Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.13.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03715	0.893
27DAP/17DAP	1.11808	0.845
39DAP/27DAP	0.95965	0.402
41DAP/39DAP	1.03036	0.67
42DAP/41DAP	0.97483	1
43DAP/42DAP	0.94853	0.695
47DAP/43DAP	0.98141	0.913
52DAP/47DAP	0.97789	0.916
57DAP/52DAP	0.89326	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96004	0.277
17DAP/reference	0.98091	0.536
27DAP/reference	1.02227	0.569
39DAP/reference	1.0576	0.243
41DAP/reference	0.95752	0.434
42DAP/reference	1.01775	0.585
43DAP/reference	1.0208	0.838
47DAP/reference	0.98305	0.418
52DAP/reference	0.95969	0.393
57DAP/reference	1.08829	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99961	1
27DAP/17DAP	1.00101	1
39DAP/27DAP	0.97932	0.898
41DAP/39DAP	1.00029	1
42DAP/41DAP	1.026	0.795
43DAP/42DAP	1.00681	0.627
47DAP/43DAP	1.00199	1
52DAP/47DAP	0.98046	0.898
57DAP/52DAP	0.93836	0.366
57DAP/7DAP	0.94118	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90728	0.122
17DAP/reference	0.96078	0.124
27DAP/reference	0.92772	0.042
39DAP/reference	0.96104	0.095
41DAP/reference	0.97886	0.133
42DAP/reference	0.91553	0.073
43DAP/reference	0.83235	0.034
47DAP/reference	0.90584	0.066
52DAP/reference	0.8671	0.049
57DAP/reference	0.85101	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96399	0.441
17DAP/reference	0.96576	0.307
27DAP/reference	0.93623	0.24
39DAP/reference	0.92475	0.189
41DAP/reference	0.92517	0.183
42DAP/reference	1.01192	1
43DAP/reference	1.02384	0.845
47DAP/reference	1.11846	0.039
52DAP/reference	0.92728	0.101
57DAP/reference	1.02992	0.552

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96438	0.311
17DAP/reference	0.98067	0.681
27DAP/reference	0.93814	0.097
39DAP/reference	0.94158	0.271
41DAP/reference	0.98913	0.754
42DAP/reference	0.89573	0.172
43DAP/reference	0.90752	0.066
47DAP/reference	0.96232	0.434
52DAP/reference	0.9317	0.482
57DAP/reference	1.02079	0.8

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02937	0.966
26DAP/20DAP	1.02325	0.974
34DAP/26DAP	1.03585	1
51DAP/34DAP	0.9644	0.674
52DAP/51DAP	0.99534	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	1.18495	0.599
57DAP/55DAP	0.96118	0.863
62DAP/57DAP	0.95165	0.994
68DAP/62DAP	1.09508	0.491
68DAP/14DAP	1.28353	0.295

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97499	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79318	0.356
Mature Green Tomato/Ripe Tomato	0.98909	0.66
Immature Eggplant/Mature Eggplant	1.15482	0.19
Ripe Pepper/Ripe Tomato	1.90257	1
Mature Eggplant/Ripe Tomato	2.40907

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96387	0.944
1-1-2/M82	0.97077	1
12-2/M82	0.91797	0.955
12-4/M82	0.94968	1
1-3/M82	1.04929	0.479
2-1-1/M82	0.97101	1
2-1/M82	1.22882	1
2-6/M82	0.98721	0.501
3-2/M82	0.92429	1
4-1-1/M82	0.95842	1
4-1/M82	0.85836	0.665
4-3-2/M82	0.99248	1
4-3/M82	1.0147	1
5-3/M82	0.98737	1
6-2/M82	1.0705	1
6-3/M82	0.97514	1
7-1/M82	0.93264	0.476
7-2/M82	0.95997	1
9-3-2/M82	0.88655	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03192
IL2-6/WTpooled	0.84792	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07393	1
IL12-4/WTpooled	0.93717	1
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.94983	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	1.61583	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93869	1
DC3000/delta hrp 6h	1.24475	1
DC3000/delta hrp 12h	0.92313	1
DC3000/delta hrp 24h	1.10898	0.283

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.41296	0.042
DC3000 delta B/DC3000 delta AB	1.2852	0.105

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.68059	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02938	1
Var 0h	0.9204	0.933
Var 12h I row2-row1	1.14795	0.187
Var 12h NI row2-row1	0.92556	0.627
Var 36h I row2-row1	1.28364	1
Var 36h NI row2-row1	1.0549	1
Var 60h I row2-row1	1.18576	1
Var 60h NI row2-row1	1.20501	0.904
Time course 0hI-0hNI	1.04202	0.867
Time course 12hI-12hNI	1.03361	0.818
Time course 36hI-36hNI	1.0137	0.881
Time course 60hI-60hNI	1.04384	0.426

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)	0.83591	0.428
transgenic ySAMdc/azygous control (breaker)	2.14085	0.248
transgenic ySAMdc/azygous control (red)	1.45305	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95646	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12376	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.81551	0.333
Manapal/WT (red)	0.88343	0.607