Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.12.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37906	0.512
27DAP/17DAP	1.15691	0.864
39DAP/27DAP	0.79374	0.382
41DAP/39DAP	1.21066	0.408
42DAP/41DAP	0.86488	0.774
43DAP/42DAP	0.85682	0.77
47DAP/43DAP	1.02367	0.934
52DAP/47DAP	1.07564	0.902
57DAP/52DAP	1.01208	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08316	0.46
17DAP/reference	1.38465	0.04
27DAP/reference	1.3192	0.021
39DAP/reference	1.43231	0.117
41DAP/reference	1.782	0.014
42DAP/reference	1.28285	0.001
43DAP/reference	1.26895	0.142
47DAP/reference	1.41695	0.001
52DAP/reference	1.8108	0.019
57DAP/reference	1.20454	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23334	0.161
27DAP/17DAP	0.96912	0.782
39DAP/27DAP	1.12007	0.596
41DAP/39DAP	0.9473	0.893
42DAP/41DAP	1.04154	0.927
43DAP/42DAP	0.91901	0.415
47DAP/43DAP	1.00393	0.99
52DAP/47DAP	1.20189	0.432
57DAP/52DAP	1.19943	0.274
57DAP/7DAP	0.7922	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85646	0.088
17DAP/reference	1.07486	0.437
27DAP/reference	1.0545	0.664
39DAP/reference	0.96345	0.474
41DAP/reference	1.00194	1
42DAP/reference	1.16437	0.405
43DAP/reference	0.91211	0.192
47DAP/reference	1.11062	0.298
52DAP/reference	0.95449	0.332
57DAP/reference	0.89225	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06965	0.582
17DAP/reference	1.42262	0.094
27DAP/reference	1.30427	0.153
39DAP/reference	1.36596	0.272
41DAP/reference	1.08041	0.614
42DAP/reference	1.29594	0.066
43DAP/reference	1.35479	0.031
47DAP/reference	1.65241	0.008
52DAP/reference	1.37773	0.018
57DAP/reference	0.94721	0.015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97778	0.607
17DAP/reference	1.09793	0.665
27DAP/reference	0.91181	0.337
39DAP/reference	1.15132	0.528
41DAP/reference	1.01388	1
42DAP/reference	0.97815	0.816
43DAP/reference	1.00342	0.66
47DAP/reference	1.01234	0.731
52DAP/reference	1.10012	0.631
57DAP/reference	1.48719	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.81755	0.566
26DAP/20DAP	0.97731	1
34DAP/26DAP	0.82225	0.584
51DAP/34DAP	1.19409	0.303
52DAP/51DAP	0.9709	1
53DAP/52DAP	0.8938	0.505
55DAP/53DAP	1.48876	0.147
57DAP/55DAP	1.0051	0.863
62DAP/57DAP	0.871	0.681
68DAP/62DAP	1.39818	0.247
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13942	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83871
Mature Green Tomato/Ripe Tomato	1.02364	0.881
Immature Eggplant/Mature Eggplant	0.76011	0.159
Ripe Pepper/Ripe Tomato	0.42899	0.224
Mature Eggplant/Ripe Tomato	2.20578	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99387	1
1-1-2/M82	1.29398	0.972
12-2/M82	1.7327	1
12-4/M82	1.03803	1
1-3/M82	0.66063
2-1-1/M82	0.52237
2-1/M82	N/A	N/A
2-6/M82	0.8858	1
3-2/M82	0.96908
4-1-1/M82	0.77839
4-1/M82	1.56873	0.512
4-3-2/M82	0.93105	1
4-3/M82	0.73964	0.611
5-3/M82	1.0517	1
6-2/M82	0.68211
6-3/M82	1.05953	0.971
7-1/M82	N/A	N/A
7-2/M82	0.87916
9-3-2/M82	0.84212	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.03572	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07761	1
IL12-4/WTpooled	0.84905	0.71
IL1-4/WTpooled	0.9163
WT/WTpooled	1.11432	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	1.55941	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03443	0.921
DC3000/delta hrp 6h	1.04439	1
DC3000/delta hrp 12h	1.13448	1
DC3000/delta hrp 24h	1.02872	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.83636	0.132
DC3000 delta B/DC3000 delta AB	1.05189	0.558

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.977	1
Exp 36h	0.93188	0.879
Exp 60h	0.98202	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0519	1
Var 0h	1.20205	0.421
Var 12h I row2-row1	0.89882	0.514
Var 12h NI row2-row1	1.12585	1
Var 36h I row2-row1	1.12207	1
Var 36h NI row2-row1	0.76604	0.478
Var 60h I row2-row1	0.79194	0.285
Var 60h NI row2-row1	0.75929	0.431
Time course 0hI-0hNI	1.01342	1
Time course 12hI-12hNI	1.06691	0.593
Time course 36hI-36hNI	1.56077	0.005
Time course 60hI-60hNI	2.52771	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)	1.03637	0.654
transgenic ySAMdc/azygous control (breaker)	0.90448	0.49
transgenic ySAMdc/azygous control (red)	0.93963	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89657	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.61138	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70491	1
Manapal/WT (break)	0.92927	1
Manapal/WT (red)	1.07023	1