Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.20.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.56976	0.073
27DAP/17DAP	1.0944	0.902
39DAP/27DAP	1.04035	0.798
41DAP/39DAP	0.90473	0.617
42DAP/41DAP	0.90561	1
43DAP/42DAP	1.25923	0.831
47DAP/43DAP	1.55178	0.201
52DAP/47DAP	1.77607	0.12
57DAP/52DAP	1.09554	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69908	0.033
17DAP/reference	0.69774	0.008
27DAP/reference	1.04621	1
39DAP/reference	0.88063	0.261
41DAP/reference	0.70429	0.018
42DAP/reference	0.81518	0.005
43DAP/reference	0.97755	0.708
47DAP/reference	1.0485	0.885
52DAP/reference	1.63178	0.026
57DAP/reference	1.14576	0.529

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27678	0.749
27DAP/17DAP	1.02981	0.969
39DAP/27DAP	0.80207	0.496
41DAP/39DAP	1.07115	0.827
42DAP/41DAP	0.80888	0.276
43DAP/42DAP	0.85196	0.399
47DAP/43DAP	1.36269	0.889
52DAP/47DAP	1.3467	0.494
57DAP/52DAP	0.87852	0.166
57DAP/7DAP	0.34314

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4586	0.051
17DAP/reference	1.86476	0.006
27DAP/reference	1.36536	0.008
39DAP/reference	1.76213	0.006
41DAP/reference	1.76875	0.012
42DAP/reference	1.86977	0.007
43DAP/reference	2.30774	0.006
47DAP/reference	1.40006	0.337
52DAP/reference	1.89926	0.007
57DAP/reference	1.90605	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.735	0.022
17DAP/reference	0.70422	0.004
27DAP/reference	0.76413	0.012
39DAP/reference	0.86614	0.105
41DAP/reference	0.95419	0.364
42DAP/reference	0.81061	0.027
43DAP/reference	0.67598	0.007
47DAP/reference	0.76104	0.021
52DAP/reference	0.8364	0.02
57DAP/reference	0.75488	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30139	0.119
17DAP/reference	1.21741	0.456
27DAP/reference	1.63625	0.02
39DAP/reference	1.48504	0.029
41DAP/reference	1.50559	0.007
42DAP/reference	1.34672	0.056
43DAP/reference	1.40472	0.237
47DAP/reference	0.93608	0.269
52DAP/reference	1.62494	0.119
57DAP/reference	1.35194	0.196

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93373	1
26DAP/20DAP	1.02017	1
34DAP/26DAP	1.46037	0.819
51DAP/34DAP	0.9414	0.579
52DAP/51DAP	1.70153	0.261
53DAP/52DAP	1.4246
55DAP/53DAP	0.72483	0.417
57DAP/55DAP	1.1766	0.911
62DAP/57DAP	1.22341	0.767
68DAP/62DAP	2.614	0.097
68DAP/14DAP	2.20782	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72703	0.269

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.18117	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.25675	0.224
Mature Eggplant/Ripe Tomato	0.07886	0.234

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	1.0067
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	1.12465	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.89276	0.277
IL2-6/WTpooled	1.03651	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.40257	1
IL12-4/WTpooled	1.71544	0.785
IL1-4/WTpooled	0.86546	0.562
WT/WTpooled	1.1424	0.999

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	0.8636	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.94691	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.04229

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23929	1
Exp 36h	1.3214	1
Exp 60h	1.22717	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	0.87526
Var 12h NI row2-row1	0.97058	0.713
Var 36h I row2-row1	0.97719
Var 36h NI row2-row1	0.74103	0.743
Var 60h I row2-row1	0.58769	0.285
Var 60h NI row2-row1	0.54806	1
Time course 0hI-0hNI	1.06476	0.603
Time course 12hI-12hNI	1.01953	0.849
Time course 36hI-36hNI	0.81782	0.651
Time course 60hI-60hNI	8.27584	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)	1.18462	0.699
transgenic ySAMdc/azygous control (breaker)	0.9496	1
transgenic ySAMdc/azygous control (red)	0.82625	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98017	0.12

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76867	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73758	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A