Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3586	0.534
27DAP/17DAP	1.54243	0.392
39DAP/27DAP	0.94334	0.663
41DAP/39DAP	0.92422	0.678
42DAP/41DAP	1.81377	0.025
43DAP/42DAP	0.86853	0.741
47DAP/43DAP	1.5712	0.369
52DAP/47DAP	0.86949	0.639
57DAP/52DAP	0.86235	0.833

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87144	0.145
17DAP/reference	0.92937	0.138
27DAP/reference	1.0982	0.132
39DAP/reference	1.0336	0.615
41DAP/reference	0.93608	0.434
42DAP/reference	0.87851	0.004
43DAP/reference	0.9231	0.17
47DAP/reference	0.93453	0.106
52DAP/reference	1.07371	0.04
57DAP/reference	1.02209	0.853

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02913	0.899
27DAP/17DAP	0.90972	0.508
39DAP/27DAP	1.31	0.068
41DAP/39DAP	0.93558	0.793
42DAP/41DAP	1.20203	0.063
43DAP/42DAP	1.24816	0.147
47DAP/43DAP	0.94603	0.617
52DAP/47DAP	1.11665	0.589
57DAP/52DAP	0.88681	0.16
57DAP/7DAP	1.14149	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84641	0.095
17DAP/reference	0.87763	0.056
27DAP/reference	0.78704	0.026
39DAP/reference	0.98306	0.552
41DAP/reference	0.88737	0.166
42DAP/reference	0.85486	0.144
43DAP/reference	0.82579	0.069
47DAP/reference	0.85031	0.168
52DAP/reference	0.80394	0.077
57DAP/reference	1.06937	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95404	0.362
17DAP/reference	0.9304	0.116
27DAP/reference	0.96638	0.407
39DAP/reference	0.93351	0.265
41DAP/reference	0.94469	0.268
42DAP/reference	0.90198	0.135
43DAP/reference	1.03174	0.777
47DAP/reference	0.86412	0.049
52DAP/reference	1.05121	0.559
57DAP/reference	0.94959	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00101	0.653
17DAP/reference	0.91108	0.308
27DAP/reference	0.93774	0.319
39DAP/reference	0.79656	0.021
41DAP/reference	0.82782	0.024
42DAP/reference	0.87678	0.22
43DAP/reference	0.89364	0.158
47DAP/reference	0.99511	0.646
52DAP/reference	0.82651	0.223
57DAP/reference	0.85701	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88851	0.915
26DAP/20DAP	0.51734	0.228
34DAP/26DAP	1.09398	0.819
51DAP/34DAP	2.11368	0.031
52DAP/51DAP	0.80816	0.151
53DAP/52DAP	2.11741	0.02
55DAP/53DAP	1.10345	0.306
57DAP/55DAP	1.28396	0.682
62DAP/57DAP	0.51555	0.002
68DAP/62DAP	0.90162	0.543
68DAP/14DAP	1.29059	0.041

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20551	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.0541	0.06
Mature Green Tomato/Ripe Tomato	0.78959	0.079
Immature Eggplant/Mature Eggplant	7.08864	0.05
Ripe Pepper/Ripe Tomato	0.9077	1
Mature Eggplant/Ripe Tomato	0.23307	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.54354	0.742
1-1-2/M82	0.96891	1
12-2/M82	1.06122	1
12-4/M82	1.07999	1
1-3/M82	1.36853	0.26
2-1-1/M82	0.89891	0.92
2-1/M82	1.26227	0.345
2-6/M82	1.12968	0.695
3-2/M82	1.29956	0.717
4-1-1/M82	0.85964	1
4-1/M82	N/A	N/A
4-3-2/M82	0.75002	0.487
4-3/M82	1.09499	1
5-3/M82	0.83241	0.642
6-2/M82	1.05928	1
6-3/M82	1.05181	1
7-1/M82	1.11415	1
7-2/M82	0.94176	0.881
9-3-2/M82	0.89844	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91319	0.243
IL2-6/WTpooled	1.27916	0.419
IL7-5/WTpooled	0.67699	0.483
IL7-3/WTpooled	0.97672	1
IL12-4/WTpooled	1.02583	0.785
IL1-4/WTpooled	1.01184	1
WT/WTpooled	1.00022	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	2.01834	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06537	0.921
DC3000/delta hrp 6h	0.77704	0.947
DC3000/delta hrp 12h	1.18873	1
DC3000/delta hrp 24h	1.03623	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1931	0.121
DC3000 delta B/DC3000 delta AB	1.22306	0.703

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	2.29402	1
Exp 60h	2.24223	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04124
Var 0h	0.89684	0.457
Var 12h I row2-row1	1.10255	0.443
Var 12h NI row2-row1	0.72519	0.713
Var 36h I row2-row1	0.9775	1
Var 36h NI row2-row1	0.7728	0.61
Var 60h I row2-row1	0.99753	1
Var 60h NI row2-row1	1.30588	0.904
Time course 0hI-0hNI	1.16154	0.662
Time course 12hI-12hNI	1.05337	0.773
Time course 36hI-36hNI	1.16141	0.07
Time course 60hI-60hNI	2.69277	0.022

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)	0.85199	0.278
transgenic ySAMdc/azygous control (breaker)	0.71348	0.251
transgenic ySAMdc/azygous control (red)	1.19594	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03397	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.44556	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.61791	0.172
Manapal/WT (break)	0.64214	0.299
Manapal/WT (red)	0.43288	0.181