Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.8.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04375	0.977
27DAP/17DAP	0.76814	0.276
39DAP/27DAP	1.22545	0.876
41DAP/39DAP	1.2443	0.545
42DAP/41DAP	1.18107	0.802
43DAP/42DAP	1.03212	1
47DAP/43DAP	0.92828	0.724
52DAP/47DAP	1.24438	0.596
57DAP/52DAP	0.77064	0.431

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42161	0.32
17DAP/reference	1.11277	0.104
27DAP/reference	1.40485	0.073
39DAP/reference	1.10162	0.593
41DAP/reference	1.73793	0.221
42DAP/reference	1.13099	0.276
43DAP/reference	1.02164	0.928
47DAP/reference	1.13785	0.254
52DAP/reference	1.01637	0.689
57DAP/reference	0.91889	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2488	0.34
27DAP/17DAP	0.91487	0.446
39DAP/27DAP	0.94796	0.66
41DAP/39DAP	1.11002	0.276
42DAP/41DAP	0.99856	0.887
43DAP/42DAP	1.05281	0.478
47DAP/43DAP	1.00519	0.973
52DAP/47DAP	1.08604	0.776
57DAP/52DAP	0.91887	0.494
57DAP/7DAP	0.87309	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85218	0.224
17DAP/reference	0.82296	0.124
27DAP/reference	0.78227	0.014
39DAP/reference	1.08672	1
41DAP/reference	1.1522	0.445
42DAP/reference	1.09473	0.686
43DAP/reference	0.93925	0.241
47DAP/reference	1.09167	0.837
52DAP/reference	1.17815	0.352
57DAP/reference	0.99712	0.67

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53252	0.005
17DAP/reference	1.2881	0.367
27DAP/reference	0.92054	0.519
39DAP/reference	1.03835	1
41DAP/reference	0.99301	0.683
42DAP/reference	0.99719	0.723
43DAP/reference	0.85195	0.385
47DAP/reference	1.02534	0.994
52DAP/reference	1.28842	0.343
57DAP/reference	0.89299	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84576	0.197
17DAP/reference	0.82007	0.571
27DAP/reference	N/A	N/A
39DAP/reference	0.87879	0.299
41DAP/reference	1.40551	0.019
42DAP/reference	1.31366	0.34
43DAP/reference	1.05796	0.738
47DAP/reference	1.25051	0.562
52DAP/reference	1.13896	0.89
57DAP/reference	0.68743	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18438	0.021
26DAP/20DAP	1.02206	1
34DAP/26DAP	0.90218	0.777
51DAP/34DAP	1.20703	0.118
52DAP/51DAP	0.91799	1
53DAP/52DAP	0.92126	0.587
55DAP/53DAP	1.00986	0.925
57DAP/55DAP	1.34543	0.324
62DAP/57DAP	0.91749	0.681
68DAP/62DAP	0.82195	0.429
68DAP/14DAP	0.73496

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.88876	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.96086	0.66
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	2.56773
12-2/M82	N/A	N/A
12-4/M82	1.64926
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	1.69968
4-3-2/M82	0.7492
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.92229
7-2/M82	N/A	N/A
9-3-2/M82	1.36312	1

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	0.8943
IL12-4/WTpooled	0.91575	1
IL1-4/WTpooled	1.13021
WT/WTpooled	1.21012	0.87

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	0.9702	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.98391	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	1.07351	1
DC3000 delta B/DC3000 delta AB	0.82811	0.04

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	1.03416	1
Var 0h	0.42531	1
Var 12h I row2-row1	0.9089	0.418
Var 12h NI row2-row1	0.98764	1
Var 36h I row2-row1	0.97503	0.805
Var 36h NI row2-row1	1.17165	1
Var 60h I row2-row1	0.98825	0.952
Var 60h NI row2-row1	0.98671	1
Time course 0hI-0hNI	1.01879	1
Time course 12hI-12hNI	0.99076	0.978
Time course 36hI-36hNI	0.96828	0.284
Time course 60hI-60hNI	0.60498	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.86804	1
transgenic ySAMdc/azygous control (red)	0.78174	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.54684	0.026

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15417	1

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)	0.88372	1
Manapal/WT (red)	1.95134	1