Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.1.8.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88758	0.436
27DAP/17DAP	0.9596	0.939
39DAP/27DAP	1.21383	0.603
41DAP/39DAP	0.93216	0.63
42DAP/41DAP	1.30801	0.552
43DAP/42DAP	0.86441	0.705
47DAP/43DAP	0.80414	0.424
52DAP/47DAP	1.19252	0.997
57DAP/52DAP	0.90228	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0055	1
17DAP/reference	1.05582	0.1
27DAP/reference	0.98655	0.711
39DAP/reference	0.98497	0.762
41DAP/reference	0.96237	0.542
42DAP/reference	0.96873	0.233
43DAP/reference	1.09973	0.038
47DAP/reference	0.97023	0.366
52DAP/reference	0.75852	0.084
57DAP/reference	0.83772	0.074

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05972	0.515
27DAP/17DAP	1.0338	0.957
39DAP/27DAP	1.02033	0.758
41DAP/39DAP	1.08948	0.849
42DAP/41DAP	1.02356	1
43DAP/42DAP	0.78837	0.027
47DAP/43DAP	0.99895	0.998
52DAP/47DAP	1.01295	0.979
57DAP/52DAP	0.99724	0.887
57DAP/7DAP	0.84384	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89341	0.27
17DAP/reference	0.78677	0.014
27DAP/reference	N/A	N/A
39DAP/reference	0.80337	0.083
41DAP/reference	0.84302	0.127
42DAP/reference	0.92894	0.1
43DAP/reference	0.70402	0.011
47DAP/reference	0.94165	0.504
52DAP/reference	0.88933	0.163
57DAP/reference	0.84954	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18871	0.043
17DAP/reference	1.07345	0.083
27DAP/reference	1.06847	0.488
39DAP/reference	1.07155	0.543
41DAP/reference	0.82337	0.029
42DAP/reference	1.03753	0.934
43DAP/reference	1.30464	0.526
47DAP/reference	0.99222	0.66
52DAP/reference	0.92215	0.037
57DAP/reference	0.89776	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83428	0.047
17DAP/reference	1.01865	1
27DAP/reference	0.74507	0.03
39DAP/reference	0.83324	0.022
41DAP/reference	0.81985	0.167
42DAP/reference	0.93609	0.22
43DAP/reference	0.6854	0.024
47DAP/reference	1.04078	0.562
52DAP/reference	1.05961	0.941
57DAP/reference	1.34131	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03429	0.966
26DAP/20DAP	1.3823	0.208
34DAP/26DAP	0.82154	0.479
51DAP/34DAP	0.86032	0.143
52DAP/51DAP	1.03177	0.792
53DAP/52DAP	0.91478	0.417
55DAP/53DAP	0.96507	0.807
57DAP/55DAP	1.04009	0.975
62DAP/57DAP	1.22973	0.303
68DAP/62DAP	1.01502	0.914
68DAP/14DAP	0.94905	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.67819	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89539	0.426
Mature Green Tomato/Ripe Tomato	1.14424	0.577
Immature Eggplant/Mature Eggplant	1.29748	0.072
Ripe Pepper/Ripe Tomato	0.8638	1
Mature Eggplant/Ripe Tomato	1.37584	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00199	1
1-1-2/M82	1.03263	1
12-2/M82	1.05549	1
12-4/M82	1.11476	1
1-3/M82	1.35689	0.277
2-1-1/M82	0.93524	0.92
2-1/M82	1.07014	1
2-6/M82	1.14932	0.695
3-2/M82	0.91796	N/A
4-1-1/M82	1.06418	1
4-1/M82	1.29502	0.512
4-3-2/M82	1.39695	N/A
4-3/M82	1.20506	1
5-3/M82	1.06326	1
6-2/M82	1.04191	1
6-3/M82	0.88811	1
7-1/M82	1.19699	N/A
7-2/M82	1.02864	1
9-3-2/M82	0.98555	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08267	0.277
IL2-6/WTpooled	0.98524	1
IL7-5/WTpooled	0.8749	1
IL7-3/WTpooled	1.12251	1
IL12-4/WTpooled	0.87099	0.581
IL1-4/WTpooled	0.98764	1
WT/WTpooled	1.07829	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	1.05252	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02096	0.921
DC3000/delta hrp 6h	0.92875	0.95
DC3000/delta hrp 12h	0.99401	1
DC3000/delta hrp 24h	1.0461	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.27166	0.087
DC3000 delta B/DC3000 delta AB	1.12407	0.302

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.77959	1
Exp 36h	1.37914	0.693
Exp 60h	1.27406	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0165	1
Var 0h	0.8265	0.933
Var 12h I row2-row1	1.1407	0.654
Var 12h NI row2-row1	0.95056	0.906
Var 36h I row2-row1	1.0507	1
Var 36h NI row2-row1	0.9728	0.791
Var 60h I row2-row1	0.8799	0.287
Var 60h NI row2-row1	1.01642	1
Time course 0hI-0hNI	0.84272	0.162
Time course 12hI-12hNI	1.0482	0.599
Time course 36hI-36hNI	1.26605	0.28
Time course 60hI-60hNI	1.4969	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)	1.07537	0.289
transgenic ySAMdc/azygous control (breaker)	1.70468	0.248
transgenic ySAMdc/azygous control (red)	1.23908	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08752	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72544	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80695	1
Manapal/WT (break)	1.15187	1
Manapal/WT (red)	1.04794	1