Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.13.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.56296	0.018
27DAP/17DAP	0.98024	0.978
39DAP/27DAP	0.97685	0.749
41DAP/39DAP	0.96372	0.841
42DAP/41DAP	0.93042	1
43DAP/42DAP	0.94668	0.77
47DAP/43DAP	1.57919	0.245
52DAP/47DAP	0.99543	0.889
57DAP/52DAP	0.96949	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13896	0.139
17DAP/reference	0.97062	0.419
27DAP/reference	1.05055	0.405
39DAP/reference	1.14075	0.029
41DAP/reference	1.06497	0.624
42DAP/reference	1.04927	0.565
43DAP/reference	1.13699	0.038
47DAP/reference	1.23126	0.002
52DAP/reference	1.0993	0.286
57DAP/reference	1.29052	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90786	0.219
27DAP/17DAP	0.88138	0.206
39DAP/27DAP	1.20487	0.422
41DAP/39DAP	1.02262	0.88
42DAP/41DAP	0.90084	0.318
43DAP/42DAP	0.85078	0.036
47DAP/43DAP	1.09322	0.581
52DAP/47DAP	0.86676	0.433
57DAP/52DAP	0.81184	0.171
57DAP/7DAP	1.02455	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96468	0.445
17DAP/reference	0.89712	0.013
27DAP/reference	1.14851	0.073
39DAP/reference	1.04009	0.669
41DAP/reference	1.1513	0.033
42DAP/reference	1.01536	0.791
43DAP/reference	1.02718	0.873
47DAP/reference	1.12503	0.292
52DAP/reference	1.23198	0.043
57DAP/reference	1.26967	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21498	0.099
17DAP/reference	1.10193	0.079
27DAP/reference	1.07543	0.552
39DAP/reference	0.94212	0.322
41DAP/reference	0.92704	0.173
42DAP/reference	1.45919	0.038
43DAP/reference	1.31871	0.179
47DAP/reference	1.54848	0.008
52DAP/reference	1.10072	0.279
57DAP/reference	1.0671	0.654

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98671	0.607
17DAP/reference	1.05205	0.675
27DAP/reference	0.88498	0.218
39DAP/reference	1.0413	0.528
41DAP/reference	1.15842	0.197
42DAP/reference	1.06508	0.576
43DAP/reference	0.90533	0.158
47DAP/reference	1.23996	0.012
52DAP/reference	0.96992	0.675
57DAP/reference	1.01292	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95886	1
26DAP/20DAP	0.56078	0.512
34DAP/26DAP	0.96752	0.927
51DAP/34DAP	1.12312	0.96
52DAP/51DAP	1.06991	1
53DAP/52DAP	0.95998	0.876
55DAP/53DAP	0.99441	0.917
57DAP/55DAP	1.12834	0.818
62DAP/57DAP	0.97635	0.994
68DAP/62DAP	0.98663	0.863
68DAP/14DAP	0.9534	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.68405	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.62718	0.058
Mature Green Tomato/Ripe Tomato	0.79569	0.079
Immature Eggplant/Mature Eggplant	1.03034	0.485
Ripe Pepper/Ripe Tomato	0.40622	0.224
Mature Eggplant/Ripe Tomato	0.60375	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15843	1
1-1-2/M82	1.02644	1
12-2/M82	1.08871	1
12-4/M82	0.97772	1
1-3/M82	1.33142	1
2-1-1/M82	0.98828
2-1/M82	0.98452	1
2-6/M82	0.99397	1
3-2/M82	0.8873	0.752
4-1-1/M82	0.92025	1
4-1/M82	1.15703	0.853
4-3-2/M82	1.12658	1
4-3/M82	0.98921	1
5-3/M82	0.97171	1
6-2/M82	0.70111	0.481
6-3/M82	0.95532	1
7-1/M82	1.01269	1
7-2/M82	0.91019	0.796
9-3-2/M82	1.12259	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.259
IL2-6/WTpooled	1.07378	0.788
IL7-5/WTpooled	0.72284	1
IL7-3/WTpooled	0.82227	0.418
IL12-4/WTpooled	0.81129	0.71
IL1-4/WTpooled	0.9566	0.834
WT/WTpooled	1.02619	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	0.85875	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.25237	0.921
DC3000/delta hrp 6h	1.01446	1
DC3000/delta hrp 12h	1.06255	1
DC3000/delta hrp 24h	0.83349	0.257

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06581	0.441
DC3000 delta B/DC3000 delta AB	1.07004	0.535

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0679	1
Exp 36h	1.11239	1
Exp 60h	0.95204	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98995	1
Var 0h	0.55637	0.98
Var 12h I row2-row1	1.01617	1
Var 12h NI row2-row1	0.95855	0.906
Var 36h I row2-row1	0.98406	1
Var 36h NI row2-row1	0.98944	0.852
Var 60h I row2-row1	0.91272	0.832
Var 60h NI row2-row1	0.99312	1
Time course 0hI-0hNI	0.86052	0.07
Time course 12hI-12hNI	0.99177	0.978
Time course 36hI-36hNI	0.88885	0.183
Time course 60hI-60hNI	0.70906	0.006

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)	0.70483	0.267
transgenic ySAMdc/azygous control (breaker)	1.20539	0.248
transgenic ySAMdc/azygous control (red)	0.83524	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05007	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.32294	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98411	1
Manapal/WT (break)	1.0393	1
Manapal/WT (red)	0.73757	0.181