Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29487	0.428
27DAP/17DAP	1.27511	0.799
39DAP/27DAP	0.82408	0.487
41DAP/39DAP	1.05501	0.797
42DAP/41DAP	1.10451	0.886
43DAP/42DAP	1.08752	1
47DAP/43DAP	1.16002	0.459
52DAP/47DAP	0.7666	0.418
57DAP/52DAP	1.0109	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03045	0.788
17DAP/reference	1.04433	0.108
27DAP/reference	1.03213	0.623
39DAP/reference	1.03101	0.393
41DAP/reference	1.0206	0.759
42DAP/reference	0.94681	0.072
43DAP/reference	1.02305	0.678
47DAP/reference	0.94839	0.127
52DAP/reference	0.94158	0.275
57DAP/reference	0.99985	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9171	0.402
27DAP/17DAP	1.12932	0.775
39DAP/27DAP	1.10532	0.558
41DAP/39DAP	0.9562	0.923
42DAP/41DAP	1.05264	0.861
43DAP/42DAP	1.07671	0.627
47DAP/43DAP	1.03681	0.92
52DAP/47DAP	0.95397	0.834
57DAP/52DAP	0.88094	0.317
57DAP/7DAP	1.48593	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24869	0.079
17DAP/reference	1.50155	0.022
27DAP/reference	1.29946	0.16
39DAP/reference	1.3542	0.008
41DAP/reference	1.19246	0.131
42DAP/reference	1.20943	0.03
43DAP/reference	1.13995	0.364
47DAP/reference	1.08341	0.353
52DAP/reference	1.30293	0.016
57DAP/reference	1.22686	0.046

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98487	0.811
17DAP/reference	0.90855	0.113
27DAP/reference	0.93932	0.304
39DAP/reference	0.9058	0.202
41DAP/reference	0.97732	0.557
42DAP/reference	0.89077	0.02
43DAP/reference	0.96982	0.569
47DAP/reference	0.9121	0.085
52DAP/reference	1.05471	0.528
57DAP/reference	1.00327	0.957

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22342	0.212
17DAP/reference	1.13286	0.474
27DAP/reference	1.13699	0.596
39DAP/reference	1.25662	0.069
41DAP/reference	0.98732	0.682
42DAP/reference	1.27192	0.214
43DAP/reference	1.11636	0.412
47DAP/reference	1.01414	1
52DAP/reference	1.17186	0.393
57DAP/reference	1.01447	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99477	1
26DAP/20DAP	0.89584	0.512
34DAP/26DAP	1.08194	1
51DAP/34DAP	0.98222	0.856
52DAP/51DAP	0.99002	1
53DAP/52DAP	1.00367	1
55DAP/53DAP	1.1064	0.584
57DAP/55DAP	1.01181	1
62DAP/57DAP	0.9486
68DAP/62DAP	1.04176	0.897
68DAP/14DAP	1.13996	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96069	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.3456	0.068
Mature Green Tomato/Ripe Tomato	0.87	0.411
Immature Eggplant/Mature Eggplant	0.93861	0.366
Ripe Pepper/Ripe Tomato	1.11015	0.251
Mature Eggplant/Ripe Tomato	0.72617	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05994	1
1-1-2/M82	1.04397	0.977
12-2/M82	1.07307	1
12-4/M82	0.94783	1
1-3/M82	0.92624	0.501
2-1-1/M82	1.20339	0.689
2-1/M82	1.1901	1
2-6/M82	1.04788	0.695
3-2/M82	1.01554
4-1-1/M82	1.01192	1
4-1/M82	1.06587
4-3-2/M82	0.8609
4-3/M82	1.19431	1
5-3/M82	0.91883	0.49
6-2/M82	0.99492	1
6-3/M82	1.02045	1
7-1/M82	0.83385	0.803
7-2/M82	1.07033	0.385
9-3-2/M82	0.88549	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.35454	0.277
IL2-6/WTpooled	0.58792	0.337
IL7-5/WTpooled	1.17776	0.495
IL7-3/WTpooled	1.21534	0.362
IL12-4/WTpooled	1.06355	0.839
IL1-4/WTpooled	0.92066	0.699
WT/WTpooled	0.97226	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	0.84312	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00182	1
DC3000/delta hrp 6h	1.03522	0.95
DC3000/delta hrp 12h	1.15187
DC3000/delta hrp 24h	0.92068	0.412

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10889	0.408
DC3000 delta B/DC3000 delta AB	1.02378	0.636

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.26251	1
Exp 36h	1.00191	1
Exp 60h	0.93984	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9993	1
Var 0h	0.88843	1
Var 12h I row2-row1	0.85631	0.363
Var 12h NI row2-row1	1.0969	0.34
Var 36h I row2-row1	1.03949	0.908
Var 36h NI row2-row1	9.83075	1
Var 60h I row2-row1	1.86779
Var 60h NI row2-row1	0.98138	1
Time course 0hI-0hNI	0.97939	0.95
Time course 12hI-12hNI	0.94046	0.173
Time course 36hI-36hNI	0.85372	0.025
Time course 60hI-60hNI	0.51342	0.005

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)	0.95295	0.454
transgenic ySAMdc/azygous control (breaker)	1.23504	0.178
transgenic ySAMdc/azygous control (red)	1.10096	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99991	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08839	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00646	1
Manapal/WT (break)	1.15881	1
Manapal/WT (red)	0.7694	0.199