Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.8.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72572	0.134
27DAP/17DAP	0.94768	0.863
39DAP/27DAP	0.95303	0.663
41DAP/39DAP	0.77792	0.396
42DAP/41DAP	1.29945	0.552
43DAP/42DAP	1.01957	0.937
47DAP/43DAP	0.71177	0.185
52DAP/47DAP	1.04376	0.724
57DAP/52DAP	1.09442	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99292	0.707
17DAP/reference	0.93398	0.26
27DAP/reference	0.99226	0.763
39DAP/reference	1.07546	0.57
41DAP/reference	0.93861	0.434
42DAP/reference	0.93125	0.072
43DAP/reference	1.09816	0.269
47DAP/reference	0.89278	0.021
52DAP/reference	1.00771	1
57DAP/reference	1.05962	0.744

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.51316	0.094
27DAP/17DAP	0.88959	0.748
39DAP/27DAP	0.96468	0.795
41DAP/39DAP	0.78509	0.024
42DAP/41DAP	1.17942	0.514
43DAP/42DAP	1.32627	0.042
47DAP/43DAP	0.85927	0.145
52DAP/47DAP	1.25101	0.36
57DAP/52DAP	0.81391	0.426
57DAP/7DAP	0.90328	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10551	0.461
17DAP/reference	1.08406	0.112
27DAP/reference	0.99792	0.656
39DAP/reference	1.03143	0.96
41DAP/reference	0.93568	0.259
42DAP/reference	1.04869	0.686
43DAP/reference	0.94546	0.279
47DAP/reference	1.01393	1
52DAP/reference	0.83928	0.049
57DAP/reference	0.88638	0.066

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88315	0.14
17DAP/reference	0.79359	0.052
27DAP/reference	0.82824	0.024
39DAP/reference	1.00649	0.769
41DAP/reference	1.01192	1
42DAP/reference	0.9218	0.15
43DAP/reference	0.93673	0.344
47DAP/reference	0.96497	0.349
52DAP/reference	0.94034	0.239
57DAP/reference	0.9207	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28651	0.047
17DAP/reference	0.98726	0.739
27DAP/reference	1.03594	0.903
39DAP/reference	0.87226	0.031
41DAP/reference	0.94951	0.417
42DAP/reference	1.11011	0.433
43DAP/reference	1.04907	0.91
47DAP/reference	1.17683	0.099
52DAP/reference	1.15203	0.377
57DAP/reference	1.14286	0.18

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00125	1
26DAP/20DAP	1.37193	0.499
34DAP/26DAP	1.14863	0.819
51DAP/34DAP	N/A	N/A
52DAP/51DAP	1.18581	0.565
53DAP/52DAP	0.75881	0.484
55DAP/53DAP	1.06553	0.806
57DAP/55DAP	1.07247	1
62DAP/57DAP	1.05898	1
68DAP/62DAP	0.98752	0.863
68DAP/14DAP	1.19641	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.26192	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09355	0.666
Mature Green Tomato/Ripe Tomato	2.0767	0.149
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.86162
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.32131	0.536
1-1-2/M82	0.90594	1
12-2/M82	1.16975	0.519
12-4/M82	0.90782	1
1-3/M82	0.76433
2-1-1/M82	0.72093
2-1/M82	N/A	N/A
2-6/M82	1.33715	0.695
3-2/M82	0.67206
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	1.10589	0.125
5-3/M82	0.90963	1
6-2/M82	1.4395
6-3/M82	N/A	N/A
7-1/M82	1.05432
7-2/M82	1.00789
9-3-2/M82	1.10157

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12891	0.229
IL2-6/WTpooled	1.10059	0.659
IL7-5/WTpooled	1.15459	0.792
IL7-3/WTpooled	1.13143	1
IL12-4/WTpooled	0.80775	0.581
IL1-4/WTpooled	1.05278	1
WT/WTpooled	1.01611	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	0.72563	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92387	0.941
DC3000/delta hrp 6h	1.13932	1
DC3000/delta hrp 12h	1.01169	1
DC3000/delta hrp 24h	0.56855	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80535	0.388
DC3000 delta B/DC3000 delta AB	0.83913	0.097

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85241	1
Exp 36h	0.67297	0.471
Exp 60h	0.6522	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95469	1
Var 0h	1.89547	0.98
Var 12h I row2-row1	0.82151	0.39
Var 12h NI row2-row1	0.99618	1
Var 36h I row2-row1	1.26397	0.908
Var 36h NI row2-row1	1.29434	0.482
Var 60h I row2-row1	0.98368	1
Var 60h NI row2-row1	0.98659	1
Time course 0hI-0hNI	0.96583	0.827
Time course 12hI-12hNI	0.98429	0.909
Time course 36hI-36hNI	0.87926	0.042
Time course 60hI-60hNI	0.18628	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)	1.38821	0.297
transgenic ySAMdc/azygous control (breaker)	2.076	0.162
transgenic ySAMdc/azygous control (red)	1.42265	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9352	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.12006	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.6398	0.093
Manapal/WT (break)	2.24419	0.183
Manapal/WT (red)	2.34277	0.142