Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.6.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23886	0.725
27DAP/17DAP	1.02549	1
39DAP/27DAP	0.80838	0.512
41DAP/39DAP	1.06838	0.37
42DAP/41DAP	0.9333	1
43DAP/42DAP	0.95157	0.892
47DAP/43DAP	0.76092	0.321
52DAP/47DAP	1.125	0.76
57DAP/52DAP	1.02316	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89736	0.167
17DAP/reference	1.08051	0.148
27DAP/reference	0.94832	0.359
39DAP/reference	1.02083	1
41DAP/reference	0.99595	1
42DAP/reference	0.95547	0.134
43DAP/reference	1.00773	0.982
47DAP/reference	0.91406	0.03
52DAP/reference	0.82859	0.079
57DAP/reference	0.90544	0.199

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7019	0.033
27DAP/17DAP	1.37281	0.08
39DAP/27DAP	0.79189	0.068
41DAP/39DAP	0.71641	0.069
42DAP/41DAP	0.96412	0.7
43DAP/42DAP	0.92885	0.399
47DAP/43DAP	0.91413	0.418
52DAP/47DAP	1.05783	0.81
57DAP/52DAP	0.98841	0.813
57DAP/7DAP	0.66474	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1041	0.776
17DAP/reference	0.92031	0.295
27DAP/reference	0.8883	0.171
39DAP/reference	1.1392	0.149
41DAP/reference	1.31993	0.153
42DAP/reference	1.14303	0.405
43DAP/reference	0.91358	0.351
47DAP/reference	1.01388	1
52DAP/reference	1.38502	0.041
57DAP/reference	1.05707	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9514	0.441
17DAP/reference	1.15033	0.031
27DAP/reference	1.01345	1
39DAP/reference	1.10775	0.746
41DAP/reference	1.08067	0.562
42DAP/reference	0.99296	0.594
43DAP/reference	1.01419	0.692
47DAP/reference	0.84471	0.023
52DAP/reference	1.00596	1
57DAP/reference	0.92189	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23874	0.218
17DAP/reference	1.01389	0.886
27DAP/reference	1.1058	0.51
39DAP/reference	0.93576	0.328
41DAP/reference	1.23977	0.486
42DAP/reference	1.21261	0.226
43DAP/reference	1.34937	0.219
47DAP/reference	0.81735	0.007
52DAP/reference	1.30266	0.318
57DAP/reference	0.93578	0.346

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13785	0.966
26DAP/20DAP	0.87703	1
34DAP/26DAP	1.00617	1
51DAP/34DAP	0.69824	0.061
52DAP/51DAP	1.18029	0.253
53DAP/52DAP	0.79857	0.094
55DAP/53DAP	0.82909	0.056
57DAP/55DAP	1.11075	0.898
62DAP/57DAP	1.61279	0.767
68DAP/62DAP	1.13485	0.788
68DAP/14DAP	1.40319	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.55957	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.15091	0.058
Mature Green Tomato/Ripe Tomato	2.21595	0.064
Immature Eggplant/Mature Eggplant	0.75295	0.117
Ripe Pepper/Ripe Tomato	1.99872	1
Mature Eggplant/Ripe Tomato	7.43423	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79251	0.613
1-1-2/M82	1.05393	1
12-2/M82	0.94901	0.955
12-4/M82	1.33226	0.655
1-3/M82	0.78362	0.378
2-1-1/M82	1.05959	1
2-1/M82	0.92117	0.325
2-6/M82	1.05338	0.505
3-2/M82	1.72493	0.426
4-1-1/M82	0.92789	1
4-1/M82	0.95008
4-3-2/M82	N/A	N/A
4-3/M82	1.04162	1
5-3/M82	0.88638	0.447
6-2/M82	1.41043
6-3/M82	1.07785	1
7-1/M82	1.33713	0.992
7-2/M82	1.16055	1
9-3-2/M82	0.86577

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.33076	0.493
IL2-6/WTpooled	0.90729	0.473
IL7-5/WTpooled	1.00722
IL7-3/WTpooled	0.95671	0.418
IL12-4/WTpooled	0.70231	0.543
IL1-4/WTpooled	1.09664	1
WT/WTpooled	0.89117	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	0.97055	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09076	0.921
DC3000/delta hrp 6h	0.92408	0.95
DC3000/delta hrp 12h	0.95876	1
DC3000/delta hrp 24h	0.57099	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.43183	0.023
DC3000 delta B/DC3000 delta AB	0.51705	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7569	0.265
Exp 36h	0.97734	0.943
Exp 60h	0.88684	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00928	1
Var 0h	0.91821	0.457
Var 12h I row2-row1	0.85219	0.338
Var 12h NI row2-row1	0.94772	0.82
Var 36h I row2-row1	0.93551	1
Var 36h NI row2-row1	1.13346	0.482
Var 60h I row2-row1	1.10465	0.562
Var 60h NI row2-row1	1.0929	0.904
Time course 0hI-0hNI	1.06409	0.662
Time course 12hI-12hNI	0.93649	0.515
Time course 36hI-36hNI	0.87635	0.031
Time course 60hI-60hNI	0.1996	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)	1.02438	0.921
transgenic ySAMdc/azygous control (breaker)	0.63896	0.134
transgenic ySAMdc/azygous control (red)	0.89265	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09228	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02249	1
Manapal/WT (break)	0.77332	0.333
Manapal/WT (red)	0.883	0.242