Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.3.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37376	0.725
27DAP/17DAP	1.3196	0.859
39DAP/27DAP	0.99552	0.798
41DAP/39DAP	1.15676	0.742
42DAP/41DAP	0.86565	1
43DAP/42DAP	1.20635	1
47DAP/43DAP	1.14937	0.769
52DAP/47DAP	1.31806	0.491
57DAP/52DAP	1.31791	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.207	0.041
17DAP/reference	1.17323	0.089
27DAP/reference	1.08967	0.246
39DAP/reference	1.05678	1
41DAP/reference	1.21887	0.365
42DAP/reference	1.47801	0.002
43DAP/reference	0.91855	0.728
47DAP/reference	1.2849	0.001
52DAP/reference	1.22854	0.205
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80749	0.277
27DAP/17DAP	0.91907	0.684
39DAP/27DAP	1.06685	0.558
41DAP/39DAP	1.17649	0.909
42DAP/41DAP	0.86631	0.451
43DAP/42DAP	1.10049	0.699
47DAP/43DAP	1.30787	0.889
52DAP/47DAP	1.02209	0.965
57DAP/52DAP	0.82547	0.047
57DAP/7DAP	0.935	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21453	0.095
17DAP/reference	1.41754	0.008
27DAP/reference	1.42005	0.023
39DAP/reference	1.38194	0.017
41DAP/reference	1.55614	0.012
42DAP/reference	1.44377	0.018
43DAP/reference	1.47866	0.012
47DAP/reference	1.04601	0.965
52DAP/reference	1.47566	0.019
57DAP/reference	1.36732	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1048	0.308
17DAP/reference	1.36033	0.01
27DAP/reference	1.22835	0.08
39DAP/reference	1.09611	0.29
41DAP/reference	1.01478	1
42DAP/reference	0.99945	0.655
43DAP/reference	1.06543	0.91
47DAP/reference	1.05733	0.311
52DAP/reference	1.23226	0.007
57DAP/reference	1.37367	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15472	0.258
17DAP/reference	1.09195	0.595
27DAP/reference	1.41731	0.029
39DAP/reference	1.31558	0.016
41DAP/reference	1.27548	0.06
42DAP/reference	1.2422	0.074
43DAP/reference	1.09782	0.779
47DAP/reference	0.9414	0.335
52DAP/reference	1.50363	0.179
57DAP/reference	0.90445	0.221

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0083	1
26DAP/20DAP	1.82238	0.14
34DAP/26DAP	0.66977	0.247
51DAP/34DAP	1.76886	0.159
52DAP/51DAP	0.81029	1
53DAP/52DAP	1.03219	0.99
55DAP/53DAP	1.02843	1
57DAP/55DAP	1.18211	0.764
62DAP/57DAP	1.27054	0.833
68DAP/62DAP	0.71517	0.406
68DAP/14DAP	0.81483	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.33619	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.08246	1
Mature Green Tomato/Ripe Tomato	1.18905
Immature Eggplant/Mature Eggplant	1.09934	0.248
Ripe Pepper/Ripe Tomato	0.51268	0.224
Mature Eggplant/Ripe Tomato	0.95355	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.88159
12-2/M82	N/A	N/A
12-4/M82	0.75489
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.60024	1
5-3/M82	1.2118
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.24116
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17799	0.225
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.40971	0.75
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.30137	1
WT/WTpooled	1.80974

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	0.8862	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92044	1
DC3000/delta hrp 6h	1.65602	1
DC3000/delta hrp 12h	1.07156	1
DC3000/delta hrp 24h	0.65563	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78874	0.66
DC3000 delta B/DC3000 delta AB	1.05876	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24191	1
Exp 36h	1.02595	1
Exp 60h	1.10746	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99093	1
Var 0h	0.87985	0.933
Var 12h I row2-row1	0.75171	0.467
Var 12h NI row2-row1	1.10006	1
Var 36h I row2-row1	0.9756	1
Var 36h NI row2-row1	1.18401	0.482
Var 60h I row2-row1	0.94869	0.306
Var 60h NI row2-row1	1.10899	0.904
Time course 0hI-0hNI	0.93632	0.656
Time course 12hI-12hNI	0.98509	0.931
Time course 36hI-36hNI	0.94903	0.366
Time course 60hI-60hNI	0.71098	0.047

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)	1.06304	0.612
transgenic ySAMdc/azygous control (breaker)	0.85204	0.173
transgenic ySAMdc/azygous control (red)	1.15463	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08431	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87475	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15	0.14
Manapal/WT (break)	1.05715	1
Manapal/WT (red)	1.1408	1