Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.13.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99552	0.728
27DAP/17DAP	1.4004	0.8
39DAP/27DAP	1.13248	0.894
41DAP/39DAP	0.84122	0.422
42DAP/41DAP	0.92144	1
43DAP/42DAP	0.94954	0.89
47DAP/43DAP	1.00223	0.953
52DAP/47DAP	1.01935	0.976
57DAP/52DAP	1.13936	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94085	0.3
17DAP/reference	1.06791	0.476
27DAP/reference	1.09146	0.179
39DAP/reference	0.96962	0.663
41DAP/reference	1.02092	0.963
42DAP/reference	0.79038	0.002
43DAP/reference	0.98064	0.745
47DAP/reference	0.87221	0.013
52DAP/reference	0.93883	0.275
57DAP/reference	1.15779	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08695	0.284
27DAP/17DAP	1.15887	0.377
39DAP/27DAP	1.11432	0.429
41DAP/39DAP	1.04359	0.727
42DAP/41DAP	1.00219	0.865
43DAP/42DAP	0.91677	0.383
47DAP/43DAP	1.0183	0.956
52DAP/47DAP	1.09646	0.635
57DAP/52DAP	1.15799	0.417
57DAP/7DAP	1.16275	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98947	0.55
17DAP/reference	1.07651	0.084
27DAP/reference	1.10639	0.014
39DAP/reference	1.14058	0.01
41DAP/reference	1.17293	0.019
42DAP/reference	1.07861	0.018
43DAP/reference	1.01288	0.974
47DAP/reference	1.06458	0.745
52DAP/reference	1.17625	0.011
57DAP/reference	1.44696	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93448	0.399
17DAP/reference	0.93536	0.214
27DAP/reference	0.89614	0.229
39DAP/reference	0.80732	0.156
41DAP/reference	1.0102	0.683
42DAP/reference	0.90098	0.089
43DAP/reference	1.1322	0.562
47DAP/reference	0.94617	0.137
52DAP/reference	0.93583	0.327
57DAP/reference	0.77667	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93581	0.268
17DAP/reference	0.95908	0.444
27DAP/reference	1.06994	0.271
39DAP/reference	1.1006	0.087
41DAP/reference	1.04136	0.257
42DAP/reference	0.9498	0.172
43DAP/reference	0.94639	0.256
47DAP/reference	0.99742	0.626
52DAP/reference	1.01038	1
57DAP/reference	1.02641	0.827

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94297	1
26DAP/20DAP	0.96076	1
34DAP/26DAP	0.9768	0.961
51DAP/34DAP	1.12634	0.458
52DAP/51DAP	0.93161	1
53DAP/52DAP	1.02126	0.961
55DAP/53DAP	0.98813	0.864
57DAP/55DAP	1.2687	0.826
62DAP/57DAP	1.10193	1
68DAP/62DAP	0.81706	0.641
68DAP/14DAP	0.99237	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88287	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.61228
Immature Eggplant/Mature Eggplant	0.28218
Ripe Pepper/Ripe Tomato	1.03295
Mature Eggplant/Ripe Tomato	0.96313

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9462	0.944
1-1-2/M82	1.12186	1
12-2/M82	1.06135	1
12-4/M82	1.02953
1-3/M82	0.66441
2-1-1/M82	1.0308	1
2-1/M82	0.99864	1
2-6/M82	0.94747	1
3-2/M82	1.00687	1
4-1-1/M82	0.97751	1
4-1/M82	1.19632
4-3-2/M82	N/A	N/A
4-3/M82	1.03704	1
5-3/M82	1.04085	1
6-2/M82	0.78333	1
6-3/M82	1.02365	1
7-1/M82	1.06385	1
7-2/M82	0.82488	0.796
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09686	0.277
IL2-6/WTpooled	1.1847	0.531
IL7-5/WTpooled	0.61468	1
IL7-3/WTpooled	0.91914	1
IL12-4/WTpooled	1.08409	0.523
IL1-4/WTpooled	0.86976	0.457
WT/WTpooled	0.98226	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	1.10647	0.083

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.86613	1
DC3000/delta hrp 6h	1.02267	1
DC3000/delta hrp 12h	1.03856	1
DC3000/delta hrp 24h	1.07844	0.516

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	1.01373	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98434	1
Exp 36h	1.54305	0.693
Exp 60h	1.18094	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10181	1
Var 0h	1.02052	1
Var 12h I row2-row1	1.21539	0.506
Var 12h NI row2-row1	1.09528	1
Var 36h I row2-row1	1.15749	0.908
Var 36h NI row2-row1	0.86552	0.584
Var 60h I row2-row1	1.15174	0.502
Var 60h NI row2-row1	1.10227	1
Time course 0hI-0hNI	1.16063	0.799
Time course 12hI-12hNI	1.02712	0.82
Time course 36hI-36hNI	1.41002	0.012
Time course 60hI-60hNI	1.39913	0.053

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)	0.97669	0.662
transgenic ySAMdc/azygous control (breaker)	1.24449	1
transgenic ySAMdc/azygous control (red)	1.07509	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00425	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83705	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0723	0.307
Manapal/WT (break)	1.05022	1
Manapal/WT (red)	0.77055	0.181