Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.12.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09348	0.77
27DAP/17DAP	0.70133	0.204
39DAP/27DAP	0.89189	0.449
41DAP/39DAP	0.77006	0.165
42DAP/41DAP	0.91221	1
43DAP/42DAP	1.01489	1
47DAP/43DAP	0.8375	0.484
52DAP/47DAP	1.15904	0.619
57DAP/52DAP	1.00911	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12843	0.078
17DAP/reference	0.93928	0.24
27DAP/reference	0.93609	0.275
39DAP/reference	0.83722	0.051
41DAP/reference	0.8122	0.011
42DAP/reference	0.91162	0.006
43DAP/reference	0.83217	0.017
47DAP/reference	0.79838	0.001
52DAP/reference	0.79568	0.033
57DAP/reference	0.77526	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22332	0.252
27DAP/17DAP	0.94091	0.684
39DAP/27DAP	0.78226	0.029
41DAP/39DAP	0.98869	1
42DAP/41DAP	1.01809	0.976
43DAP/42DAP	0.93676	0.321
47DAP/43DAP	0.97846	0.843
52DAP/47DAP	1.00487	1
57DAP/52DAP	1.03863	0.798
57DAP/7DAP	1.00702	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.78422	0.025
17DAP/reference	1.26329	0.012
27DAP/reference	0.97012	0.43
39DAP/reference	0.90477	0.23
41DAP/reference	0.71378	0.017
42DAP/reference	0.68256	0.014
43DAP/reference	0.69345	0.016
47DAP/reference	0.60607	0.03
52DAP/reference	0.91183	0.213
57DAP/reference	0.86044	0.083

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94643	0.503
17DAP/reference	0.95707	0.41
27DAP/reference	1.2148	0.133
39DAP/reference	0.81835	0.087
41DAP/reference	1.06438	1
42DAP/reference	0.8927	0.108
43DAP/reference	0.62699	0.027
47DAP/reference	0.82144	0.01
52DAP/reference	0.70148	0.004
57DAP/reference	0.68202	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.17618	0.015
17DAP/reference	2.5368	0.151
27DAP/reference	2.316	0.016
39DAP/reference	1.87216	0.011
41DAP/reference	1.34441	0.043
42DAP/reference	0.92873	0.552
43DAP/reference	1.06173	0.646
47DAP/reference	0.71658	0.005
52DAP/reference	0.77693	0.119
57DAP/reference	1.48534	0.2

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03015	0.966
26DAP/20DAP	1.01143	1
34DAP/26DAP	0.93402	0.479
51DAP/34DAP	1.00403	0.988
52DAP/51DAP	1.01486	0.848
53DAP/52DAP	1.03468
55DAP/53DAP	0.84344	0.632
57DAP/55DAP	1.0208	0.818
62DAP/57DAP	1.05685	0.622
68DAP/62DAP	1.17428	0.792
68DAP/14DAP	0.9861	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09202	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.38761	0.058
Mature Green Tomato/Ripe Tomato	4.1372	0.021
Immature Eggplant/Mature Eggplant	0.79598	0.066
Ripe Pepper/Ripe Tomato	6.1506	1
Mature Eggplant/Ripe Tomato	12.2022	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98188	0.961
1-1-2/M82	0.9101	1
12-2/M82	1.15296	1
12-4/M82	0.92841	1
1-3/M82	1.03511	1
2-1-1/M82	1.06349	0.764
2-1/M82	0.93384
2-6/M82	1.02194	0.452
3-2/M82	0.99486	1
4-1-1/M82	1.13342	1
4-1/M82	1.08603	0.853
4-3-2/M82	0.94301	1
4-3/M82	1.01336	1
5-3/M82	1.07483	1
6-2/M82	0.9527	1
6-3/M82	1.06263	1
7-1/M82	1.01491	1
7-2/M82	0.98131	1
9-3-2/M82	0.91305	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84049	0.321
IL2-6/WTpooled	1.2289	0.788
IL7-5/WTpooled	1.32457	0.792
IL7-3/WTpooled	0.44121	0.294
IL12-4/WTpooled	0.94478	1
IL1-4/WTpooled	0.97284	1
WT/WTpooled	1.04685	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	1.08443	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98044	1
DC3000/delta hrp 6h	1.00419	1
DC3000/delta hrp 12h	1.09985
DC3000/delta hrp 24h	0.95739	0.682

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98158	0.955
DC3000 delta B/DC3000 delta AB	0.64509	0.04

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01451	1
Exp 36h	0.98369	1
Exp 60h	1.12026	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03091	1
Var 0h	1.23686	0.339
Var 12h I row2-row1	0.95713	0.467
Var 12h NI row2-row1	1.02819	0.649
Var 36h I row2-row1	0.94182	1
Var 36h NI row2-row1	1.19755	1
Var 60h I row2-row1	2.62171
Var 60h NI row2-row1	0.95904	1
Time course 0hI-0hNI	0.99445	1
Time course 12hI-12hNI	1.03974	0.779
Time course 36hI-36hNI	1.04913	0.355
Time course 60hI-60hNI	0.72418	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)	1.11308	0.699
transgenic ySAMdc/azygous control (breaker)	5.03208	0.162
transgenic ySAMdc/azygous control (red)	1.54709	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.83646	0.136

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.70871	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.65087	0.093
Manapal/WT (break)	8.91064	0.14
Manapal/WT (red)	13.2673	0.137