Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.10.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89155	0.464
27DAP/17DAP	0.48849	0.027
39DAP/27DAP	0.57052	0.241
41DAP/39DAP	0.54138	0.041
42DAP/41DAP	0.8477	1
43DAP/42DAP	1.21077	0.929
47DAP/43DAP	0.48755	0.049
52DAP/47DAP	1.45071	0.691
57DAP/52DAP	0.98264	0.966

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4666	0.011
17DAP/reference	0.81527	0.111
27DAP/reference	0.62407	0.031
39DAP/reference	0.60592	0.023
41DAP/reference	0.43363	0.008
42DAP/reference	0.44504	0.001
43DAP/reference	0.37932	0.012
47DAP/reference	0.51888	0.007
52DAP/reference	0.32669	0.012
57DAP/reference	0.40685	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97387	0.697
27DAP/17DAP	0.86066	0.508
39DAP/27DAP	0.48637	0.028
41DAP/39DAP	1.34379	0.037
42DAP/41DAP	0.79441	0.033
43DAP/42DAP	0.66122	0.022
47DAP/43DAP	0.98511	0.93
52DAP/47DAP	0.91555	0.778
57DAP/52DAP	0.90226	0.473
57DAP/7DAP	0.52188	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.85324	0.025
17DAP/reference	1.43702	0.006
27DAP/reference	1.41317	0.008
39DAP/reference	1.73529	0.009
41DAP/reference	1.34967	0.28
42DAP/reference	1.66564	0.014
43DAP/reference	1.651	0.007
47DAP/reference	1.35432	0.671
52DAP/reference	1.89804	0.021
57DAP/reference	1.43287	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06641	0.704
17DAP/reference	0.80416	0.068
27DAP/reference	0.7407	0.051
39DAP/reference	0.46482	0.007
41DAP/reference	0.62779	0.038
42DAP/reference	0.39857	0.01
43DAP/reference	0.3455	0.002
47DAP/reference	0.44081	0.01
52DAP/reference	0.43136	0.003
57DAP/reference	0.33405	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.58548	0.015
17DAP/reference	1.91548	0.075
27DAP/reference	1.84118	0.017
39DAP/reference	1.69074	0.012
41DAP/reference	1.15289	0.286
42DAP/reference	1.12728	0.994
43DAP/reference	1.00571	0.545
47DAP/reference	0.43412	0.004
52DAP/reference	0.84519	0.334
57DAP/reference	0.9271	0.315

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15622	0.966
26DAP/20DAP	0.76463	0.512
34DAP/26DAP	1.00206	1
51DAP/34DAP	0.818	0.209
52DAP/51DAP	0.87331	1
53DAP/52DAP	1.00347	1
55DAP/53DAP	1.14991	0.355
57DAP/55DAP	0.86495	0.309
62DAP/57DAP	1.12638	0.723
68DAP/62DAP	1.1958	0.936
68DAP/14DAP	0.58932	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.75274	0.062

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.76762	0.058
Mature Green Tomato/Ripe Tomato	27.1548	0.015
Immature Eggplant/Mature Eggplant	0.31922	0.058
Ripe Pepper/Ripe Tomato	12.6478	1
Mature Eggplant/Ripe Tomato	27.6833	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.12762	1
12-2/M82	0.61144
12-4/M82	0.81561	1
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	1.26592
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	N/A	N/A
5-3/M82	1.77665	0.467
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.80407
7-2/M82	0.18275
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15572	0.277
IL2-6/WTpooled	1.17448	0.456
IL7-5/WTpooled	0.99454	1
IL7-3/WTpooled	0.98848	1
IL12-4/WTpooled	1.02616	0.737
IL1-4/WTpooled	0.95421	0.834
WT/WTpooled	1.00771	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	0.78875	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90242	0.839
DC3000/delta hrp 6h	0.89472	0.95
DC3000/delta hrp 12h	1.07594	1
DC3000/delta hrp 24h	1.0523	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.5262	0.026
DC3000 delta B/DC3000 delta AB	0.44771	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84916	1
Exp 36h	0.92422	0.699
Exp 60h	0.86624	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00484	1
Var 0h	1.0126	1
Var 12h I row2-row1	0.8385	0.565
Var 12h NI row2-row1	1.10364	1
Var 36h I row2-row1	0.8803	0.805
Var 36h NI row2-row1	0.93435	0.645
Var 60h I row2-row1	1.30434	0.562
Var 60h NI row2-row1	0.96775	1
Time course 0hI-0hNI	0.96339	0.699
Time course 12hI-12hNI	0.96175	0.682
Time course 36hI-36hNI	0.97687	0.29
Time course 60hI-60hNI	0.56642	0.015

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)	1.08196	0.571
transgenic ySAMdc/azygous control (breaker)	4.80086	0.165
transgenic ySAMdc/azygous control (red)	1.58327	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.53389	0.085

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.3252	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.40312	0.093
Manapal/WT (break)	16.7331	0.126
Manapal/WT (red)	4.04176	0.222