Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.6.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16895	0.838
27DAP/17DAP	1.15135	0.881
39DAP/27DAP	0.77286	0.399
41DAP/39DAP	1.30821	0.657
42DAP/41DAP	1.22365	0.912
43DAP/42DAP	1.06868	0.937
47DAP/43DAP	0.99293	0.821
52DAP/47DAP	1.53218	0.307
57DAP/52DAP	0.95999	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08882	0.587
17DAP/reference	1.47581	0.014
27DAP/reference	1.179	0.33
39DAP/reference	1.29331	0.209
41DAP/reference	1.254	0.171
42DAP/reference	1.07088	0.449
43DAP/reference	0.96018	0.448
47DAP/reference	1.16468	0.243
52DAP/reference	1.04312	0.991
57DAP/reference	0.94184	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04198	0.515
27DAP/17DAP	1.00702	0.976
39DAP/27DAP	0.99276	1
41DAP/39DAP	0.95602	0.861
42DAP/41DAP	1.01363	1
43DAP/42DAP	0.95145	0.399
47DAP/43DAP	0.95269	0.559
52DAP/47DAP	1.02551	0.892
57DAP/52DAP	0.99098	0.833
57DAP/7DAP	1.32114	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81885	0.146
17DAP/reference	0.93479	0.253
27DAP/reference	0.93692	0.231
39DAP/reference	0.87588	0.073
41DAP/reference	0.87802	0.094
42DAP/reference	0.72378	0.01
43DAP/reference	0.73453	0.026
47DAP/reference	0.96318	0.671
52DAP/reference	0.87654	0.137
57DAP/reference	0.79674	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08783	0.719
17DAP/reference	1.21281	0.04
27DAP/reference	1.22908	0.123
39DAP/reference	1.16839	0.67
41DAP/reference	1.02075	0.702
42DAP/reference	1.25116	0.039
43DAP/reference	1.10763	0.681
47DAP/reference	1.09699	0.332
52DAP/reference	1.27169	0.145
57DAP/reference	1.14129	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85994	0.104
17DAP/reference	0.97724	0.668
27DAP/reference	0.90403	0.319
39DAP/reference	0.85369	0.046
41DAP/reference	1.12946	0.222
42DAP/reference	0.93316	0.445
43DAP/reference	1.07924	0.599
47DAP/reference	1.28319	0.115
52DAP/reference	0.81385	0.142
57DAP/reference	1.05936	0.539

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05262	1
26DAP/20DAP	0.86595	0.512
34DAP/26DAP	0.99128	1
51DAP/34DAP	1.02998	0.814
52DAP/51DAP	0.96952	1
53DAP/52DAP	0.92363	0.386
55DAP/53DAP	0.9136	0.489
57DAP/55DAP	1.00229	0.935
62DAP/57DAP	1.06967	1
68DAP/62DAP	0.58862	0.314
68DAP/14DAP	0.65482	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91495	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.89997	0.522
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.65184
Mature Eggplant/Ripe Tomato	1.03982

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02096	1
1-1-2/M82	0.89773	0.804
12-2/M82	1.14202	1
12-4/M82	1.15437	0.611
1-3/M82	0.8915	0.441
2-1-1/M82	1.15151	1
2-1/M82	N/A	N/A
2-6/M82	1.17495	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.04286	1
4-1/M82	0.78848	0.867
4-3-2/M82	1.07721
4-3/M82	1.00058	1
5-3/M82	1.01981	1
6-2/M82	0.93617	1
6-3/M82	0.9893	1
7-1/M82	0.97427
7-2/M82	1.10246	0.385
9-3-2/M82	0.85402

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11864	0.365
IL2-6/WTpooled	0.95283	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.82977	0.294
IL12-4/WTpooled	0.96913	1
IL1-4/WTpooled	1.25666
WT/WTpooled	0.98856	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	1.12171	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99265	1
DC3000/delta hrp 6h	1.06346	0.95
DC3000/delta hrp 12h	0.99081	1
DC3000/delta hrp 24h	1.23977	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96252	0.629
DC3000 delta B/DC3000 delta AB	0.9829	0.892

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05036	1
Exp 36h	1.0704	1
Exp 60h	0.66328	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93494	1
Var 0h	0.65646	1
Var 12h I row2-row1	0.91129	0.418
Var 12h NI row2-row1	0.97785	0.906
Var 36h I row2-row1	0.93016	0.805
Var 36h NI row2-row1	1.15957	1
Var 60h I row2-row1	1.16792	0.562
Var 60h NI row2-row1	0.98502	0.977
Time course 0hI-0hNI	1.06861	0.63
Time course 12hI-12hNI	0.97424	0.82
Time course 36hI-36hNI	0.88251	0.041
Time course 60hI-60hNI	0.70913	0.015

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)	0.80559	0.314
transgenic ySAMdc/azygous control (breaker)	1.04392	1
transgenic ySAMdc/azygous control (red)	1.03383	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95794	0.393

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88308	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74417	1
Manapal/WT (break)	0.81333	1
Manapal/WT (red)	1.11791	1