Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.1.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0504	0.801
27DAP/17DAP	1.2783	0.688
39DAP/27DAP	1.05827	1
41DAP/39DAP	0.95839	0.811
42DAP/41DAP	1.24291	0.614
43DAP/42DAP	0.78978	0.468
47DAP/43DAP	0.98016	0.89
52DAP/47DAP	0.74943	0.339
57DAP/52DAP	1.17471	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90311	0.402
17DAP/reference	0.99825	0.904
27DAP/reference	0.99695	0.797
39DAP/reference	0.8104	0.083
41DAP/reference	1.08057	0.963
42DAP/reference	1.17172	0.782
43DAP/reference	0.89999	0.17
47DAP/reference	1.0955	0.91
52DAP/reference	1.17631	0.607
57DAP/reference	1.33117	0.066

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04552	0.899
27DAP/17DAP	0.96164	0.614
39DAP/27DAP	1.31773	0.076
41DAP/39DAP	1.02094	0.909
42DAP/41DAP	0.96101	0.7
43DAP/42DAP	0.80431	0.044
47DAP/43DAP	1.04573	0.805
52DAP/47DAP	0.96093	0.857
57DAP/52DAP	0.90332	0.498
57DAP/7DAP	0.89163	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19321	0.385
17DAP/reference	1.19911	0.361
27DAP/reference	1.35393	0.03
39DAP/reference	1.30477	0.081
41DAP/reference	1.07538	0.593
42DAP/reference	1.26054	0.233
43DAP/reference	1.29694	0.093
47DAP/reference	1.32398	0.158
52DAP/reference	1.27355	0.159
57DAP/reference	1.10857	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43759	0.732
17DAP/reference	0.80089	0.134
27DAP/reference	0.92048	0.381
39DAP/reference	1.23879	0.059
41DAP/reference	1.32862	0.062
42DAP/reference	1.16329	0.267
43DAP/reference	0.91148	0.361
47DAP/reference	1.03299	0.4
52DAP/reference	1.10512	0.667
57DAP/reference	0.90589	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13557	0.329
17DAP/reference	0.92105	0.499
27DAP/reference	1.33581	0.081
39DAP/reference	1.27433	0.016
41DAP/reference	0.97845	0.56
42DAP/reference	1.24382	0.146
43DAP/reference	1.33353	0.154
47DAP/reference	1.06813	0.847
52DAP/reference	1.65769	0.198
57DAP/reference	1.5129	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82447	1
26DAP/20DAP	1.23175	0.226
34DAP/26DAP	1.06836	1
51DAP/34DAP	0.99998	0.96
52DAP/51DAP	0.92981	1
53DAP/52DAP	0.9457	0.767
55DAP/53DAP	0.88502	0.243
57DAP/55DAP	1.15508	0.543
62DAP/57DAP	1.13484	1
68DAP/62DAP	1.2378	0.907
68DAP/14DAP	1.33443	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15288	0.077

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.72237	0.023
Immature Eggplant/Mature Eggplant	3.82781
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.39291

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.73298
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	1.79664
4-3/M82	N/A	N/A
5-3/M82	1.14806
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.02919
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	1.76205	0.395
IL7-5/WTpooled	1.19737
IL7-3/WTpooled	1.15914	1
IL12-4/WTpooled	1.00735	1
IL1-4/WTpooled	1.67153	0.426
WT/WTpooled	1.05514	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	1.27407	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03099	1
DC3000/delta hrp 6h	0.86639	0.95
DC3000/delta hrp 12h	0.88159	1
DC3000/delta hrp 24h	2.51568	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.38701	0.06
DC3000 delta B/DC3000 delta AB	0.94176	0.288

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.29009	1
Exp 36h	2.10201	0.693
Exp 60h	1.44988	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99747	1
Var 0h	1.03588	1
Var 12h I row2-row1	1.16211	0.506
Var 12h NI row2-row1	1.24489	0.266
Var 36h I row2-row1	1.2527	0.291
Var 36h NI row2-row1	0.85645	0.421
Var 60h I row2-row1	0.74892	0.293
Var 60h NI row2-row1	0.87281	0.292
Time course 0hI-0hNI	0.94475	0.617
Time course 12hI-12hNI	1.31823	0.015
Time course 36hI-36hNI	1.91524	0.004
Time course 60hI-60hNI	2.87929	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)	0.8402	0.348
transgenic ySAMdc/azygous control (breaker)	1.70394	0.248
transgenic ySAMdc/azygous control (red)	1.34731	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.26408	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29789	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87096	1
Manapal/WT (break)	1.24442	0.14
Manapal/WT (red)	1.16568	1