Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.5.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6582	0.095
27DAP/17DAP	0.54668	0.073
39DAP/27DAP	0.75073	0.41
41DAP/39DAP	1.30747	0.37
42DAP/41DAP	1.07703	0.994
43DAP/42DAP	1.01768	0.937
47DAP/43DAP	0.94444	0.794
52DAP/47DAP	0.98714	0.924
57DAP/52DAP	1.09083	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86358	0.078
17DAP/reference	1.02288	0.585
27DAP/reference	0.97364	0.668
39DAP/reference	0.96081	0.391
41DAP/reference	1.03828	0.759
42DAP/reference	0.99135	0.517
43DAP/reference	1.02105	0.646
47DAP/reference	0.98879	0.602
52DAP/reference	0.92908	0.275
57DAP/reference	0.89857	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.60064	0.037
27DAP/17DAP	1.76237	0.023
39DAP/27DAP	0.74447	0.058
41DAP/39DAP	0.65672	0.047
42DAP/41DAP	1.02367	0.924
43DAP/42DAP	1.12739	0.212
47DAP/43DAP	1.02301	0.957
52DAP/47DAP	1.00253	0.987
57DAP/52DAP	0.98804	0.823
57DAP/7DAP	0.76434	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84731
17DAP/reference	0.93736	0.013
27DAP/reference	0.91059	0.012
39DAP/reference	0.97649	0.146
41DAP/reference	0.84344	0.024
42DAP/reference	0.89511	0.014
43DAP/reference	1.0067	1
47DAP/reference	0.76782	0.04
52DAP/reference	0.9206	0.232
57DAP/reference	0.96114	0.26

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0281	0.758
17DAP/reference	1.00253	0.924
27DAP/reference	1.01057	1
39DAP/reference	0.9473	0.314
41DAP/reference	0.96855	0.451
42DAP/reference	0.95873	0.392
43DAP/reference	0.93275	0.43
47DAP/reference	0.88727	0.017
52DAP/reference	0.9492	0.093
57DAP/reference	0.97014	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92323	0.046
17DAP/reference	0.93461	0.224
27DAP/reference	0.91236	0.03
39DAP/reference	0.94365	0.222
41DAP/reference	1.01129	1
42DAP/reference	0.92802	0.059
43DAP/reference	0.92208	0.056
47DAP/reference	0.8764	0.017
52DAP/reference	0.91427	0.296
57DAP/reference	0.76047	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00285	1
26DAP/20DAP	1.44018	0.136
34DAP/26DAP	0.90589	0.584
51DAP/34DAP	1.15755	0.429
52DAP/51DAP	0.93411	1
53DAP/52DAP	0.94171	0.772
55DAP/53DAP	0.86272	0.106
57DAP/55DAP	1.03708	1
62DAP/57DAP	1.03959	0.868
68DAP/62DAP	0.97523	0.863
68DAP/14DAP	0.96353	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.33167	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.68648	0.077
Immature Eggplant/Mature Eggplant	0.68028
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	0.98732	0.961
1-1-2/M82	0.9484	1
12-2/M82	1.17447
12-4/M82	1.06873	1
1-3/M82	0.57465
2-1-1/M82	1.16324
2-1/M82	1.18319
2-6/M82	1.21485	0.505
3-2/M82	0.92838	1
4-1-1/M82	N/A	N/A
4-1/M82	1.03488	1
4-3-2/M82	0.97087	1
4-3/M82	0.97231	1
5-3/M82	0.89869	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.84429
7-2/M82	1.07184
9-3-2/M82	0.81338	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81086	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	2.32494
IL7-3/WTpooled	0.8816	1
IL12-4/WTpooled	0.86039	1
IL1-4/WTpooled	0.98447	1
WT/WTpooled	0.99982	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	0.90091	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97674	1
DC3000/delta hrp 6h	0.84108	0.926
DC3000/delta hrp 12h	1.05447	1
DC3000/delta hrp 24h	1.16574	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.4523	0.023
DC3000 delta B/DC3000 delta AB	0.53333	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93831	1
Exp 36h	0.50577	0.434
Exp 60h	0.6341	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01832	1
Var 0h	1.1905	0.339
Var 12h I row2-row1	0.90851	0.514
Var 12h NI row2-row1	0.86478	0.627
Var 36h I row2-row1	1.08287	0.742
Var 36h NI row2-row1	1.29972	0.482
Var 60h I row2-row1	1.02894	0.562
Var 60h NI row2-row1	1.03659	0.904
Time course 0hI-0hNI	1.02955	0.833
Time course 12hI-12hNI	0.94082	0.33
Time course 36hI-36hNI	0.7556	0.055
Time course 60hI-60hNI	0.19848	0.005

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)	0.76606	0.246
transgenic ySAMdc/azygous control (breaker)	1.20503	0.248
transgenic ySAMdc/azygous control (red)	1.33616	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96517	0.277

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.69492	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.70577	0.09
Manapal/WT (break)	1.73025	0.183
Manapal/WT (red)	1.23645	0.15