Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.13.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9355	0.475
27DAP/17DAP	1.07351	0.881
39DAP/27DAP	1.02951	1
41DAP/39DAP	0.93384	0.72
42DAP/41DAP	1.05722	0.912
43DAP/42DAP	0.96317	0.906
47DAP/43DAP	0.91378	0.693
52DAP/47DAP	1.12265	0.707
57DAP/52DAP	1.03072	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8741	0.05
17DAP/reference	0.87997	0.26
27DAP/reference	0.90835	0.098
39DAP/reference	0.85562	0.031
41DAP/reference	0.9029	0.085
42DAP/reference	1.04031	0.241
43DAP/reference	1.00244	0.942
47DAP/reference	1.05564	0.463
52DAP/reference	1.0856	0.092
57DAP/reference	1.09642	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0399	0.438
27DAP/17DAP	1.00025	1
39DAP/27DAP	1.00753	0.854
41DAP/39DAP	0.87877	0.434
42DAP/41DAP	0.99293	0.887
43DAP/42DAP	0.98229	0.854
47DAP/43DAP	0.98299	0.939
52DAP/47DAP	1.0104	0.986
57DAP/52DAP	0.9477	0.494
57DAP/7DAP	0.99725	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19554	0.227
17DAP/reference	1.32657	0.006
27DAP/reference	1.25528	0.009
39DAP/reference	1.4872	0.005
41DAP/reference	1.52627	0.015
42DAP/reference	1.65271	0.006
43DAP/reference	1.68716	0.007
47DAP/reference	1.37811	0.37
52DAP/reference	1.55353	0.007
57DAP/reference	1.58047	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8751	0.09
17DAP/reference	0.8686	0.045
27DAP/reference	0.94809	0.24
39DAP/reference	1.05873	0.571
41DAP/reference	1.01228	1
42DAP/reference	1.0004	1
43DAP/reference	0.85639	0.121
47DAP/reference	0.93001	0.025
52DAP/reference	0.99034	0.576
57DAP/reference	0.81641	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14507	0.273
17DAP/reference	1.06766	0.746
27DAP/reference	1.43986	0.023
39DAP/reference	1.4312	0.015
41DAP/reference	1.27038	0.01
42DAP/reference	1.19675	0.272
43DAP/reference	1.35658	0.016
47DAP/reference	0.96344	0.434
52DAP/reference	1.42761	0.091
57DAP/reference	1.33946	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96397	1
26DAP/20DAP	1.05803	0.875
34DAP/26DAP	0.97671	0.98
51DAP/34DAP	1.08963	0.387
52DAP/51DAP	1.06542	0.542
53DAP/52DAP	1.00867	0.961
55DAP/53DAP	1.06528	0.893
57DAP/55DAP	0.85957	0.313
62DAP/57DAP	1.13525	0.393
68DAP/62DAP	1.33653	0.515
68DAP/14DAP	1.26986	0.099

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03487	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01281	1
Mature Green Tomato/Ripe Tomato	0.63964	0.016
Immature Eggplant/Mature Eggplant	1.0636	0.462
Ripe Pepper/Ripe Tomato	0.34319	0.224
Mature Eggplant/Ripe Tomato	0.46642	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97059	0.944
1-1-2/M82	1.05804	1
12-2/M82	0.9802	1
12-4/M82	0.98049	0.619
1-3/M82	1.08458	1
2-1-1/M82	0.93611	0.784
2-1/M82	0.96676	1
2-6/M82	1.00264	1
3-2/M82	1.02807	0.717
4-1-1/M82	1.04484	1
4-1/M82	0.7782	1
4-3-2/M82	0.85289	1
4-3/M82	0.95862	1
5-3/M82	0.98559	1
6-2/M82	0.97952	1
6-3/M82	1.04682	1
7-1/M82	1.03026	1
7-2/M82	0.91309	0.881
9-3-2/M82	1.01085	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1048	1
IL2-6/WTpooled	1.17259	0.584
IL7-5/WTpooled	1.22564	0.792
IL7-3/WTpooled	0.90324	1
IL12-4/WTpooled	1.12795	0.737
IL1-4/WTpooled	0.70854	0.562
WT/WTpooled	0.96457	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	1.29457	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84712	0.105
DC3000/delta hrp 6h	1.18908	1
DC3000/delta hrp 12h	0.99039	1
DC3000/delta hrp 24h	1.01145	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94469	0.46
DC3000 delta B/DC3000 delta AB	0.89742	0.147

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06997	1
Exp 36h	0.97501	0.943
Exp 60h	0.95385	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00189	1
Var 0h	0.59711	0.98
Var 12h I row2-row1	1.21478	0.187
Var 12h NI row2-row1	1.05569	1
Var 36h I row2-row1	0.99376	1
Var 36h NI row2-row1	0.91683	0.478
Var 60h I row2-row1	1.31065	0.562
Var 60h NI row2-row1	0.92354	0.756
Time course 0hI-0hNI	0.99824	0.973
Time course 12hI-12hNI	1.0947	0.49
Time course 36hI-36hNI	0.94123	0.344
Time course 60hI-60hNI	0.88331	0.047

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)	0.70444	0.299
transgenic ySAMdc/azygous control (breaker)	0.68073	0.142
transgenic ySAMdc/azygous control (red)	1.07232	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9616	0.128

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8979	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98648	1
Manapal/WT (break)	0.76823	1
Manapal/WT (red)	0.64271	0.181