Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.11.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31159	0.63
27DAP/17DAP	1.99524	0.399
39DAP/27DAP	0.75041	0.286
41DAP/39DAP	0.94097	0.72
42DAP/41DAP	1.19073	0.894
43DAP/42DAP	1.40033	0.259
47DAP/43DAP	2.6887	0.156
52DAP/47DAP	1.23724	0.518
57DAP/52DAP	1.49831	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95005	0.442
17DAP/reference	1.12471	0.086
27DAP/reference	1.09868	0.339
39DAP/reference	1.05286	0.747
41DAP/reference	1.07494	0.393
42DAP/reference	0.85821	0.006
43DAP/reference	1.03477	0.899
47DAP/reference	1.0203	1
52DAP/reference	1.033	0.84
57DAP/reference	0.97133	0.503

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92541	0.542
27DAP/17DAP	1.74407	0.381
39DAP/27DAP	1.01458	0.932
41DAP/39DAP	0.92644	0.781
42DAP/41DAP	1.18363	0.55
43DAP/42DAP	1.09689	0.585
47DAP/43DAP	0.88889	0.305
52DAP/47DAP	1.08892	0.844
57DAP/52DAP	1.1361	0.971
57DAP/7DAP	1.66862	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98352	0.613
17DAP/reference	0.88087	0.167
27DAP/reference	0.92885	0.283
39DAP/reference	0.8172	0.064
41DAP/reference	0.68879	0.014
42DAP/reference	0.79171	0.01
43DAP/reference	0.82189	0.04
47DAP/reference	0.80744	0.128
52DAP/reference	0.92205	0.179
57DAP/reference	0.94203	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98812	0.811
17DAP/reference	1.0873	0.773
27DAP/reference	0.99351	0.642
39DAP/reference	0.87692	0.165
41DAP/reference	0.99129	0.584
42DAP/reference	0.99172	0.594
43DAP/reference	1.0478	0.89
47DAP/reference	0.94047	0.214
52DAP/reference	0.84555	0.078
57DAP/reference	1.05781	0.848

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94091	0.249
17DAP/reference	0.85101	0.239
27DAP/reference	0.8178	0.113
39DAP/reference	0.93589	0.328
41DAP/reference	0.87486	0.086
42DAP/reference	0.92659	0.287
43DAP/reference	0.86293	0.098
47DAP/reference	1.0006	0.687
52DAP/reference	0.90955	0.433
57DAP/reference	0.97286	0.516

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22147	0.966
26DAP/20DAP	1.44699
34DAP/26DAP	1.2051	1
51DAP/34DAP	0.85632	0.667
52DAP/51DAP	1.21081	0.542
53DAP/52DAP	1.13783	0.552
55DAP/53DAP	1.01429	0.894
57DAP/55DAP	0.86466	0.458
62DAP/57DAP	1.08532	0.678
68DAP/62DAP	0.91489	0.769
68DAP/14DAP	1.23793	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.06391	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.41831	0.021
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.14789	0.224
Mature Eggplant/Ripe Tomato	0.1512	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0633	1
1-1-2/M82	1.1645	1
12-2/M82	1.00256
12-4/M82	1.06028
1-3/M82	0.99858
2-1-1/M82	1.08015	1
2-1/M82	1.51707
2-6/M82	1.09054	1
3-2/M82	1.18289	0.463
4-1-1/M82	1.40007	1
4-1/M82	1.2024
4-3-2/M82	0.99501
4-3/M82	1.03981	1
5-3/M82	0.97465	1
6-2/M82	1.3028
6-3/M82	0.99106	1
7-1/M82	1.63605	0.598
7-2/M82	1.04209	1
9-3-2/M82	1.05302	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.55344	0.321
IL2-6/WTpooled	0.96885	1
IL7-5/WTpooled	1.5179
IL7-3/WTpooled	1.10576	0.362
IL12-4/WTpooled	0.98249	0.71
IL1-4/WTpooled	0.85048	0.834
WT/WTpooled	0.98555	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	1.25033	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9779	1
DC3000/delta hrp 6h	0.99847	0.95
DC3000/delta hrp 12h	1.04909
DC3000/delta hrp 24h	1.23903	0.158

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.53428	0.489
Exp 60h	0.81801	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.12407	1
Var 0h	0.61854	0.933
Var 12h I row2-row1	0.83539	0.418
Var 12h NI row2-row1	0.96021	0.906
Var 36h I row2-row1	0.8629	1
Var 36h NI row2-row1	0.60586	1
Var 60h I row2-row1	0.91423	0.285
Var 60h NI row2-row1	0.5981	1
Time course 0hI-0hNI	1.04775	0.574
Time course 12hI-12hNI	1.01095	0.888
Time course 36hI-36hNI	1.24729	0.025
Time course 60hI-60hNI	11.158	0.08

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)	1.37312	0.3
transgenic ySAMdc/azygous control (breaker)	1.06418	1
transgenic ySAMdc/azygous control (red)	1.03956	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.82965	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94211	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.66641	0.172
Manapal/WT (break)	0.79363	0.333
Manapal/WT (red)	0.78465	0.184