Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.4.4.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72282	0.226
27DAP/17DAP	0.81138	0.504
39DAP/27DAP	0.93981	0.652
41DAP/39DAP	1.21246	0.535
42DAP/41DAP	1.09606	0.992
43DAP/42DAP	1.09927	1
47DAP/43DAP	1.08023	0.965
52DAP/47DAP	1.3715	0.662
57DAP/52DAP	1.58381	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01239	1
17DAP/reference	0.82021	0.012
27DAP/reference	0.89812	0.152
39DAP/reference	0.81178	0.011
41DAP/reference	0.67171	0.01
42DAP/reference	0.8196	0.002
43DAP/reference	0.93617	0.5
47DAP/reference	0.86226	0.013
52DAP/reference	1.0775	0.371
57DAP/reference	1.08623	0.529

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18123	0.515
27DAP/17DAP	1.22063	0.73
39DAP/27DAP	0.92463	0.628
41DAP/39DAP	1.03914	0.895
42DAP/41DAP	1.05997	1
43DAP/42DAP	1.01479	1
47DAP/43DAP	1.1753	0.805
52DAP/47DAP	1.05366	1
57DAP/52DAP	1.36048	0.228
57DAP/7DAP	0.9965	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09872	0.292
17DAP/reference	1.0715	0.134
27DAP/reference	1.06125	0.049
39DAP/reference	1.04145	0.267
41DAP/reference	1.0488	0.375
42DAP/reference	1.0158	0.889
43DAP/reference	1.08518	0.432
47DAP/reference	1.15443	0.254
52DAP/reference	1.23281	0.052
57DAP/reference	1.14252	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87015	0.286
17DAP/reference	0.80949	0.159
27DAP/reference	0.9747	0.554
39DAP/reference	0.93459	0.036
41DAP/reference	0.95545	0.422
42DAP/reference	1.06096	0.68
43DAP/reference	0.92005	0.394
47DAP/reference	0.89538	0.164
52DAP/reference	0.90503	0.111
57DAP/reference	0.78294	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12598	0.218
17DAP/reference	0.97362	0.658
27DAP/reference	0.94571	0.165
39DAP/reference	1.00236	1
41DAP/reference	0.97446	0.56
42DAP/reference	1.21769	0.078
43DAP/reference	0.95266	0.503
47DAP/reference	0.97404	0.421
52DAP/reference	1.14882	0.448
57DAP/reference	1.17705	0.144

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13913	0.752
26DAP/20DAP	2.24686	0.097
34DAP/26DAP	1.01619	1
51DAP/34DAP	1.64731	0.047
52DAP/51DAP	1.07498	0.792
53DAP/52DAP	1.27199	0.398
55DAP/53DAP	1.01827	1
57DAP/55DAP	1.08793	0.955
62DAP/57DAP	0.57942	0.028
68DAP/62DAP	1.33523	0.193
68DAP/14DAP	2.2543	0.071

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.34268	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9283	0.605
Mature Green Tomato/Ripe Tomato	1.13065	0.66
Immature Eggplant/Mature Eggplant	1.10999	0.398
Ripe Pepper/Ripe Tomato	0.70719	0.293
Mature Eggplant/Ripe Tomato	0.9762	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93482	N/A
1-1-2/M82	1.09533	N/A
12-2/M82	1.07337	N/A
12-4/M82	0.95462	1
1-3/M82	N/A	N/A
2-1-1/M82	0.63085	N/A
2-1/M82	0.96839	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	0.93475	0.611
5-3/M82	1.06251	0.572
6-2/M82	0.88883	N/A
6-3/M82	1.23196	1
7-1/M82	N/A	N/A
7-2/M82	1.14261	N/A
9-3-2/M82	0.97892	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0813	0.365
IL2-6/WTpooled	0.64226	0.348
IL7-5/WTpooled	1.14609	1
IL7-3/WTpooled	1.17628	1
IL12-4/WTpooled	1.15754	0.785
IL1-4/WTpooled	0.8766	0.834
WT/WTpooled	1.07356	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	0.91395	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18599	0.724
DC3000/delta hrp 6h	1.08517	1
DC3000/delta hrp 12h	0.90735	1
DC3000/delta hrp 24h	1.07763	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22624	0.355
DC3000 delta B/DC3000 delta AB	1.67286	0.279

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.8961	1
Exp 36h	1.44822	1
Exp 60h	1.25033	0.563

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	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.11143	0.339
transgenic ySAMdc/azygous control (breaker)	1.02618	1
transgenic ySAMdc/azygous control (red)	0.94657	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.24905	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91487	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93331	1
Manapal/WT (break)	0.77585	0.299
Manapal/WT (red)	0.73823	0.181