Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.16.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00421	0.891
27DAP/17DAP	0.86492	0.67
39DAP/27DAP	0.93323	0.583
41DAP/39DAP	0.75788	0.164
42DAP/41DAP	0.93824	1
43DAP/42DAP	1.09854	0.974
47DAP/43DAP	0.80642	0.39
52DAP/47DAP	1.01782	0.932
57DAP/52DAP	1.08678	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03705	0.48
17DAP/reference	1.01775	0.696
27DAP/reference	1.00126	1
39DAP/reference	1.02107	0.557
41DAP/reference	1.00485	0.855
42DAP/reference	0.99881	0.645
43DAP/reference	1.01528	0.866
47DAP/reference	1.06038	0.081
52DAP/reference	1.01585	0.695
57DAP/reference	1.15866	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02153	0.749
27DAP/17DAP	0.95718	0.782
39DAP/27DAP	0.9878	0.932
41DAP/39DAP	1.09503	0.656
42DAP/41DAP	1.01361	0.935
43DAP/42DAP	0.97393	0.709
47DAP/43DAP	0.98258	0.911
52DAP/47DAP	0.96925	0.857
57DAP/52DAP	0.98906	0.793
57DAP/7DAP	0.97555	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87416	0.138
17DAP/reference	0.76514	0.012
27DAP/reference	0.78064	0.01
39DAP/reference	0.80272	0.013
41DAP/reference	0.84084	0.027
42DAP/reference	0.82882	0.046
43DAP/reference	0.73874	0.011
47DAP/reference	0.84229	0.128
52DAP/reference	0.7921	0.013
57DAP/reference	0.77639	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02877	0.55
17DAP/reference	0.9407	0.024
27DAP/reference	0.95318	0.381
39DAP/reference	1.00882	1
41DAP/reference	0.96144	0.322
42DAP/reference	1.0161	0.951
43DAP/reference	1.09321	0.276
47DAP/reference	1.09896	0.059
52DAP/reference	0.95576	0.259
57DAP/reference	0.95848	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85933	0.061
17DAP/reference	0.93729	0.381
27DAP/reference	0.79877	0.048
39DAP/reference	0.8533	0.021
41DAP/reference	0.84946	0.025
42DAP/reference	0.75627	0.028
43DAP/reference	0.8049	0.049
47DAP/reference	0.98412	0.525
52DAP/reference	0.76452	0.177
57DAP/reference	0.95785	0.444

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97455	1
26DAP/20DAP	1.11378	0.558
34DAP/26DAP	1.03691	1
51DAP/34DAP	0.97503	0.77
52DAP/51DAP	0.9724	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.91702
57DAP/55DAP	0.96657
62DAP/57DAP	0.99939	1
68DAP/62DAP	1.17073	0.713
68DAP/14DAP	0.98432	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0821	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69856	0.187
Mature Green Tomato/Ripe Tomato	4.41512	0.015
Immature Eggplant/Mature Eggplant	1.24605	0.181
Ripe Pepper/Ripe Tomato	1.6644	0.258
Mature Eggplant/Ripe Tomato	1.51718	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92359	0.944
1-1-2/M82	0.97926	1
12-2/M82	0.90964	0.955
12-4/M82	0.93809	0.358
1-3/M82	0.99891	1
2-1-1/M82	0.84334	0.565
2-1/M82	1.2837	1
2-6/M82	0.98373	1
3-2/M82	1.11587	0.426
4-1-1/M82	1.0676	1
4-1/M82	0.99119
4-3-2/M82	1.44768	0.508
4-3/M82	0.91038	1
5-3/M82	0.9936	1
6-2/M82	1.00299	1
6-3/M82	0.95883	1
7-1/M82	1.02123
7-2/M82	0.92543	0.881
9-3-2/M82	1.29122	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.29595	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.67626	0.294
IL12-4/WTpooled	1.08675	0.538
IL1-4/WTpooled	1.0152
WT/WTpooled	1.09495	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	1.19036	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02645	0.921
DC3000/delta hrp 6h	1.42094	1
DC3000/delta hrp 12h	1.00552	1
DC3000/delta hrp 24h	1.02303	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10885	0.081
DC3000 delta B/DC3000 delta AB	1.03417	0.586

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.77055	1
Exp 36h	1.82944	0.326
Exp 60h	1.30215	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99186	1
Var 0h	1.0279	1
Var 12h I row2-row1	1.25243	0.242
Var 12h NI row2-row1	0.88919	0.627
Var 36h I row2-row1	1.0062	1
Var 36h NI row2-row1	0.86681	0.61
Var 60h I row2-row1	1.11533	1
Var 60h NI row2-row1	1.09181	1
Time course 0hI-0hNI	1.01865	1
Time course 12hI-12hNI	1.05934	0.724
Time course 36hI-36hNI	1.19301	0.006
Time course 60hI-60hNI	1.80807	0.009

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)	0.99288	0.862
transgenic ySAMdc/azygous control (breaker)	1.06949	1
transgenic ySAMdc/azygous control (red)	1.17441	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0034	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29836	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73316	0.172
Manapal/WT (break)	0.82844	1
Manapal/WT (red)	0.91041	0.315