Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.4.6.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08781	0.798
27DAP/17DAP	1.17859	0.801
39DAP/27DAP	1.02698	0.876
41DAP/39DAP	1.11816	0.603
42DAP/41DAP	0.89561	1
43DAP/42DAP	1.13374	1
47DAP/43DAP	0.92388	0.724
52DAP/47DAP	1.23537	0.553
57DAP/52DAP	0.97257	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95726	0.432
17DAP/reference	1.15012	0.014
27DAP/reference	1.03232	0.794
39DAP/reference	1.08622	0.57
41DAP/reference	1.07588	0.221
42DAP/reference	0.86038	0.023
43DAP/reference	1.07234	0.202
47DAP/reference	0.88128	0.06
52DAP/reference	0.93774	0.167
57DAP/reference	0.88772	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97587	0.732
27DAP/17DAP	1.28194	0.071
39DAP/27DAP	0.85426	0.044
41DAP/39DAP	0.99332	1
42DAP/41DAP	0.94443	0.565
43DAP/42DAP	0.96255	0.576
47DAP/43DAP	0.98017	0.902
52DAP/47DAP	1.07172	0.73
57DAP/52DAP	0.99136	0.838
57DAP/7DAP	0.87109	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81133	0.086
17DAP/reference	0.94746	0.253
27DAP/reference	1.07705	0.551
39DAP/reference	0.74197	0.011
41DAP/reference	0.83364	0.039
42DAP/reference	0.68713	0.014
43DAP/reference	0.66398	0.01
47DAP/reference	0.85879	0.168
52DAP/reference	0.85124	0.04
57DAP/reference	0.85708	0.118

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11278	0.531
17DAP/reference	0.99322	0.766
27DAP/reference	1.00832	0.79
39DAP/reference	0.86998	0.129
41DAP/reference	1.03499	0.766
42DAP/reference	0.85688	0.067
43DAP/reference	1.52357	0.047
47DAP/reference	0.93351	0.11
52DAP/reference	1.22775	0.24
57DAP/reference	1.09562	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58329	0.02
17DAP/reference	1.09595	0.289
27DAP/reference	1.21724	0.111
39DAP/reference	0.98752	0.544
41DAP/reference	1.99513	0.035
42DAP/reference	1.37063	0.45
43DAP/reference	2.44853	0.087
47DAP/reference	1.00393	0.731
52DAP/reference	0.97784	0.637
57DAP/reference	0.79146	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92603	1
26DAP/20DAP	1.18283	0.635
34DAP/26DAP	1.18138	1
51DAP/34DAP	0.79683	0.112
52DAP/51DAP	0.83986	1
53DAP/52DAP	0.84073	0.212
55DAP/53DAP	0.88539	0.417
57DAP/55DAP	1.55156	0.092
62DAP/57DAP	0.90738	0.871
68DAP/62DAP	0.95081	0.787
68DAP/14DAP	0.76454	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.57754	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.11489	0.948
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.00418	1
Mature Eggplant/Ripe Tomato	1.72427	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.2246	0.526
1-1-2/M82	1.06064	N/A
12-2/M82	1.53662	0.448
12-4/M82	1.13586	1
1-3/M82	0.81853	0.378
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.80448	0.501
3-2/M82	1.10939	0.967
4-1-1/M82	0.83145	1
4-1/M82	1.11536	1
4-3-2/M82	N/A	N/A
4-3/M82	0.95985	N/A
5-3/M82	1.11579	1
6-2/M82	0.69495	1
6-3/M82	0.98924	1
7-1/M82	0.92444	N/A
7-2/M82	0.91555	1
9-3-2/M82	0.70096	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.80833	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.26829	1
IL12-4/WTpooled	0.82747	0.71
IL1-4/WTpooled	0.86992	N/A
WT/WTpooled	1.0448	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	1.00994	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03112	0.921
DC3000/delta hrp 6h	1.00665	0.95
DC3000/delta hrp 12h	1.02228	1
DC3000/delta hrp 24h	1.04596	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16497	0.045
DC3000 delta B/DC3000 delta AB	1.27877	0.158

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78767	0.328
Exp 36h	1.36053	0.489
Exp 60h	1.3086	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97291	1
Var 0h	1.07819	1
Var 12h I row2-row1	1.2056	0.235
Var 12h NI row2-row1	1.13622	0.649
Var 36h I row2-row1	0.91165	1
Var 36h NI row2-row1	1.10138	0.852
Var 60h I row2-row1	0.99577	1
Var 60h NI row2-row1	0.93165	0.932
Time course 0hI-0hNI	1.06052	0.537
Time course 12hI-12hNI	1.13426	0.083
Time course 36hI-36hNI	1.81579	0.005
Time course 60hI-60hNI	1.91167	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)	0.99563	0.931
transgenic ySAMdc/azygous control (breaker)	1.03072	1
transgenic ySAMdc/azygous control (red)	1.11868	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96909	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38771	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20757	1
Manapal/WT (break)	1.15469	1
Manapal/WT (red)	1.43943	0.164