Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.2.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9629	0.76
27DAP/17DAP	1.13061	0.905
39DAP/27DAP	1.19266	0.762
41DAP/39DAP	0.99548	0.791
42DAP/41DAP	0.80449	0.774
43DAP/42DAP	0.95831	0.887
47DAP/43DAP	1.10618	0.856
52DAP/47DAP	1.2355	0.804
57DAP/52DAP	1.36701	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81867	0.027
17DAP/reference	0.86248	0.053
27DAP/reference	1.05947	0.782
39DAP/reference	1.00657	1
41DAP/reference	0.77644	0.039
42DAP/reference	0.96315	0.259
43DAP/reference	1.05003	0.471
47DAP/reference	1.21247	0.002
52DAP/reference	1.09586	0.8
57DAP/reference	1.19249	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03559	0.947
27DAP/17DAP	0.99348	0.943
39DAP/27DAP	1.00387	1
41DAP/39DAP	1.07783	0.876
42DAP/41DAP	1.12094	0.495
43DAP/42DAP	0.93732	0.503
47DAP/43DAP	1.08129	0.664
52DAP/47DAP	0.9737	0.9
57DAP/52DAP	1.05699	0.662
57DAP/7DAP	1.0905	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4748	0.082
17DAP/reference	0.36923	0.011
27DAP/reference	0.90647	0.248
39DAP/reference	0.46458	0.011
41DAP/reference	1.11646	0.701
42DAP/reference	2.33264	0.1
43DAP/reference	2.24102	0.01
47DAP/reference	1.26994	0.05
52DAP/reference	0.49719	0.013
57DAP/reference	0.33692	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77312	0.145
17DAP/reference	0.84648	0.052
27DAP/reference	0.94205	0.34
39DAP/reference	1.00588	1
41DAP/reference	0.98714	0.493
42DAP/reference	0.98155	0.534
43DAP/reference	0.69618	0.014
47DAP/reference	0.9717	0.459
52DAP/reference	0.98069	0.5
57DAP/reference	0.91007	0.156

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42348	0.032
17DAP/reference	0.85009	0.239
27DAP/reference	0.51802	0.033
39DAP/reference	0.48062	0.01
41DAP/reference	0.45426	0.019
42DAP/reference	1.86419	0.032
43DAP/reference	1.94924	0.019
47DAP/reference	1.11087	0.187
52DAP/reference	1.04714	1
57DAP/reference	1.31314	0.124

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03492	1
26DAP/20DAP	1.64842	0.1
34DAP/26DAP	0.80914	0.189
51DAP/34DAP	1.01167	0.978
52DAP/51DAP	0.92124	1
53DAP/52DAP	0.90109	0.435
55DAP/53DAP	0.99525	0.796
57DAP/55DAP	1.37063	0.249
62DAP/57DAP	1.19959	0.767
68DAP/62DAP	1.27231	0.945
68DAP/14DAP	1.879	0.051

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.3314	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83217	0.312
Mature Green Tomato/Ripe Tomato	1.12029	0.752
Immature Eggplant/Mature Eggplant	0.91259	0.197
Ripe Pepper/Ripe Tomato	0.63089	0.224
Mature Eggplant/Ripe Tomato	1.16777	1

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	1.00133
4-3/M82	N/A	N/A
5-3/M82	0.97025
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.00652
7-2/M82	N/A	N/A
9-3-2/M82	1.03288

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95015	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.70792	0.418
IL12-4/WTpooled	1.06317	0.891
IL1-4/WTpooled	0.88483
WT/WTpooled	1.04855	0.874

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	1.12975	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.26587	0.894
DC3000/delta hrp 6h	1.02521	0.95
DC3000/delta hrp 12h	0.9809	1
DC3000/delta hrp 24h	1.21644	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2808	0.11
DC3000 delta B/DC3000 delta AB	0.93571	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14176	1
Exp 36h	0.9976	1
Exp 60h	1.12849	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97252	1
Var 0h	0.92788	1
Var 12h I row2-row1	0.98417	1
Var 12h NI row2-row1	1.22558	0.266
Var 36h I row2-row1	0.96257	1
Var 36h NI row2-row1	0.6693	0.645
Var 60h I row2-row1	0.91178	0.285
Var 60h NI row2-row1	0.87583	0.866
Time course 0hI-0hNI	0.88516	0.188
Time course 12hI-12hNI	0.9975	1
Time course 36hI-36hNI	1.19717	0.101
Time course 60hI-60hNI	1.23147	0.025

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)	0.93623	0.428
transgenic ySAMdc/azygous control (breaker)	0.95101	1
transgenic ySAMdc/azygous control (red)	0.94934	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01581	0.911

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73351	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99432	1
Manapal/WT (break)	0.82787	0.333
Manapal/WT (red)	1.01214	1