Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22596	0.575
27DAP/17DAP	1.36802	0.613
39DAP/27DAP	1.275	0.444
41DAP/39DAP	1.1338	0.696
42DAP/41DAP	0.91832	1
43DAP/42DAP	0.92287	0.865
47DAP/43DAP	1.30037	0.689
52DAP/47DAP	0.85552	0.612
57DAP/52DAP	1.17739	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90162	0.08
17DAP/reference	0.88812	0.053
27DAP/reference	1.06648	0.435
39DAP/reference	0.96773	0.624
41DAP/reference	0.85397	0.018
42DAP/reference	0.93107	0.169
43DAP/reference	0.91834	0.273
47DAP/reference	1.0516	0.794
52DAP/reference	1.02581	0.912
57DAP/reference	1.14324	0.097

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25052	0.264
27DAP/17DAP	0.88167	0.724
39DAP/27DAP	1.13787	0.519
41DAP/39DAP	0.97448	0.973
42DAP/41DAP	1.01557	0.926
43DAP/42DAP	0.85522	0.043
47DAP/43DAP	1.13892	0.601
52DAP/47DAP	0.87297	0.528
57DAP/52DAP	1.16412	0.871
57DAP/7DAP	1.24537	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01517	1
17DAP/reference	0.87211	0.094
27DAP/reference	1.01686	0.8
39DAP/reference	0.92181	0.17
41DAP/reference	0.89557	0.049
42DAP/reference	0.92079	0.262
43DAP/reference	0.8706	0.086
47DAP/reference	1.20281	0.049
52DAP/reference	1.0685	0.428
57DAP/reference	1.10265	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94564	0.457
17DAP/reference	0.81821	0.017
27DAP/reference	0.97699	0.393
39DAP/reference	0.92002	0.265
41DAP/reference	1.20195	0.285
42DAP/reference	0.98128	0.534
43DAP/reference	0.78905	0.02
47DAP/reference	0.94062	0.319
52DAP/reference	0.86755	0.037
57DAP/reference	0.90524	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9153	0.335
17DAP/reference	0.92036	0.477
27DAP/reference	1.00797	0.843
39DAP/reference	0.9419	0.464
41DAP/reference	0.84038	0.077
42DAP/reference	1.04439	1
43DAP/reference	1.09506	0.655
47DAP/reference	0.88582	0.045
52DAP/reference	0.86436	0.303
57DAP/reference	1.19562	0.046

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91533	1
26DAP/20DAP	1.25492	1
34DAP/26DAP	1.11758	1
51DAP/34DAP	0.74392	0.385
52DAP/51DAP	1.36851	0.51
53DAP/52DAP	1.01501	0.99
55DAP/53DAP	1.12961	1
57DAP/55DAP	0.95944	0.831
62DAP/57DAP	0.96807	0.994
68DAP/62DAP	1.30399	0.565
68DAP/14DAP	1.13948	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.56989	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.98364	0.058
Mature Green Tomato/Ripe Tomato	0.70424	0.038
Immature Eggplant/Mature Eggplant	1.29652	0.058
Ripe Pepper/Ripe Tomato	0.08618	0.224
Mature Eggplant/Ripe Tomato	0.69233	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78858	0.634
1-1-2/M82	1.05316	1
12-2/M82	0.61906
12-4/M82	1.32655	1
1-3/M82	1.66958	0.277
2-1-1/M82	0.8675
2-1/M82	1.06437	1
2-6/M82	0.81161	0.501
3-2/M82	1.35905
4-1-1/M82	0.86235
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.90726	0.268
5-3/M82	1.06261	1
6-2/M82	1.43932
6-3/M82	0.47917	0.387
7-1/M82	1.12306
7-2/M82	1.14601	0.385
9-3-2/M82	1.22411

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.99248	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00166	1
DC3000/delta hrp 6h	1.02047	1
DC3000/delta hrp 12h	0.95968	1
DC3000/delta hrp 24h	1.0935	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00479	0.955
DC3000 delta B/DC3000 delta AB	0.94185	0.638

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10426	1
Exp 36h	1.369	1
Exp 60h	1.00295	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.24702	0.259
Var 12h I row2-row1	1.11708	0.283
Var 12h NI row2-row1	0.95573
Var 36h I row2-row1	1.0879	1
Var 36h NI row2-row1	1.26049	1
Var 60h I row2-row1	1.27426	0.562
Var 60h NI row2-row1	0.93396	0.516
Time course 0hI-0hNI	0.98384	0.981
Time course 12hI-12hNI	0.94284	0.701
Time course 36hI-36hNI	1.01459	0.975
Time course 60hI-60hNI	1.24031	1

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)	1.06617	0.571
transgenic ySAMdc/azygous control (breaker)	1.51339	0.248
transgenic ySAMdc/azygous control (red)	0.93881	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1816	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99353	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12862	1
Manapal/WT (break)	1.37972	1
Manapal/WT (red)	1.25114	0.413