Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.20.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87715	0.339
27DAP/17DAP	0.88043	0.69
39DAP/27DAP	1.39989	0.782
41DAP/39DAP	0.96906	0.83
42DAP/41DAP	1.76103	0.031
43DAP/42DAP	1.3195	0.619
47DAP/43DAP	1.86784	0.334
52DAP/47DAP	0.74556	0.367
57DAP/52DAP	0.95687	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01581	0.814
17DAP/reference	1.0293	0.342
27DAP/reference	1.05029	0.339
39DAP/reference	1.05356	0.243
41DAP/reference	0.97145	0.667
42DAP/reference	1.00602	0.731
43DAP/reference	0.99612	0.882
47DAP/reference	1.01974	0.433
52DAP/reference	1.12841	0.633
57DAP/reference	1.01539	0.829

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10454	0.5
27DAP/17DAP	1.0096	0.968
39DAP/27DAP	0.96809	0.579
41DAP/39DAP	1.00703	0.921
42DAP/41DAP	1.03082	0.773
43DAP/42DAP	1.0167	0.273
47DAP/43DAP	0.97694	0.712
52DAP/47DAP	1.0076	0.979
57DAP/52DAP	0.99187	0.823
57DAP/7DAP	0.96166	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96301	0.361
17DAP/reference	0.86921	0.056
27DAP/reference	0.91422	0.159
39DAP/reference	0.97831	0.552
41DAP/reference	0.99219	0.619
42DAP/reference	0.93343	0.262
43DAP/reference	1.01479	1
47DAP/reference	0.98914	0.671
52DAP/reference	1.11532	0.375
57DAP/reference	1.14986	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94307	0.197
17DAP/reference	0.96381	0.337
27DAP/reference	0.90858	0.119
39DAP/reference	0.9989	0.702
41DAP/reference	0.96886	0.364
42DAP/reference	1.01809	0.969
43DAP/reference	0.96594	0.507
47DAP/reference	1.08891	0.051
52DAP/reference	0.937	0.066
57DAP/reference	1.05305	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89082	0.214
17DAP/reference	0.95325	0.537
27DAP/reference	0.84716	0.055
39DAP/reference	1.09159	0.528
41DAP/reference	1.1726	0.502
42DAP/reference	1.02563	0.943
43DAP/reference	1.24581	0.308
47DAP/reference	1.04975	0.355
52DAP/reference	1.06475	0.735
57DAP/reference	1.05105	0.481

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98567	1
26DAP/20DAP	1.0014	1
34DAP/26DAP	1.00999	1
51DAP/34DAP	0.97983	0.816
52DAP/51DAP	0.9297	0.151
53DAP/52DAP	0.93416	0.767
55DAP/53DAP	0.92467	0.417
57DAP/55DAP	1.00588	0.968
62DAP/57DAP	0.86928	0.088
68DAP/62DAP	0.98014	0.834
68DAP/14DAP	1.09226	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98873	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14799	0.666
Mature Green Tomato/Ripe Tomato	0.34266	0.017
Immature Eggplant/Mature Eggplant	1.14101	0.363
Ripe Pepper/Ripe Tomato	1.40211	0.258
Mature Eggplant/Ripe Tomato	1.51696	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00848	1
1-1-2/M82	1.26753	1
12-2/M82	0.99236	1
12-4/M82	1.68499	1
1-3/M82	0.99916	1
2-1-1/M82	1.02001	1
2-1/M82	0.98977	1
2-6/M82	0.95203	1
3-2/M82	1.03489	0.388
4-1-1/M82	0.90696	1
4-1/M82	1.33341	1
4-3-2/M82	0.96469
4-3/M82	0.94064	0.72
5-3/M82	0.95869	1
6-2/M82	1.03832	1
6-3/M82	0.99087	1
7-1/M82	0.7947	1
7-2/M82	0.83197	0.796
9-3-2/M82	1.51249	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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.85044
WT/WTpooled	N/A	N/A

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	0.81698	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06798	0.921
DC3000/delta hrp 6h	1.49709	1
DC3000/delta hrp 12h	0.91398	1
DC3000/delta hrp 24h	1.13057	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15149	0.06
DC3000 delta B/DC3000 delta AB	1.19473	0.206

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0391	1
Exp 36h	0.96223	0.943
Exp 60h	1.11053	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01575	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.153	0.163
Var 12h NI row2-row1	1.00684	1
Var 36h I row2-row1	0.94419	1
Var 36h NI row2-row1	0.9293	0.645
Var 60h I row2-row1	1.05451	1
Var 60h NI row2-row1	1.0943	0.904
Time course 0hI-0hNI	1.04108	0.867
Time course 12hI-12hNI	0.9639	0.734
Time course 36hI-36hNI	0.8689	0.169
Time course 60hI-60hNI	1.17148	0.069

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)	0.90708	0.309
transgenic ySAMdc/azygous control (breaker)	1.00642	1
transgenic ySAMdc/azygous control (red)	1.11613	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02289	0.421

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68706	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03708	1
Manapal/WT (break)	0.80094	0.333
Manapal/WT (red)	0.72228	0.181