Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.2.12.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12154	0.725
27DAP/17DAP	0.90377	0.7
39DAP/27DAP	1.17933	0.765
41DAP/39DAP	0.91913	0.623
42DAP/41DAP	1.16616	0.886
43DAP/42DAP	0.99875	0.937
47DAP/43DAP	1.13183	0.715
52DAP/47DAP	1.07286	0.999
57DAP/52DAP	0.99118	0.932

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14302	0.105
17DAP/reference	1.0985	0.08
27DAP/reference	1.04719	0.559
39DAP/reference	1.07719	0.262
41DAP/reference	1.22151	0.079
42DAP/reference	1.10209	0.002
43DAP/reference	1.01981	0.928
47DAP/reference	1.00077	0.72
52DAP/reference	1.09902	0.045
57DAP/reference	0.89868	0.024

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1068	0.87
27DAP/17DAP	1.06888	0.681
39DAP/27DAP	0.95297	0.587
41DAP/39DAP	0.89456	0.42
42DAP/41DAP	1.05581	0.763
43DAP/42DAP	0.989	0.902
47DAP/43DAP	1.08991	0.681
52DAP/47DAP	0.98725	0.93
57DAP/52DAP	1.00588	0.926
57DAP/7DAP	0.9322	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97242	0.326
17DAP/reference	0.97949	0.253
27DAP/reference	0.9318	0.066
39DAP/reference	0.844	0.011
41DAP/reference	0.93448	0.111
42DAP/reference	0.93072	0.066
43DAP/reference	0.84158	0.017
47DAP/reference	0.90419	0.222
52DAP/reference	0.90582	0.163
57DAP/reference	0.95285	0.411

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10601	0.048
17DAP/reference	1.13386	0.029
27DAP/reference	1.13543	0.323
39DAP/reference	1.05964	0.502
41DAP/reference	1.1438	0.394
42DAP/reference	1.16404	0.094
43DAP/reference	1.14589	0.373
47DAP/reference	1.07491	0.128
52DAP/reference	1.17815	0.014
57DAP/reference	1.25982	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21944	0.062
17DAP/reference	1.10703	0.612
27DAP/reference	1.06991	0.447
39DAP/reference	1.01223	0.858
41DAP/reference	0.96337	0.293
42DAP/reference	0.99581	0.816
43DAP/reference	1.02138	0.895
47DAP/reference	0.94051	0.215
52DAP/reference	0.92669	0.385
57DAP/reference	0.77824	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88211	0.807
26DAP/20DAP	0.90661	0.512
34DAP/26DAP	0.9821	0.988
51DAP/34DAP	0.95324	0.714
52DAP/51DAP	0.88265	1
53DAP/52DAP	1.23847	0.444
55DAP/53DAP	0.93482	0.577
57DAP/55DAP	1.08483	0.914
62DAP/57DAP	0.82113	0.088
68DAP/62DAP	0.876	0.505
68DAP/14DAP	0.76082	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02523	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.76551	0.058
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.56813	0.078
Ripe Pepper/Ripe Tomato	0.9069	0.224
Mature Eggplant/Ripe Tomato	1.5411	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	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	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93172	0.321
IL2-6/WTpooled	1.01591	1
IL7-5/WTpooled	1.01275	1
IL7-3/WTpooled	0.95229	0.418
IL12-4/WTpooled	0.96407	1
IL1-4/WTpooled	0.98031	0.834
WT/WTpooled	0.95818	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	0.92208	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.24631	0.921
DC3000/delta hrp 6h	1.06154	1
DC3000/delta hrp 12h	0.88691	1
DC3000/delta hrp 24h	1.24371	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.72036	0.043
DC3000 delta B/DC3000 delta AB	0.61409	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03409	1
Exp 36h	1.38853	0.693
Exp 60h	1.10381	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01187	1
Var 0h	0.93251	1
Var 12h I row2-row1	0.84171	0.338
Var 12h NI row2-row1	0.99201	1
Var 36h I row2-row1	0.97157	1
Var 36h NI row2-row1	1.1603	0.482
Var 60h I row2-row1	0.959	0.832
Var 60h NI row2-row1	1.00013	1
Time course 0hI-0hNI	1.02313	0.852
Time course 12hI-12hNI	0.94565	0.586
Time course 36hI-36hNI	0.9024	0.071
Time course 60hI-60hNI	0.41532	0.005

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)	1.44455	0.267
transgenic ySAMdc/azygous control (breaker)	0.8988	0.251
transgenic ySAMdc/azygous control (red)	0.95731	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95816	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14866	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98837	1
Manapal/WT (break)	0.89929	1
Manapal/WT (red)	0.96845	0.863