60h	0.86188	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9849	1
Var 0h	0.85688	1
Var 12h I row2-row1	0.95964	0.77
Var 12h NI row2-row1	1.03316	1
Var 36h I row2-row1	1.15183	1
Var 36h NI row2-row1	0.9036	0.706
Var 60h I row2-row1	0.99219	1
Var 60h NI row2-row1	1.05749	1
Time course 0hI-0hNI	0.9877	0.97
Time course 12hI-12hNI	0.99002	0.968
Time course 36hI-36hNI	1.06402	0.401
Time course 60hI-60hNI	1.13799	0.053

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)	1.10124	0.699
transgenic ySAMdc/azygous control (breaker)	2.73211	0.172
transgenic ySAMdc/azygous control (red)	1.08738	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.25438	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11518	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.26818	0.105
Manapal/WT (break)	1.16894	1
Manapal/WT (red)	1.52581	1