Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.18.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07169	0.863
27DAP/17DAP	1.01448	1
39DAP/27DAP	1.0111	0.782
41DAP/39DAP	0.82376	0.436
42DAP/41DAP	1.09364	0.941
43DAP/42DAP	1.06017	1
47DAP/43DAP	1.36216	0.405
52DAP/47DAP	0.9016	0.702
57DAP/52DAP	1.09297	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91199	0.205
17DAP/reference	1.07584	0.049
27DAP/reference	1.03192	0.684
39DAP/reference	1.00665	0.8
41DAP/reference	0.9897	0.814
42DAP/reference	0.90269	0.019
43DAP/reference	1.02556	0.899
47DAP/reference	0.88573	0.014
52DAP/reference	0.88641	0.183
57DAP/reference	0.77039	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87998	0.336
27DAP/17DAP	0.99823	0.969
39DAP/27DAP	1.12855	0.441
41DAP/39DAP	1.15513	0.719
42DAP/41DAP	1.05807	0.893
43DAP/42DAP	1.02014	0.788
47DAP/43DAP	1.01409	1
52DAP/47DAP	1.00894	0.991
57DAP/52DAP	1.02042	0.957
57DAP/7DAP	1.27676	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84509	0.071
17DAP/reference	0.8799	0.025
27DAP/reference	0.82489	0.011
39DAP/reference	0.93888	0.049
41DAP/reference	0.90063	0.046
42DAP/reference	0.87803	0.017
43DAP/reference	0.89936	0.051
47DAP/reference	0.90398	0.383
52DAP/reference	0.91983	0.028
57DAP/reference	0.89987	0.036

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01919	0.933
17DAP/reference	0.93075	0.245
27DAP/reference	0.90275	0.249
39DAP/reference	0.87803	0.119
41DAP/reference	0.82058	0.067
42DAP/reference	0.86314	0.021
43DAP/reference	1.02717	0.957
47DAP/reference	0.85969	0.036
52DAP/reference	0.96359	0.28
57DAP/reference	1.07117	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82997	0.028
17DAP/reference	1.0066	0.918
27DAP/reference	0.82794	0.03
39DAP/reference	0.85207	0.063
41DAP/reference	0.90531	0.132
42DAP/reference	0.74882	0.036
43DAP/reference	0.78745	0.12
47DAP/reference	0.96517	0.452
52DAP/reference	0.76737	0.132
57DAP/reference	0.58467	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91779	0.773
26DAP/20DAP	0.84238	0.317
34DAP/26DAP	1.01088	1
51DAP/34DAP	0.92159	0.537
52DAP/51DAP	1.17629	0.207
53DAP/52DAP	1.04719	0.806
55DAP/53DAP	1.13142	0.33
57DAP/55DAP	0.98328	0.88
62DAP/57DAP	1.18693	0.158
68DAP/62DAP	0.91572	0.7
68DAP/14DAP	0.91754	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77786	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.98728	0.66
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.78581
Mature Eggplant/Ripe Tomato	1.05385	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80217	0.605
1-1-2/M82	0.86572	1
12-2/M82	1.12396	1
12-4/M82	1.21354	1
1-3/M82	0.81346	0.378
2-1-1/M82	0.88571
2-1/M82	N/A	N/A
2-6/M82	1.07213	0.505
3-2/M82	N/A	N/A
4-1-1/M82	1.03983	1
4-1/M82	1.21535
4-3-2/M82	N/A	N/A
4-3/M82	0.68671	0.72
5-3/M82	0.92839	1
6-2/M82	1.03546	1
6-3/M82	1.06035	1
7-1/M82	N/A	N/A
7-2/M82	0.79844
9-3-2/M82	0.96042

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94806	1
IL2-6/WTpooled	0.89863	1
IL7-5/WTpooled	1.65353	0.792
IL7-3/WTpooled	0.95242	0.31
IL12-4/WTpooled	0.94851	0.71
IL1-4/WTpooled	0.94206	0.834
WT/WTpooled	1.02336	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	0.90389	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93691	1
DC3000/delta hrp 6h	0.24986
DC3000/delta hrp 12h	1.31397	1
DC3000/delta hrp 24h	1.01976	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1033	0.648
DC3000 delta B/DC3000 delta AB	0.9502	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.88674	1
Exp 60h	1.22146	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95087	1
Var 0h	0.83467	0.933
Var 12h I row2-row1	1.25336	0.296
Var 12h NI row2-row1	0.77339	0.546
Var 36h I row2-row1	0.84725	0.805
Var 36h NI row2-row1	1.18357	1
Var 60h I row2-row1	1.40692	0.562
Var 60h NI row2-row1	1.36127	0.904
Time course 0hI-0hNI	1.12661	0.764
Time course 12hI-12hNI	1.05333	0.762
Time course 36hI-36hNI	0.92298	0.102
Time course 60hI-60hNI	1.09329	0.254

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)	0.99199	0.862
transgenic ySAMdc/azygous control (breaker)	0.90839	0.251
transgenic ySAMdc/azygous control (red)	0.84503	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06083	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77654	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90334	0.172
Manapal/WT (break)	1.05478	1
Manapal/WT (red)	1.04689	1