Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.9.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67235	0.015
27DAP/17DAP	0.80624	0.46
39DAP/27DAP	0.89857	0.608
41DAP/39DAP	0.84518	0.422
42DAP/41DAP	1.04624	0.974
43DAP/42DAP	1.03446	1
47DAP/43DAP	1.21883	0.52
52DAP/47DAP	0.7671	0.403
57DAP/52DAP	1.00016	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.71644	0.007
17DAP/reference	1.28761	0.096
27DAP/reference	1.25953	0.018
39DAP/reference	0.97017	0.638
41DAP/reference	0.85744	0.085
42DAP/reference	1.07779	0.338
43DAP/reference	0.80954	0.061
47DAP/reference	0.91114	0.148
52DAP/reference	0.69681	0.014
57DAP/reference	0.84324	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7849	0.055
27DAP/17DAP	0.95754	0.748
39DAP/27DAP	0.75965	0.029
41DAP/39DAP	0.80202	0.059
42DAP/41DAP	0.97647	0.777
43DAP/42DAP	1.05087	0.513
47DAP/43DAP	0.96338	0.787
52DAP/47DAP	0.8994	0.612
57DAP/52DAP	1.12707	0.36
57DAP/7DAP	0.65017	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68343	0.027
17DAP/reference	1.14245	0.134
27DAP/reference	0.91321	0.033
39DAP/reference	0.78549	0.027
41DAP/reference	0.838	0.116
42DAP/reference	0.83266	0.058
43DAP/reference	0.95086	0.21
47DAP/reference	0.96081	0.383
52DAP/reference	0.749	0.012
57DAP/reference	0.88061	0.054

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52651	0.049
17DAP/reference	1.42639	0.01
27DAP/reference	1.14758	0.126
39DAP/reference	0.8924	0.189
41DAP/reference	1.03573	1
42DAP/reference	1.07417	0.274
43DAP/reference	0.79302	0.036
47DAP/reference	0.97513	0.487
52DAP/reference	0.66552	0.004
57DAP/reference	0.764	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.25983	0.015
17DAP/reference	1.44397	0.06
27DAP/reference	1.12071	0.1
39DAP/reference	0.94448	0.271
41DAP/reference	0.9051	0.185
42DAP/reference	0.95331	0.445
43DAP/reference	0.95314	0.416
47DAP/reference	0.86781	0.043
52DAP/reference	0.85708	0.228
57DAP/reference	0.83817	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04082	0.966
26DAP/20DAP	1.76469	0.099
34DAP/26DAP	1.03684	1
51DAP/34DAP	0.6603	0.058
52DAP/51DAP	1.00611	1
53DAP/52DAP	0.70319	0.049
55DAP/53DAP	0.67536	0.037
57DAP/55DAP	1.18258	0.764
62DAP/57DAP	1.04475	0.8
68DAP/62DAP	0.8203	0.227
68DAP/14DAP	0.68151	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65322	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.53454	0.058
Mature Green Tomato/Ripe Tomato	1.43278	0.022
Immature Eggplant/Mature Eggplant	0.32152	0.057
Ripe Pepper/Ripe Tomato	5.80036	1
Mature Eggplant/Ripe Tomato	15.8334	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13976
1-1-2/M82	0.67761
12-2/M82	N/A	N/A
12-4/M82	0.71722	0.319
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	0.82511
4-3-2/M82	0.69706
4-3/M82	N/A	N/A
5-3/M82	0.98589
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.90554
7-2/M82	N/A	N/A
9-3-2/M82	0.78254	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17191	0.277
IL2-6/WTpooled	0.76259	0.383
IL7-5/WTpooled	0.90875	1
IL7-3/WTpooled	1.26611	0.362
IL12-4/WTpooled	1.12292	0.531
IL1-4/WTpooled	0.9424	0.699
WT/WTpooled	1.05024	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	0.84541	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95544	1
DC3000/delta hrp 6h	1.31568	1
DC3000/delta hrp 12h	1.50614	1
DC3000/delta hrp 24h	0.45283	0.038

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44801	0.024
DC3000 delta B/DC3000 delta AB	0.50519	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90372	1
Exp 36h	0.62223	0.406
Exp 60h	0.50378	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01536	1
Var 0h	1.32653	0.98
Var 12h I row2-row1	0.81906	0.338
Var 12h NI row2-row1	0.90823	0.82
Var 36h I row2-row1	1.03546	1
Var 36h NI row2-row1	1.0856	1
Var 60h I row2-row1	1.29162	0.562
Var 60h NI row2-row1	1.36988	0.904
Time course 0hI-0hNI	0.97667	0.908
Time course 12hI-12hNI	1.0051	1
Time course 36hI-36hNI	0.79783	0.023
Time course 60hI-60hNI	0.26839	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)	0.88543	0.33
transgenic ySAMdc/azygous control (breaker)	1.10561	1
transgenic ySAMdc/azygous control (red)	0.97868	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8725	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.85589	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08951	1
Manapal/WT (break)	1.16353	1
Manapal/WT (red)	1.50476	1