Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.14.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02103	0.997
27DAP/17DAP	0.97182	0.984
39DAP/27DAP	0.79148	0.447
41DAP/39DAP	1.22672	0.638
42DAP/41DAP	1.04918	1
43DAP/42DAP	0.98355	0.918
47DAP/43DAP	1.19654	0.584
52DAP/47DAP	1.15659	0.794
57DAP/52DAP	0.92812	0.779

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23646	0.126
17DAP/reference	0.97695	0.63
27DAP/reference	1.01914	0.771
39DAP/reference	1.02846	0.393
41DAP/reference	1.10247	0.158
42DAP/reference	1.23954	0.001
43DAP/reference	0.99168	0.84
47DAP/reference	1.03442	0.509
52DAP/reference	1.05769	0.498
57DAP/reference	0.9718	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98466	0.763
27DAP/17DAP	1.04022	0.915
39DAP/27DAP	1.0169	0.832
41DAP/39DAP	0.9533	0.839
42DAP/41DAP	1.05237	0.893
43DAP/42DAP	0.94079	0.482
47DAP/43DAP	1.04022	0.906
52DAP/47DAP	1.00836	0.979
57DAP/52DAP	0.99548	0.857
57DAP/7DAP	1.09612	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98265	0.613
17DAP/reference	0.94182	0.039
27DAP/reference	0.95953	0.094
39DAP/reference	0.94322	0.031
41DAP/reference	0.8902	0.038
42DAP/reference	0.94397	0.06
43DAP/reference	0.95219	0.095
47DAP/reference	0.94669	0.222
52DAP/reference	0.91598	0.066
57DAP/reference	0.93652	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14808	0.043
17DAP/reference	1.15861	0.127
27DAP/reference	1.10903	0.735
39DAP/reference	1.0308	0.935
41DAP/reference	1.00959	0.735
42DAP/reference	0.98479	0.594
43DAP/reference	1.22365	0.081
47DAP/reference	0.95943	0.319
52DAP/reference	1.10596	0.074
57DAP/reference	1.09172	0.423

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96512	0.082
17DAP/reference	1.08437	0.551
27DAP/reference	0.90544	0.04
39DAP/reference	0.93991	0.083
41DAP/reference	0.92469	0.025
42DAP/reference	1.03566	0.671
43DAP/reference	1.0137	0.949
47DAP/reference	1.04875	0.228
52DAP/reference	0.94448	0.385
57DAP/reference	1.22241	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12308	0.966
26DAP/20DAP	1.01175	1
34DAP/26DAP	0.95723	0.909
51DAP/34DAP	1.03005	0.854
52DAP/51DAP	1.01779	0.888
53DAP/52DAP	1.10364	0.608
55DAP/53DAP	1.10807	0.15
57DAP/55DAP	0.89675	0.496
62DAP/57DAP	1.08392	0.622
68DAP/62DAP	0.75395	0.314
68DAP/14DAP	0.99565	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9808	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.54296	0.114
Mature Green Tomato/Ripe Tomato	1.04356	0.814
Immature Eggplant/Mature Eggplant	1.97613	0.05
Ripe Pepper/Ripe Tomato	1.2431	1
Mature Eggplant/Ripe Tomato	0.56181	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00831	1
1-1-2/M82	0.95704	1
12-2/M82	1.20034	1
12-4/M82	0.93201	1
1-3/M82	1.02175	1
2-1-1/M82	0.94665
2-1/M82	N/A	N/A
2-6/M82	0.93418	0.501
3-2/M82	0.98615
4-1-1/M82	1.01238
4-1/M82	0.88896	1
4-3-2/M82	1.05069	1
4-3/M82	0.98061	1
5-3/M82	0.98134	1
6-2/M82	0.96358	1
6-3/M82	1.00932	1
7-1/M82	1.0195
7-2/M82	1.02797	1
9-3-2/M82	1.00106	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.64736	0.277
IL2-6/WTpooled	0.83422	0.473
IL7-5/WTpooled	1.01819	0.792
IL7-3/WTpooled	1.02103	1
IL12-4/WTpooled	0.89645	0.581
IL1-4/WTpooled	1.23786	1
WT/WTpooled	1.03398	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	0.94416	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96831	1
DC3000/delta hrp 6h	1.02161	1
DC3000/delta hrp 12h	0.95547	1
DC3000/delta hrp 24h	1.01466	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.93556	0.46
DC3000 delta B/DC3000 delta AB	0.96117	0.483

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02533	1
Exp 36h	0.85615	0.699
Exp 60h	1.02257	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97939	1
Var 0h	1.11965	0.98
Var 12h I row2-row1	0.98589	0.856
Var 12h NI row2-row1	1.04876	1
Var 36h I row2-row1	0.83394	0.805
Var 36h NI row2-row1	0.99563	1
Var 60h I row2-row1	1.0081	1
Var 60h NI row2-row1	1.03874	0.904
Time course 0hI-0hNI	1.03909	0.764
Time course 12hI-12hNI	0.9698	0.716
Time course 36hI-36hNI	1.0242	0.799
Time course 60hI-60hNI	0.77543	0.007

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)	0.86399	0.246
transgenic ySAMdc/azygous control (breaker)	1.07476	1
transgenic ySAMdc/azygous control (red)	1.34212	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03334	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33732	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.02839	0.086
Manapal/WT (break)	1.84416	0.183
Manapal/WT (red)	1.43869	0.164