Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.14.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15912	0.755
27DAP/17DAP	1.18697	0.793
39DAP/27DAP	0.93965	0.641
41DAP/39DAP	1.21808	0.676
42DAP/41DAP	0.97049	1
43DAP/42DAP	1.03403	1
47DAP/43DAP	1.20372	0.633
52DAP/47DAP	1.17127	0.837
57DAP/52DAP	1.02699	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96197	0.371
17DAP/reference	1.03965	0.239
27DAP/reference	0.98393	0.428
39DAP/reference	1.00463	0.857
41DAP/reference	1.0634	0.093
42DAP/reference	0.98501	0.372
43DAP/reference	0.9816	0.675
47DAP/reference	1.00846	1
52DAP/reference	0.89271	0.195
57DAP/reference	1.08399	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88162	0.595
27DAP/17DAP	1.04681	0.909
39DAP/27DAP	1.22378	0.262
41DAP/39DAP	0.97951	0.973
42DAP/41DAP	1.02513	1
43DAP/42DAP	1.15368	0.25
47DAP/43DAP	0.97431	0.823
52DAP/47DAP	0.9368	0.565
57DAP/52DAP	0.90887	0.168
57DAP/7DAP	0.96737	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90503	0.146
17DAP/reference	0.92567	0.013
27DAP/reference	0.89811	0.01
39DAP/reference	0.92281	0.014
41DAP/reference	0.93855	0.064
42DAP/reference	0.95183	0.03
43DAP/reference	0.92594	0.022
47DAP/reference	0.91355	0.101
52DAP/reference	0.96237	0.213
57DAP/reference	0.92288	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96487	0.518
17DAP/reference	0.94184	0.08
27DAP/reference	0.9118	0.22
39DAP/reference	0.90665	0.119
41DAP/reference	0.87857	0.141
42DAP/reference	0.88461	0.032
43DAP/reference	0.9184	0.152
47DAP/reference	0.94073	0.048
52DAP/reference	0.9574	0.28
57DAP/reference	1.05676	0.423

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97655	0.335
17DAP/reference	0.95941	0.55
27DAP/reference	0.93558	0.076
39DAP/reference	1.02132	0.65
41DAP/reference	0.92243	0.293
42DAP/reference	0.84648	0.071
43DAP/reference	0.88126	0.106
47DAP/reference	0.94409	0.348
52DAP/reference	0.89844	0.289
57DAP/reference	0.76032	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02386	0.966
26DAP/20DAP	0.87544	0.512
34DAP/26DAP	1.10043	0.819
51DAP/34DAP	1.01125	1
52DAP/51DAP	0.91569	1
53DAP/52DAP	1.09441	0.413
55DAP/53DAP	1.04485	0.781
57DAP/55DAP	1.00925	0.97
62DAP/57DAP	0.98727	0.994
68DAP/62DAP	1.08595	0.85
68DAP/14DAP	1.02636	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9821	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.66478	0.066
Immature Eggplant/Mature Eggplant	1.50372	0.528
Ripe Pepper/Ripe Tomato	0.64703	0.293
Mature Eggplant/Ripe Tomato	0.82292	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9146	0.944
1-1-2/M82	0.85873	0.958
12-2/M82	1.03765	1
12-4/M82	0.98252	1
1-3/M82	0.86516	0.378
2-1-1/M82	1.11561	0.764
2-1/M82	1.32517
2-6/M82	0.91049	0.501
3-2/M82	0.94128	0.752
4-1-1/M82	1.06953	1
4-1/M82	0.84859	1
4-3-2/M82	1.01562	1
4-3/M82	0.9562	0.292
5-3/M82	0.94867	1
6-2/M82	1.03145	1
6-3/M82	1.01772	1
7-1/M82	0.88955
7-2/M82	0.90521	0.578
9-3-2/M82	0.87976

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.53853	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.89047	1
IL12-4/WTpooled	1.06108	1
IL1-4/WTpooled	0.96449	1
WT/WTpooled	1.0373	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	1.05618

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99246	1
DC3000/delta hrp 6h	1.26371	1
DC3000/delta hrp 12h	0.98255	1
DC3000/delta hrp 24h	1.08906	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.43938	0.384
DC3000 delta B/DC3000 delta AB	1.03686	0.544

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94079	1
Exp 36h	6.85217	0.693
Exp 60h	1.01999	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98027	1
Var 0h	0.81954	0.933
Var 12h I row2-row1	1.0764	0.254
Var 12h NI row2-row1	0.88739	0.627
Var 36h I row2-row1	1.00039	1
Var 36h NI row2-row1	1.02551	1
Var 60h I row2-row1	1.19693	0.562
Var 60h NI row2-row1	1.21369	0.904
Time course 0hI-0hNI	1.049	0.852
Time course 12hI-12hNI	1.00422	1
Time course 36hI-36hNI	0.98753	0.632
Time course 60hI-60hNI	1.03405	0.575

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)	0.96988	0.789
transgenic ySAMdc/azygous control (breaker)	1.53465	0.248
transgenic ySAMdc/azygous control (red)	1.14468	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95558	0.133

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30442	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92216	1
Manapal/WT (break)	0.80275	0.333
Manapal/WT (red)	0.94761	0.607