Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.10.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0388	0.947
27DAP/17DAP	0.88407	0.72
39DAP/27DAP	1.40417	0.299
41DAP/39DAP	0.77502	0.233
42DAP/41DAP	1.17861	0.941
43DAP/42DAP	1.12407	1
47DAP/43DAP	0.93806	0.768
52DAP/47DAP	0.89279	0.662
57DAP/52DAP	1.36011	0.648

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04303	1
17DAP/reference	0.68666	0.021
27DAP/reference	0.54513	0.011
39DAP/reference	0.66955	0.031
41DAP/reference	0.47392	0.008
42DAP/reference	0.93872	0.176
43DAP/reference	0.82435	0.039
47DAP/reference	1.00884	0.636
52DAP/reference	0.65783	0.022
57DAP/reference	0.83191	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05848	0.736
27DAP/17DAP	1.11703	0.645
39DAP/27DAP	0.84646	0.05
41DAP/39DAP	1.13325	0.883
42DAP/41DAP	1.09387	0.783
43DAP/42DAP	0.85449	0.026
47DAP/43DAP	0.98514	0.928
52DAP/47DAP	0.82853	0.103
57DAP/52DAP	0.92005	0.577
57DAP/7DAP	0.77038	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97371	0.55
17DAP/reference	0.87794	0.144
27DAP/reference	0.99299	0.614
39DAP/reference	0.66465	0.011
41DAP/reference	0.73844	0.029
42DAP/reference	0.77923	0.013
43DAP/reference	0.76922	0.026
47DAP/reference	0.95503	0.671
52DAP/reference	0.62408	0.012
57DAP/reference	0.5446	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87787	0.182
17DAP/reference	0.63758	0.003
27DAP/reference	0.95981	0.467
39DAP/reference	0.68449	0.009
41DAP/reference	0.7525	0.007
42DAP/reference	0.9062	0.15
43DAP/reference	0.69595	0.029
47DAP/reference	1.40892	0.282
52DAP/reference	0.5318	0.003
57DAP/reference	0.79629	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13534	0.493
17DAP/reference	0.84771	0.205
27DAP/reference	0.88016	0.069
39DAP/reference	0.87294	0.028
41DAP/reference	0.75508	0.032
42DAP/reference	0.71146	0.028
43DAP/reference	0.79484	0.032
47DAP/reference	0.83476	0.052
52DAP/reference	1.03417	1
57DAP/reference	0.92239	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98885	1
26DAP/20DAP	1.02919	1
34DAP/26DAP	1.05754	1
51DAP/34DAP	0.80023	0.482
52DAP/51DAP	0.90032	1
53DAP/52DAP	0.99574	0.998
55DAP/53DAP	1.44489	0.208
57DAP/55DAP	0.96965	0.819
62DAP/57DAP	0.94379	0.871
68DAP/62DAP	1.38488	0.657
68DAP/14DAP	1.1828	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.64297	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.17431	0.054
Mature Green Tomato/Ripe Tomato	1.2735	0.119
Immature Eggplant/Mature Eggplant	8.43864	0.05
Ripe Pepper/Ripe Tomato	1.37153	1
Mature Eggplant/Ripe Tomato	0.46932	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11089
1-1-2/M82	1.14641	1
12-2/M82	0.92657	0.955
12-4/M82	1.18688	1
1-3/M82	2.2452	1
2-1-1/M82	0.8997
2-1/M82	N/A	N/A
2-6/M82	1.82902	0.352
3-2/M82	1.00042
4-1-1/M82	1.6783	1
4-1/M82	N/A	N/A
4-3-2/M82	1.47394
4-3/M82	2.20299	0.268
5-3/M82	0.70989	0.447
6-2/M82	2.64927
6-3/M82	0.53571
7-1/M82	1.04111
7-2/M82	2.55864	0.302
9-3-2/M82	1.55357

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	7.42288
IL12-4/WTpooled	1.67336
IL1-4/WTpooled	1.06834	1
WT/WTpooled	1.66686

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	1.01229	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97125	1
DC3000/delta hrp 6h	0.90575	0.95
DC3000/delta hrp 12h	1.00973	1
DC3000/delta hrp 24h	0.69939	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.7652	0.048
DC3000 delta B/DC3000 delta AB	0.72463	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08603	1
Exp 36h	1.90252	0.693
Exp 60h	1.33919	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00021	1
Var 0h	0.99952	1
Var 12h I row2-row1	0.91331	0.39
Var 12h NI row2-row1	0.9968	1
Var 36h I row2-row1	1.27558	0.41
Var 36h NI row2-row1	0.97567	0.852
Var 60h I row2-row1	0.97772	0.952
Var 60h NI row2-row1	0.89765	0.818
Time course 0hI-0hNI	1.00684	1
Time course 12hI-12hNI	0.99987	1
Time course 36hI-36hNI	1.17267	0.114
Time course 60hI-60hNI	0.80525	0.161

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)	0.69953	0.229
transgenic ySAMdc/azygous control (breaker)	0.4425	0.137
transgenic ySAMdc/azygous control (red)	0.84088	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.77635	0.196

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66102	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.26397	0.096
Manapal/WT (break)	1.68968	0.13
Manapal/WT (red)	2.23023	0.222