Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.9.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.7574	0.148
27DAP/17DAP	1.11874	0.868
39DAP/27DAP	1.38139	0.287
41DAP/39DAP	0.60671	0.05
42DAP/41DAP	1.27798	0.903
43DAP/42DAP	1.15442	0.993
47DAP/43DAP	1.32763	0.538
52DAP/47DAP	0.9906	0.779
57DAP/52DAP	1.21523	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4541	0.097
17DAP/reference	0.98534	0.597
27DAP/reference	0.96677
39DAP/reference	0.98143	0.611
41DAP/reference	1.30627	0.312
42DAP/reference	1.09482	0.045
43DAP/reference	0.98291	0.745
47DAP/reference	1.11969	0.002
52DAP/reference	1.20958	0.079
57DAP/reference	1.17049	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.50064	0.036
27DAP/17DAP	1.22607	0.403
39DAP/27DAP	1.03457	0.728
41DAP/39DAP	1.3398	0.763
42DAP/41DAP	1.03408	1
43DAP/42DAP	0.87301	0.105
47DAP/43DAP	1.0158	0.951
52DAP/47DAP	1.24589	0.439
57DAP/52DAP	1.09177	0.563
57DAP/7DAP	1.29285	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3135	0.045
17DAP/reference	1.06691	0.822
27DAP/reference	1.26444	0.011
39DAP/reference	1.23879	0.044
41DAP/reference	1.2367	0.031
42DAP/reference	1.32554	0.016
43DAP/reference	1.32494	0.029
47DAP/reference	1.00756	1
52DAP/reference	1.28524	0.016
57DAP/reference	1.28354	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09401	0.304
17DAP/reference	1.1765	0.028
27DAP/reference	0.9363	0.483
39DAP/reference	1.09451	0.529
41DAP/reference	0.98617	0.531
42DAP/reference	1.10526	0.476
43DAP/reference	0.98569	0.706
47DAP/reference	1.0333	0.695
52DAP/reference	1.0641	0.343
57DAP/reference	1.03155	0.609

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3269	0.029
17DAP/reference	1.09337	0.224
27DAP/reference	1.11041	0.198
39DAP/reference	1.14779	0.094
41DAP/reference	1.10995	0.286
42DAP/reference	1.14917	0.154
43DAP/reference	1.01936	0.895
47DAP/reference	0.99838	0.708
52DAP/reference	1.26417	0.233
57DAP/reference	1.42012	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99752	1
26DAP/20DAP	1.79451	0.098
34DAP/26DAP	0.90462	0.548
51DAP/34DAP	0.75945	0.081
52DAP/51DAP	0.77172	0.151
53DAP/52DAP	1.06994	0.47
55DAP/53DAP	0.71806	0.045
57DAP/55DAP	1.03158	1
62DAP/57DAP	0.92887	0.681
68DAP/62DAP	0.98945	0.81
68DAP/14DAP	0.91264	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.85007	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05858	0.666
Mature Green Tomato/Ripe Tomato	0.90961	0.66
Immature Eggplant/Mature Eggplant	1.199	0.321
Ripe Pepper/Ripe Tomato	1.73237	1
Mature Eggplant/Ripe Tomato	1.19249	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.98174
12-2/M82	N/A	N/A
12-4/M82	1.18525
1-3/M82	0.94176
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	1.00115	1
4-1-1/M82	N/A	N/A
4-1/M82	1.17814
4-3-2/M82	0.77566	0.487
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.02943
7-2/M82	N/A	N/A
9-3-2/M82	1.03229	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.25106	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85061	1
IL12-4/WTpooled	0.88107	0.71
IL1-4/WTpooled	0.83459
WT/WTpooled	0.93729	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	1.05504	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82891	1
DC3000/delta hrp 6h	1.05196	1
DC3000/delta hrp 12h	1.10884	1
DC3000/delta hrp 24h	1.26205	0.243

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09833	0.06
DC3000 delta B/DC3000 delta AB	1.2775	0.112

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95521	1
Exp 36h	0.77172	0.406
Exp 60h	0.79761	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0023	1
Var 0h	0.78582	1
Var 12h I row2-row1	0.91962	0.338
Var 12h NI row2-row1	1.05518	0.649
Var 36h I row2-row1	1.08619	1
Var 36h NI row2-row1	0.93674	0.645
Var 60h I row2-row1	0.83001	0.285
Var 60h NI row2-row1	0.883	0.756
Time course 0hI-0hNI	1.06115	0.297
Time course 12hI-12hNI	0.9855	0.914
Time course 36hI-36hNI	1.25533	0.056
Time course 60hI-60hNI	1.66415	0.008

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)	0.87105	0.362
transgenic ySAMdc/azygous control (breaker)	0.88709	0.173
transgenic ySAMdc/azygous control (red)	1.04538	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94452	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.53197	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02632	1
Manapal/WT (break)	1.52224	0.13
Manapal/WT (red)	1.51173	0.164