Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68642	0.211
27DAP/17DAP	0.87796	0.717
39DAP/27DAP	1.10336	0.938
41DAP/39DAP	1.29128	0.289
42DAP/41DAP	0.90403	1
43DAP/42DAP	1.28048	0.327
47DAP/43DAP	0.82901	0.473
52DAP/47DAP	1.02252	0.903
57DAP/52DAP	1.1509	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25905	0.23
17DAP/reference	0.98577	0.777
27DAP/reference	1.07877	0.82
39DAP/reference	1.14267	0.706
41DAP/reference	0.87386	0.267
42DAP/reference	0.92468	0.145
43DAP/reference	0.97563	0.745
47DAP/reference	1.01436	1
52DAP/reference	0.94892	0.319
57DAP/reference	1.01643	0.853

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01112	0.847
27DAP/17DAP	0.95378	0.782
39DAP/27DAP	1.0836	0.603
41DAP/39DAP	0.90675	0.481
42DAP/41DAP	1.27025	0.07
43DAP/42DAP	1.18872	0.052
47DAP/43DAP	0.94591	0.701
52DAP/47DAP	1.08772	0.681
57DAP/52DAP	1.11155	0.606
57DAP/7DAP	0.97842	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97541	0.495
17DAP/reference	0.88577	0.144
27DAP/reference	0.97289	0.348
39DAP/reference	1.01222	0.909
41DAP/reference	1.10475	0.524
42DAP/reference	1.06977	0.534
43DAP/reference	1.00379	0.727
47DAP/reference	0.81002	0.101
52DAP/reference	0.80357	0.013
57DAP/reference	0.87503	0.105

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94884	0.518
17DAP/reference	1.0289	0.898
27DAP/reference	0.91703	0.257
39DAP/reference	0.92336	0.281
41DAP/reference	0.96524	0.393
42DAP/reference	0.87553	0.042
43DAP/reference	1.08075	0.846
47DAP/reference	0.95157	0.379
52DAP/reference	0.88398	0.203
57DAP/reference	0.82592	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97102	0.29
17DAP/reference	1.03767	0.767
27DAP/reference	0.99587	0.763
39DAP/reference	1.06373	0.307
41DAP/reference	0.9369	0.459
42DAP/reference	0.91612	0.108
43DAP/reference	0.85661	0.036
47DAP/reference	0.78045	0.009
52DAP/reference	0.86321	0.284
57DAP/reference	1.07327	0.255

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15363	0.015
26DAP/20DAP	0.95942	1
34DAP/26DAP	1.20558	1
51DAP/34DAP	1.0573	0.949
52DAP/51DAP	1.10016	0.662
53DAP/52DAP	0.85226	0.179
55DAP/53DAP	1.12865	0.584
57DAP/55DAP	1.04692	0.955
62DAP/57DAP	0.83418	0.28
68DAP/62DAP	0.82611	0.195
68DAP/14DAP	0.84167	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99809	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.26765	0.018
Immature Eggplant/Mature Eggplant	0.3732	0.058
Ripe Pepper/Ripe Tomato	0.51937	0.293
Mature Eggplant/Ripe Tomato	1.71677	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.72088
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.03172	0.788
IL7-5/WTpooled	0.558
IL7-3/WTpooled	0.8239	0.418
IL12-4/WTpooled	1.00874	0.891
IL1-4/WTpooled	1.11808	1
WT/WTpooled	0.96603	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	1.81336	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.30429
DC3000/delta hrp 6h	1.17839	1
DC3000/delta hrp 12h	1.37492	1
DC3000/delta hrp 24h	0.48121	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21865	0.183
DC3000 delta B/DC3000 delta AB	1.05481	0.498

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16619	1
Exp 36h	1.10105	1
Exp 60h	1.27048	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02258	1
Var 0h	0.79565	1
Var 12h I row2-row1	0.83803	0.514
Var 12h NI row2-row1	1.02898	1
Var 36h I row2-row1	1.01004	1
Var 36h NI row2-row1	0.86244	0.549
Var 60h I row2-row1	0.75873	0.832
Var 60h NI row2-row1	0.83265	0.818
Time course 0hI-0hNI	1.06079	0.451
Time course 12hI-12hNI	0.99333	1
Time course 36hI-36hNI	1.85633	0.007
Time course 60hI-60hNI	2.95056	0.008

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)	1.02258	0.863
transgenic ySAMdc/azygous control (breaker)	1.23035	0.178
transgenic ySAMdc/azygous control (red)	1.01417	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84093	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01346	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.95144	0.083
Manapal/WT (break)	1.61978	0.123
Manapal/WT (red)	0.86114	0.424