Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.7.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76749	0.178
27DAP/17DAP	1.35261	0.742
39DAP/27DAP	0.76762	0.443
41DAP/39DAP	0.68224	0.258
42DAP/41DAP	0.72004	0.774
43DAP/42DAP	1.16203	1
47DAP/43DAP	1.19157	0.584
52DAP/47DAP	6.00622	0.401
57DAP/52DAP	1.44538	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97815	0.562
17DAP/reference	1.06991	0.031
27DAP/reference	0.98195	0.595
39DAP/reference	0.9891	0.828
41DAP/reference	1.09551	0.287
42DAP/reference	0.9063	0.001
43DAP/reference	1.00634	1
47DAP/reference	0.94938	0.116
52DAP/reference	0.85671	0.121
57DAP/reference	0.82292	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01547	0.801
27DAP/17DAP	1.04897	0.928
39DAP/27DAP	1.14764	0.553
41DAP/39DAP	0.90856	0.599
42DAP/41DAP	0.86858	0.365
43DAP/42DAP	1.20476	0.297
47DAP/43DAP	0.99526	0.985
52DAP/47DAP	1.01521	0.962
57DAP/52DAP	1.0844	0.813
57DAP/7DAP	1.76375	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8946	0.224
17DAP/reference	0.77501	0.094
27DAP/reference	0.82234	0.031
39DAP/reference	0.95736	0.474
41DAP/reference	0.62121	0.026
42DAP/reference	0.95074	0.458
43DAP/reference	0.93877	0.334
47DAP/reference	0.87489	0.128
52DAP/reference	0.85958	0.106
57DAP/reference	1.0494	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04372	0.842
17DAP/reference	1.0371	0.396
27DAP/reference	0.90647	0.22
39DAP/reference	0.87955	0.11
41DAP/reference	0.82155	0.08
42DAP/reference	0.86553	0.016
43DAP/reference	1.07861	0.681
47DAP/reference	0.90161	0.01
52DAP/reference	1.02947	0.596
57DAP/reference	1.1621	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92898	0.422
17DAP/reference	0.9799	0.668
27DAP/reference	1.00006	0.763
39DAP/reference	0.98056	0.591
41DAP/reference	0.93043	0.459
42DAP/reference	1.07066	0.816
43DAP/reference	0.78048	0.066
47DAP/reference	0.94138	0.371
52DAP/reference	0.82235	0.376
57DAP/reference	0.55184	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04552	0.966
26DAP/20DAP	2.17614
34DAP/26DAP	1.25113	1
51DAP/34DAP	1.47938	0.042
52DAP/51DAP	1.11867	0.77
53DAP/52DAP	0.81242	0.52
55DAP/53DAP	0.80943	0.273
57DAP/55DAP	1.03433	0.851
62DAP/57DAP	1.00646	1
68DAP/62DAP	0.9238	0.7
68DAP/14DAP	1.00013	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.58395	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.16115
Mature Green Tomato/Ripe Tomato	1.16109
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.04136
Mature Eggplant/Ripe Tomato	1.70999

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.96613
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.04016	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	1.29359
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94087	1
IL7-5/WTpooled	1.06146	0.792
IL7-3/WTpooled	0.95133	1
IL12-4/WTpooled	0.67759	0.566
IL1-4/WTpooled	1.02222	1
WT/WTpooled	1.01504	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.63985
DC3000/delta hrp 6h	0.45537
DC3000/delta hrp 12h	0.96197	1
DC3000/delta hrp 24h	N/A	N/A

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	0.93749	0.589
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	1.0731	1
Var 0h	0.48066
Var 12h I row2-row1	0.94	0.565
Var 12h NI row2-row1	1.03478	0.161
Var 36h I row2-row1	0.987	1
Var 36h NI row2-row1	0.97719	0.852
Var 60h I row2-row1	1.05484	0.543
Var 60h NI row2-row1	0.74969	0.586
Time course 0hI-0hNI	0.84734	0.866
Time course 12hI-12hNI	0.92506	0.201
Time course 36hI-36hNI	0.843	0.028
Time course 60hI-60hNI	0.67311	0.007

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)	1.06488	0.511
transgenic ySAMdc/azygous control (breaker)	0.98079	1
transgenic ySAMdc/azygous control (red)	1.09908	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01673	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24664	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95882	1
Manapal/WT (break)	0.86922	0.333
Manapal/WT (red)	1.20411	0.413