Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.14.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00772	0.911
27DAP/17DAP	1.44245	0.688
39DAP/27DAP	0.84191	0.507
41DAP/39DAP	1.4096	0.282
42DAP/41DAP	1.04054	1
43DAP/42DAP	0.94845	0.892
47DAP/43DAP	0.90662	0.634
52DAP/47DAP	1.56383	0.46
57DAP/52DAP	0.91488	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8701	0.109
17DAP/reference	0.94578	0.368
27DAP/reference	0.90551	0.101
39DAP/reference	0.91327	0.051
41DAP/reference	0.89899	0.201
42DAP/reference	0.79022	0.009
43DAP/reference	1.02057	0.812
47DAP/reference	0.82661	0.003
52DAP/reference	0.88861	0.258
57DAP/reference	0.97353	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91166	0.428
27DAP/17DAP	1.09367	0.822
39DAP/27DAP	1.08884	0.541
41DAP/39DAP	1.05926	0.914
42DAP/41DAP	0.98876	0.819
43DAP/42DAP	1.08531	0.297
47DAP/43DAP	1.02801	0.934
52DAP/47DAP	1.03727	0.862
57DAP/52DAP	1.04748	0.763
57DAP/7DAP	1.26096	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91456	0.074
17DAP/reference	0.85701	0.025
27DAP/reference	0.88221	0.01
39DAP/reference	0.89138	0.018
41DAP/reference	0.89681	0.082
42DAP/reference	0.8666	0.024
43DAP/reference	0.78757	0.022
47DAP/reference	1.03005	1
52DAP/reference	0.8715	0.017
57DAP/reference	0.79334	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80645	0.105
17DAP/reference	0.69558	0.012
27DAP/reference	0.79453	0.044
39DAP/reference	0.87912	0.091
41DAP/reference	0.97166	0.422
42DAP/reference	0.98924	0.594
43DAP/reference	0.79851	0.114
47DAP/reference	0.92306	0.208
52DAP/reference	0.87032	0.018
57DAP/reference	0.72999	0.02

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80244	0.044
17DAP/reference	0.93605	0.335
27DAP/reference	0.91317	0.155
39DAP/reference	0.7906	0.008
41DAP/reference	0.89563	0.04
42DAP/reference	0.86395	0.134
43DAP/reference	0.8019	0.042
47DAP/reference	1.03607	1
52DAP/reference	0.82937	0.139
57DAP/reference	1.18181	0.452

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86099	0.672
26DAP/20DAP	0.92235	0.512
34DAP/26DAP	1.03908	1
51DAP/34DAP	0.96494	0.722
52DAP/51DAP	0.9542	1
53DAP/52DAP	1.19967	0.319
55DAP/53DAP	0.90977	0.293
57DAP/55DAP	1.13243	0.927
62DAP/57DAP	1.2908	0.569
68DAP/62DAP	1.24077	0.89
68DAP/14DAP	0.86929	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93274	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.95551	0.569
Immature Eggplant/Mature Eggplant	1.71947
Ripe Pepper/Ripe Tomato	0.4312	0.293
Mature Eggplant/Ripe Tomato	0.43614	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91003	0.944
1-1-2/M82	0.95773	1
12-2/M82	1.28777	0.2
12-4/M82	1.14168	1
1-3/M82	0.89134	0.501
2-1-1/M82	1.32157	0.764
2-1/M82	N/A	N/A
2-6/M82	1.1084	1
3-2/M82	0.85334	0.455
4-1-1/M82	1.04362	1
4-1/M82	0.83379	1
4-3-2/M82	0.76915	0.698
4-3/M82	0.74042	1
5-3/M82	0.96492	1
6-2/M82	1.04078
6-3/M82	0.99405	1
7-1/M82	0.95622	0.509
7-2/M82	1.1477	0.385
9-3-2/M82	0.78575	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.3143	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.81956	0.294
IL12-4/WTpooled	1.01571	1
IL1-4/WTpooled	0.80714
WT/WTpooled	1.02326	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	1.84	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00851	1
DC3000/delta hrp 6h	0.71294	0.95
DC3000/delta hrp 12h	1.16649	1
DC3000/delta hrp 24h	1.02415	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96634	1
DC3000 delta B/DC3000 delta AB	0.97739	0.826

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91887	1
Exp 36h	1.24882	1
Exp 60h	1.22233	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96697	1
Var 0h	0.88916	0.933
Var 12h I row2-row1	1.21876	0.263
Var 12h NI row2-row1	0.88482	0.713
Var 36h I row2-row1	0.88055	1
Var 36h NI row2-row1	0.95613	0.791
Var 60h I row2-row1	1.31526	1
Var 60h NI row2-row1	1.53642	0.904
Time course 0hI-0hNI	1.17731	0.662
Time course 12hI-12hNI	1.00583	1
Time course 36hI-36hNI	0.9302	0.19
Time course 60hI-60hNI	1.2862	0.015

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)	1.11512	0.863
transgenic ySAMdc/azygous control (breaker)	0.72737	0.15
transgenic ySAMdc/azygous control (red)	1.10349	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02098	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01159	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00548	1
Manapal/WT (break)	0.64993	1
Manapal/WT (red)	0.70926	0.181