Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.10.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15097	0.838
27DAP/17DAP	0.77456	0.344
39DAP/27DAP	0.96099	0.67
41DAP/39DAP	1.45803	0.284
42DAP/41DAP	1.1922	0.912
43DAP/42DAP	0.76645	0.649
47DAP/43DAP	0.81961	0.449
52DAP/47DAP	1.80605	0.371
57DAP/52DAP	0.84933	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98398	0.601
17DAP/reference	0.92692	0.111
27DAP/reference	0.94968	0.295
39DAP/reference	0.94237	0.37
41DAP/reference	0.90784	0.267
42DAP/reference	0.97148	0.295
43DAP/reference	1.07938	0.217
47DAP/reference	0.87325	0.011
52DAP/reference	0.82719	0.026
57DAP/reference	0.94708	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04073	0.581
27DAP/17DAP	0.86287	0.724
39DAP/27DAP	1.09184	0.548
41DAP/39DAP	1.04923	0.79
42DAP/41DAP	1.07254	0.635
43DAP/42DAP	0.94176	0.351
47DAP/43DAP	1.00026	0.99
52DAP/47DAP	1.15531	0.539
57DAP/52DAP	1.04685	0.777
57DAP/7DAP	1.05808	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31715	0.085
17DAP/reference	1.57692	0.006
27DAP/reference	1.59995	0.006
39DAP/reference	1.70327	0.005
41DAP/reference	1.73282	0.011
42DAP/reference	1.8115	0.006
43DAP/reference	1.98679	0.006
47DAP/reference	1.30676	0.224
52DAP/reference	1.76735	0.007
57DAP/reference	1.47282	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18847	0.078
17DAP/reference	1.10426	0.081
27DAP/reference	0.91183	0.203
39DAP/reference	0.87685	0.119
41DAP/reference	0.83372	0.029
42DAP/reference	0.83515	0.023
43DAP/reference	1.13555	0.222
47DAP/reference	0.93184	0.102
52DAP/reference	1.01284	0.988
57DAP/reference	1.29815	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17158	0.03
17DAP/reference	1.19194	0.173
27DAP/reference	1.33385	0.023
39DAP/reference	1.4171	0.011
41DAP/reference	1.43809	0.016
42DAP/reference	1.28281	0.199
43DAP/reference	1.30074	0.336
47DAP/reference	1.00537	0.731
52DAP/reference	1.42972	0.094
57DAP/reference	0.92913	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88734	0.52
26DAP/20DAP	1.16183	0.477
34DAP/26DAP	0.96029	0.927
51DAP/34DAP	1.00897	0.978
52DAP/51DAP	0.91632	1
53DAP/52DAP	1.27998	0.138
55DAP/53DAP	1.13242	0.13
57DAP/55DAP	0.93126	0.688
62DAP/57DAP	1.13959	0.217
68DAP/62DAP	0.91403	0.668
68DAP/14DAP	0.74301	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13608	0.151

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.30025	0.071
Mature Green Tomato/Ripe Tomato	1.19398	1
Immature Eggplant/Mature Eggplant	1.29421	0.174
Ripe Pepper/Ripe Tomato	5.25761	0.256
Mature Eggplant/Ripe Tomato	1.69738	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9561	0.944
1-1-2/M82	0.9554	1
12-2/M82	0.99407	1
12-4/M82	1.04315	1
1-3/M82	0.78833	0.378
2-1-1/M82	0.92798	1
2-1/M82	N/A	N/A
2-6/M82	1.18833	0.695
3-2/M82	0.93407	0.752
4-1-1/M82	1.06332	1
4-1/M82	0.75471	1
4-3-2/M82	0.85212	1
4-3/M82	0.95223	1
5-3/M82	0.91839	0.642
6-2/M82	1.06591
6-3/M82	N/A	N/A
7-1/M82	0.99833	1
7-2/M82	1.01342	1
9-3-2/M82	0.89495	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.70968
IL2-6/WTpooled	1.79242	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.30051	1
IL12-4/WTpooled	1.40577	0.42
IL1-4/WTpooled	2.1064	1
WT/WTpooled	1.03778	0.957

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	1.05906	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98846	1
DC3000/delta hrp 6h	1.0791	1
DC3000/delta hrp 12h	1.02547	1
DC3000/delta hrp 24h	0.98609	0.966

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0127
DC3000 delta B/DC3000 delta AB	1.09061	0.403

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85911	1
Exp 36h	0.80955	0.426
Exp 60h	0.78064	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99128	1
Var 0h	1.01313	1
Var 12h I row2-row1	0.94988	0.418
Var 12h NI row2-row1	1.02239	1
Var 36h I row2-row1	0.8822	1
Var 36h NI row2-row1	0.9016	0.584
Var 60h I row2-row1	0.95831	0.439
Var 60h NI row2-row1	0.95735	0.977
Time course 0hI-0hNI	1.05735	0.799
Time course 12hI-12hNI	1.04422	0.678
Time course 36hI-36hNI	1.2202	0.006
Time course 60hI-60hNI	1.51062	0.011

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)	0.99035	0.789
transgenic ySAMdc/azygous control (breaker)	0.81975	0.142
transgenic ySAMdc/azygous control (red)	0.97672	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95597	0.131

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.63372	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13138	0.096
Manapal/WT (break)	1.10577	1
Manapal/WT (red)	1.36796	0.164