Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.15.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14004	0.904
27DAP/17DAP	1.34388	0.829
39DAP/27DAP	1.02949	0.84
41DAP/39DAP	1.21333	0.711
42DAP/41DAP	1.47596	0.062
43DAP/42DAP	1.43146	0.835
47DAP/43DAP	1.17391	0.793
52DAP/47DAP	0.72114	0.341
57DAP/52DAP	0.93513	0.938

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6552	0.024
17DAP/reference	0.79072	0.091
27DAP/reference	0.83779	0.034
39DAP/reference	0.88672	0.267
41DAP/reference	0.77553	0.267
42DAP/reference	0.79332	0.005
43DAP/reference	1.14637	0.34
47DAP/reference	0.97937	0.445
52DAP/reference	1.03541	0.912
57DAP/reference	1.05588	0.582

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99885	0.847
27DAP/17DAP	0.79159	0.508
39DAP/27DAP	1.01448	0.811
41DAP/39DAP	0.90526	0.713
42DAP/41DAP	0.97363	0.746
43DAP/42DAP	1.36032	0.176
47DAP/43DAP	0.93947	0.781
52DAP/47DAP	1.19804	0.532
57DAP/52DAP	1.63709	0.146
57DAP/7DAP	1.12366	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88096	0.168
17DAP/reference	1.01972	1
27DAP/reference	1.06883	0.551
39DAP/reference	0.98236	0.552
41DAP/reference	1.02628	1
42DAP/reference	0.9881	0.582
43DAP/reference	1.21325	0.035
47DAP/reference	0.91748	0.504
52DAP/reference	0.965	0.398
57DAP/reference	1.18449	0.288

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91928	0.518
17DAP/reference	0.95007	0.499
27DAP/reference	0.76976	0.067
39DAP/reference	0.75082	0.095
41DAP/reference	1.04038	1
42DAP/reference	0.92277	0.135
43DAP/reference	1.48812	0.121
47DAP/reference	0.93949	0.075
52DAP/reference	1.04462	0.747
57DAP/reference	0.88737	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10775	0.296
17DAP/reference	1.07302	0.578
27DAP/reference	1.11275	0.552
39DAP/reference	1.05128	0.422
41DAP/reference	0.96714	0.512
42DAP/reference	1.13619	0.307
43DAP/reference	0.97612	0.545
47DAP/reference	1.15612	0.443
52DAP/reference	0.90228	0.31
57DAP/reference	0.83506	0.124

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86835	0.981
26DAP/20DAP	0.59308
34DAP/26DAP	1.41613	0.304
51DAP/34DAP	0.88729	0.649
52DAP/51DAP	1.38504
53DAP/52DAP	0.76502	0.062
55DAP/53DAP	1.38467	0.241
57DAP/55DAP	0.77711	0.225
62DAP/57DAP	1.1803	0.678
68DAP/62DAP	1.26365	0.653
68DAP/14DAP	1.18111	0.762

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.64504	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.54666	0.226
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79993
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	1.05097
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	0.88311
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	0.69261	0.243
IL2-6/WTpooled	0.95681	1
IL7-5/WTpooled	3.05059	1
IL7-3/WTpooled	1.04769	1
IL12-4/WTpooled	0.78892	1
IL1-4/WTpooled	1.72101	1
WT/WTpooled	0.79784	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	1.18486	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04239	1
DC3000/delta hrp 6h	0.99364	0.95
DC3000/delta hrp 12h	0.97795	1
DC3000/delta hrp 24h	1.05589	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.0564	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93044	1
Exp 36h	1.56437	1
Exp 60h	0.98078	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96218	1
Var 0h	1.04687	1
Var 12h I row2-row1	0.91028	0.565
Var 12h NI row2-row1	0.92739	0.82
Var 36h I row2-row1	1.23221	0.742
Var 36h NI row2-row1	0.82824	0.645
Var 60h I row2-row1	1.0032	1
Var 60h NI row2-row1	0.87199	1
Time course 0hI-0hNI	1.02334	0.867
Time course 12hI-12hNI	0.93852	0.501
Time course 36hI-36hNI	1.16575	0.101
Time course 60hI-60hNI	0.83551	0.081

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)	0.98911	0.862
transgenic ySAMdc/azygous control (breaker)	0.89399	0.49
transgenic ySAMdc/azygous control (red)	0.87737	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97633	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88809	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.66997	0.093
Manapal/WT (break)	1.86272	0.123
Manapal/WT (red)	1.11384	1