Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.10.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17207	0.709
27DAP/17DAP	0.90998	0.81
39DAP/27DAP	1.01446	0.899
41DAP/39DAP	0.89959	0.59
42DAP/41DAP	1.66112	0.908
43DAP/42DAP	1.13391	0.861
47DAP/43DAP	0.82918	0.526
52DAP/47DAP	1.24947	0.575
57DAP/52DAP	1.01059	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87586	0.083
17DAP/reference	0.73723	0.031
27DAP/reference	0.82998	0.089
39DAP/reference	0.72414	0.058
41DAP/reference	0.67857	0.021
42DAP/reference	0.91505	0.157
43DAP/reference	0.81506	0.163
47DAP/reference	0.9349	0.224
52DAP/reference	0.70845	0.089
57DAP/reference	0.95167	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35556	0.057
27DAP/17DAP	0.88456	0.195
39DAP/27DAP	0.84412	0.132
41DAP/39DAP	0.97389	0.986
42DAP/41DAP	0.91813	0.412
43DAP/42DAP	0.94692	0.576
47DAP/43DAP	1.08764	0.359
52DAP/47DAP	1.07232	0.703
57DAP/52DAP	1.32265	0.085
57DAP/7DAP	0.90492	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16131	0.11
17DAP/reference	1.31602	0.014
27DAP/reference	1.17623	0.012
39DAP/reference	1.68533	0.006
41DAP/reference	1.54288	0.035
42DAP/reference	1.60623	0.014
43DAP/reference	1.85595	0.007
47DAP/reference	1.2637	0.717
52DAP/reference	1.53148	0.013
57DAP/reference	1.54367	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01751	0.811
17DAP/reference	1.03663	0.766
27DAP/reference	0.92763	0.393
39DAP/reference	0.87656	0.214
41DAP/reference	1.01335	0.718
42DAP/reference	1.07184	0.843
43DAP/reference	0.92184	0.414
47DAP/reference	0.84839	0.079
52DAP/reference	0.73923	0.131
57DAP/reference	0.8562	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33196	0.016
17DAP/reference	1.22186	0.153
27DAP/reference	1.33472	0.018
39DAP/reference	1.42108	0.005
41DAP/reference	1.25996	0.024
42DAP/reference	1.3848	0.163
43DAP/reference	1.40931	0.067
47DAP/reference	0.89837	0.259
52DAP/reference	1.48416	0.148
57DAP/reference	1.09794	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96115	1
26DAP/20DAP	1.2598	0.273
34DAP/26DAP	1.03242	1
51DAP/34DAP	1.26181	0.365
52DAP/51DAP	1.0116	0.915
53DAP/52DAP	1.14153	0.144
55DAP/53DAP	0.96435	0.784
57DAP/55DAP	1.0328	0.935
62DAP/57DAP	0.85249	0.28
68DAP/62DAP	0.9597	0.787
68DAP/14DAP	1.32619	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85845	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88356	0.539
Mature Green Tomato/Ripe Tomato	1.03836	0.948
Immature Eggplant/Mature Eggplant	1.11357	0.267
Ripe Pepper/Ripe Tomato	0.60614	0.293
Mature Eggplant/Ripe Tomato	0.78509	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0453	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.05822	1
1-3/M82	0.99632
2-1-1/M82	0.57109
2-1/M82	1.57768
2-6/M82	N/A	N/A
3-2/M82	0.9427
4-1-1/M82	N/A	N/A
4-1/M82	1.32641
4-3-2/M82	1.01383	1
4-3/M82	1.16349	1
5-3/M82	0.97225	1
6-2/M82	1.15769
6-3/M82	1.07475
7-1/M82	0.95803
7-2/M82	1.08462	1
9-3-2/M82	1.00261	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.91178	1
IL7-5/WTpooled	1.05191
IL7-3/WTpooled	1.22803	1
IL12-4/WTpooled	0.84629	0.71
IL1-4/WTpooled	0.99747	1
WT/WTpooled	0.93195	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	1.01474	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03484	0.921
DC3000/delta hrp 6h	0.78734	0.914
DC3000/delta hrp 12h	1.01673	1
DC3000/delta hrp 24h	0.91296	0.455

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.82804	0.03
DC3000 delta B/DC3000 delta AB	0.84348	0.039

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02212	1
Exp 36h	0.8746	0.749
Exp 60h	0.79926	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01826	1
Var 0h	0.55028	0.421
Var 12h I row2-row1	0.90534	0.338
Var 12h NI row2-row1	1.01713	1
Var 36h I row2-row1	0.82826	1
Var 36h NI row2-row1	1.12209	1
Var 60h I row2-row1	0.829	0.293
Var 60h NI row2-row1	0.98306	1
Time course 0hI-0hNI	1.00416	1
Time course 12hI-12hNI	1.03192	0.724
Time course 36hI-36hNI	0.92584	0.15
Time course 60hI-60hNI	0.42155	0.006

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)	0.95814	0.299
transgenic ySAMdc/azygous control (breaker)	0.78034	0.134
transgenic ySAMdc/azygous control (red)	0.98672	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.7508	0.112

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.96782	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1479	0.09
Manapal/WT (break)	0.8443	1
Manapal/WT (red)	0.82642	0.199