Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.5.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74808	0.148
27DAP/17DAP	1.69671	0.804
39DAP/27DAP	0.90508	0.631
41DAP/39DAP	0.79684	0.512
42DAP/41DAP	1.27122	0.983
43DAP/42DAP	1.07526	1
47DAP/43DAP	1.28942	0.746
52DAP/47DAP	1.16432	0.787
57DAP/52DAP	1.13914	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.45969	0.027
17DAP/reference	0.69124	0.016
27DAP/reference	0.683	0.012
39DAP/reference	0.66574	0.017
41DAP/reference	0.86654	0.267
42DAP/reference	0.58816	0.003
43DAP/reference	0.70502	0.025
47DAP/reference	0.65061	0.004
52DAP/reference	0.52133	0.012
57DAP/reference	0.70272	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47173	0.036
27DAP/17DAP	0.91765	0.446
39DAP/27DAP	0.8542	0.35
41DAP/39DAP	1.05344	0.895
42DAP/41DAP	0.97824	0.715
43DAP/42DAP	0.93481	0.415
47DAP/43DAP	0.8388	0.41
52DAP/47DAP	2.00167	0.048
57DAP/52DAP	1.7983	0.094
57DAP/7DAP	1.30033	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6182	0.066
17DAP/reference	0.59421	0.012
27DAP/reference	0.77781	0.015
39DAP/reference	0.55735	0.011
41DAP/reference	0.50129	0.009
42DAP/reference	0.57884	0.01
43DAP/reference	0.42399	0.01
47DAP/reference	0.38278	0.03
52DAP/reference	0.47184	0.012
57DAP/reference	0.37884	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62596	0.053
17DAP/reference	0.56111	0.028
27DAP/reference	0.67075	0.087
39DAP/reference	0.65901	0.102
41DAP/reference	0.85909	0.124
42DAP/reference	0.82474	0.15
43DAP/reference	0.82059	0.043
47DAP/reference	0.55576	0.016
52DAP/reference	0.4884	0.008
57DAP/reference	0.59832	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66343	0.048
17DAP/reference	0.58816	0.103
27DAP/reference	0.46662	0.024
39DAP/reference	0.45325	0.013
41DAP/reference	0.59172	0.018
42DAP/reference	0.56515	0.015
43DAP/reference	0.52956	0.031
47DAP/reference	0.28961	0.004
52DAP/reference	0.72631	0.211
57DAP/reference	0.43215	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.75296
26DAP/20DAP	3.50894	0.62
34DAP/26DAP	2.98837	1
51DAP/34DAP	1.46541	0.936
52DAP/51DAP	2.7864	0.036
53DAP/52DAP	0.7377	0.128
55DAP/53DAP	1.22015	0.076
57DAP/55DAP	0.28028	0.019
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.53415	0.429
68DAP/14DAP	0.50516

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.38282	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.86237
Mature Eggplant/Ripe Tomato	0.52166	0.234

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	N/A	N/A
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	1.26554
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.95505
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.0262	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.87331
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09085	1
IL2-6/WTpooled	1.08116	0.395
IL7-5/WTpooled	3.02153
IL7-3/WTpooled	1.24463	1
IL12-4/WTpooled	0.80542	0.581
IL1-4/WTpooled	0.9835	1
WT/WTpooled	0.83877	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	0.79405	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95896	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.01255	1
DC3000/delta hrp 24h	1.09504	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03994	0.355
DC3000 delta B/DC3000 delta AB	1.11785	0.55

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	1.00487	1
Var 0h	0.57143	1
Var 12h I row2-row1	0.78676	0.467
Var 12h NI row2-row1	1.05221	1
Var 36h I row2-row1	0.9148	0.805
Var 36h NI row2-row1	1.57318	0.276
Var 60h I row2-row1	0.97402	0.952
Var 60h NI row2-row1	0.84888	0.977
Time course 0hI-0hNI	0.87168	0.133
Time course 12hI-12hNI	0.90984	0.454
Time course 36hI-36hNI	0.8636	0.032
Time course 60hI-60hNI	0.48952	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)	4.79105	1
transgenic ySAMdc/azygous control (breaker)	1.70163	1
transgenic ySAMdc/azygous control (red)	1.56175	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96136	0.27

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)	N/A	N/A
Manapal/WT (break)	1.11408	1
Manapal/WT (red)	1.0851	1