Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.15.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08084	0.863
27DAP/17DAP	1.07253	0.88
39DAP/27DAP	1.0015	0.84
41DAP/39DAP	1.62924	0.236
42DAP/41DAP	0.88307	1
43DAP/42DAP	0.97573	0.925
47DAP/43DAP	0.96241	0.847
52DAP/47DAP	0.95085	0.814
57DAP/52DAP	1.05065	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93441	0.167
17DAP/reference	0.97597	0.368
27DAP/reference	0.92296	0.406
39DAP/reference	1.03031	0.294
41DAP/reference	1.01708	0.587
42DAP/reference	0.96789	0.056
43DAP/reference	0.96234	0.538
47DAP/reference	1.02595	0.541
52DAP/reference	1.08375	0.407
57DAP/reference	1.06462	0.249

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03993	0.455
27DAP/17DAP	0.9833	0.854
39DAP/27DAP	1.00039	1
41DAP/39DAP	1.04969	0.748
42DAP/41DAP	0.99193	0.87
43DAP/42DAP	0.98576	0.801
47DAP/43DAP	1.03308	0.765
52DAP/47DAP	0.99555	0.969
57DAP/52DAP	1.03058	0.846
57DAP/7DAP	1.0436	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95148	0.168
17DAP/reference	0.95345	0.108
27DAP/reference	1.01099	0.804
39DAP/reference	1.01349	0.779
41DAP/reference	1.04093	0.325
42DAP/reference	0.98726	0.582
43DAP/reference	0.99563	0.608
47DAP/reference	0.96168	0.504
52DAP/reference	1.00733	0.886
57DAP/reference	1.00909	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9539	0.457
17DAP/reference	1.02975	0.459
27DAP/reference	0.91953	0.111
39DAP/reference	0.94998	0.183
41DAP/reference	0.91156	0.08
42DAP/reference	1.02509	0.826
43DAP/reference	0.97842	0.516
47DAP/reference	1.05425	0.169
52DAP/reference	0.97309	0.351
57DAP/reference	0.97871	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00556	1
17DAP/reference	0.93909	0.205
27DAP/reference	1.04174	0.408
39DAP/reference	0.93258	0.464
41DAP/reference	0.98641	0.682
42DAP/reference	0.95617	0.287
43DAP/reference	1.00089	1
47DAP/reference	0.93329	0.207
52DAP/reference	0.95975	0.424
57DAP/reference	0.89906	0.084

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06635	0.966
26DAP/20DAP	0.99541	1
34DAP/26DAP	0.9802	0.927
51DAP/34DAP	1.01668	0.962
52DAP/51DAP	1.03643	0.588
53DAP/52DAP	1.01122	0.935
55DAP/53DAP	0.93981	0.53
57DAP/55DAP	0.93032	0.748
62DAP/57DAP	0.84962	0.05
68DAP/62DAP	1.23551	0.626
68DAP/14DAP	1.03507	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08282	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70911
Mature Green Tomato/Ripe Tomato	0.88996	0.317
Immature Eggplant/Mature Eggplant	2.17925	0.061
Ripe Pepper/Ripe Tomato	0.5939	0.224
Mature Eggplant/Ripe Tomato	0.95452	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91623	0.503
1-1-2/M82	0.94001	1
12-2/M82	0.95788	0.955
12-4/M82	1.01997	1
1-3/M82	1.04492	1
2-1-1/M82	0.915	0.465
2-1/M82	1.01022	1
2-6/M82	0.99541	1
3-2/M82	1.10539	0.463
4-1-1/M82	1.00017	1
4-1/M82	1.08167	1
4-3-2/M82	0.95186	1
4-3/M82	0.91012	0.72
5-3/M82	1.01729	1
6-2/M82	1.06984	1
6-3/M82	1.00249	1
7-1/M82	1.0288	1
7-2/M82	0.94581	0.796
9-3-2/M82	0.8644	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72888	0.243
IL2-6/WTpooled	1.21071	0.584
IL7-5/WTpooled	1.10651	0.792
IL7-3/WTpooled	1.55	1
IL12-4/WTpooled	1.07262	1
IL1-4/WTpooled	1.01882	1
WT/WTpooled	0.86955	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	1.143	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02327	0.921
DC3000/delta hrp 6h	1.01107	0.95
DC3000/delta hrp 12h	0.89252	1
DC3000/delta hrp 24h	1.05486	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1118	0.042
DC3000 delta B/DC3000 delta AB	1.15252	0.261

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0067	1
Var 0h	0.40679	0.933
Var 12h I row2-row1	1.09469	0.406
Var 12h NI row2-row1	1.16312	1
Var 36h I row2-row1	0.92372	1
Var 36h NI row2-row1	0.97646	0.743
Var 60h I row2-row1	1.0803	0.562
Var 60h NI row2-row1	0.99011	1
Time course 0hI-0hNI	1.06839	0.867
Time course 12hI-12hNI	1.04359	0.803
Time course 36hI-36hNI	1.04268	0.453
Time course 60hI-60hNI	1.18676	0.022

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)	1.00894	0.384
transgenic ySAMdc/azygous control (breaker)	0.9699	1
transgenic ySAMdc/azygous control (red)	1.16581	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00403	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.34766	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04605	1
Manapal/WT (break)	1.38687	1
Manapal/WT (red)	0.79026	0.181