Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99056	0.728
27DAP/17DAP	1.56701	0.842
39DAP/27DAP	1.02828	0.782
41DAP/39DAP	1.1673	0.715
42DAP/41DAP	1.20655	0.843
43DAP/42DAP	0.97914	0.864
47DAP/43DAP	2.34665	0.201
52DAP/47DAP	2.86758	0.02
57DAP/52DAP	0.66375	0.513

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87064	0.132
17DAP/reference	1.08533	0.092
27DAP/reference	0.98976	0.741
39DAP/reference	1.06799	0.497
41DAP/reference	1.0677	0.552
42DAP/reference	1.01731	1
43DAP/reference	1.0436	0.758
47DAP/reference	1.39325	0.017
52DAP/reference	1.3153	0.205
57DAP/reference	0.94058	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97806	0.697
27DAP/17DAP	1.21056	0.518
39DAP/27DAP	1.06227	0.611
41DAP/39DAP	1.15265	0.868
42DAP/41DAP	0.85734	0.203
43DAP/42DAP	1.23116	0.192
47DAP/43DAP	1.07122	0.939
52DAP/47DAP	3.12	0.041
57DAP/52DAP	4.4028	0.029
57DAP/7DAP	4.10741	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83745	0.095
17DAP/reference	0.72502	0.011
27DAP/reference	0.67695	0.01
39DAP/reference	0.83526	0.014
41DAP/reference	0.87901	0.086
42DAP/reference	0.861	0.09
43DAP/reference	0.71588	0.012
47DAP/reference	0.7736	0.079
52DAP/reference	0.7122	0.012
57DAP/reference	0.7701	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94057	0.487
17DAP/reference	0.93463	0.378
27DAP/reference	1.04462	0.765
39DAP/reference	0.74577	0.067
41DAP/reference	0.85844	0.13
42DAP/reference	0.93343	0.355
43DAP/reference	1.04643	0.846
47DAP/reference	1.06295	0.413
52DAP/reference	0.77031	0.06
57DAP/reference	1.11294	0.508

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81859	0.158
17DAP/reference	0.91868	0.335
27DAP/reference	0.80269	0.14
39DAP/reference	0.91205	0.328
41DAP/reference	0.7858	0.02
42DAP/reference	0.72234	0.019
43DAP/reference	0.66613	0.018
47DAP/reference	1.24389	0.055
52DAP/reference	1.15464	0.908
57DAP/reference	1.37952	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14815	0.966
26DAP/20DAP	0.8039	0.512
34DAP/26DAP	1.10713	1
51DAP/34DAP	1.19692	0.251
52DAP/51DAP	1.26357	0.123
53DAP/52DAP	1.20117	0.537
55DAP/53DAP	0.99086	0.886
57DAP/55DAP	1.0105	0.955
62DAP/57DAP	0.98154	0.871
68DAP/62DAP	0.76307	0.29
68DAP/14DAP	0.76974	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.29048	0.105

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40384	0.113
Mature Green Tomato/Ripe Tomato	0.04902	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.1152	0.224
Mature Eggplant/Ripe Tomato	0.06252	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98805	0.961
1-1-2/M82	0.93705	1
12-2/M82	1.41547	1
12-4/M82	0.9713	0.619
1-3/M82	0.78073	0.378
2-1-1/M82	1.11513	0.375
2-1/M82	N/A	N/A
2-6/M82	1.10082	0.594
3-2/M82	0.78872
4-1-1/M82	1.4369	0.968
4-1/M82	1.0959
4-3-2/M82	0.92354
4-3/M82	1.07634	1
5-3/M82	0.76283	0.642
6-2/M82	0.87407	0.481
6-3/M82	1.09028	1
7-1/M82	0.87575
7-2/M82	1.00566	1
9-3-2/M82	1.46424	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77669
IL2-6/WTpooled	1.30232	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99553	1
IL12-4/WTpooled	0.63717
IL1-4/WTpooled	1.20743	1
WT/WTpooled	1.02624	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	0.76521	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02634	0.921
DC3000/delta hrp 6h	1.76024
DC3000/delta hrp 12h	1.23481	1
DC3000/delta hrp 24h	0.96754	0.818

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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	1.12291	1
Var 0h	0.94195	1
Var 12h I row2-row1	1.11091	0.263
Var 12h NI row2-row1	0.38834	1
Var 36h I row2-row1	1.64794	1
Var 36h NI row2-row1	0.69161	0.743
Var 60h I row2-row1	1.42101	0.562
Var 60h NI row2-row1	1.35219	0.904
Time course 0hI-0hNI	1.068	0.764
Time course 12hI-12hNI	0.97009	0.86
Time course 36hI-36hNI	0.94895	0.418
Time course 60hI-60hNI	1.1098	0.359

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)	1.44106	0.261
transgenic ySAMdc/azygous control (breaker)	0.43796	0.139
transgenic ySAMdc/azygous control (red)	1.02586	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02261	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.24296	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.43825	1
Manapal/WT (break)	0.76731	1
Manapal/WT (red)	1.0746	1