Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.1.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17618	0.725
27DAP/17DAP	0.93428	0.885
39DAP/27DAP	0.85407	0.414
41DAP/39DAP	1.06937	0.772
42DAP/41DAP	1.19217	0.825
43DAP/42DAP	0.93838	0.468
47DAP/43DAP	1.171	0.49
52DAP/47DAP	0.99312	0.957
57DAP/52DAP	1.1643	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79962	0.083
17DAP/reference	0.90648	0.368
27DAP/reference	1.02308	0.925
39DAP/reference	1.49761	0.018
41DAP/reference	1.34712	0.024
42DAP/reference	1.8441	0.001
43DAP/reference	1.74083	0.01
47DAP/reference	2.4845	0.001
52DAP/reference	1.57254	0.013
57DAP/reference	1.4351	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99191	0.763
27DAP/17DAP	0.92078	0.748
39DAP/27DAP	1.21743	0.548
41DAP/39DAP	0.92504	0.764
42DAP/41DAP	1.17621	0.172
43DAP/42DAP	0.92986	0.246
47DAP/43DAP	0.90887	0.305
52DAP/47DAP	0.98635	0.925
57DAP/52DAP	0.90212	0.352
57DAP/7DAP	0.89476	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6961	0.1
17DAP/reference	0.78086	0.044
27DAP/reference	1.49854	0.012
39DAP/reference	0.76303	0.056
41DAP/reference	0.84989	0.133
42DAP/reference	0.92351	0.169
43DAP/reference	1.11524	0.923
47DAP/reference	1.25529	0.386
52DAP/reference	1.23798	0.352
57DAP/reference	0.68588	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9843	0.756
17DAP/reference	1.24653	0.143
27DAP/reference	1.38593	0.029
39DAP/reference	0.8932	0.235
41DAP/reference	1.28634	0.146
42DAP/reference	1.14615	0.24
43DAP/reference	2.24926	0.017
47DAP/reference	1.23964	0.031
52DAP/reference	1.11673	0.194
57DAP/reference	1.08807	0.737

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68926	0.043
17DAP/reference	0.99279	0.508
27DAP/reference	0.56314	0.035
39DAP/reference	0.67832	0.021
41DAP/reference	1.2176	0.621
42DAP/reference	2.12311	0.006
43DAP/reference	1.79232	0.033
47DAP/reference	2.82226	0.005
52DAP/reference	2.36956	0.031
57DAP/reference	2.04049	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13572	0.966
26DAP/20DAP	0.82204	0.244
34DAP/26DAP	1.14397	0.819
51DAP/34DAP	1.22515	0.251
52DAP/51DAP	1.04512	0.758
53DAP/52DAP	0.86985	0.27
55DAP/53DAP	1.00764	1
57DAP/55DAP	0.91946	0.629
62DAP/57DAP	1.07844	0.767
68DAP/62DAP	0.94006	0.747
68DAP/14DAP	0.82461	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69125	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.00051	0.015
Immature Eggplant/Mature Eggplant	1.43184	0.259
Ripe Pepper/Ripe Tomato	0.11737	0.224
Mature Eggplant/Ripe Tomato	0.035	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0862	0.526
1-1-2/M82	0.94976	1
12-2/M82	0.96795	0.955
12-4/M82	0.99644	1
1-3/M82	1.45763	0.248
2-1-1/M82	0.87412	0.465
2-1/M82	1.03456	1
2-6/M82	0.95367	1
3-2/M82	0.98304	1
4-1-1/M82	0.97479	1
4-1/M82	1.16705	1
4-3-2/M82	0.9513	1
4-3/M82	0.94899	1
5-3/M82	0.93916	1
6-2/M82	1.01044	1
6-3/M82	0.98462	1
7-1/M82	0.96836	1
7-2/M82	0.93265	0.796
9-3-2/M82	0.89761	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.24671
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.64345	0.293
IL12-4/WTpooled	0.73352	0.71
IL1-4/WTpooled	0.65036
WT/WTpooled	1.09211	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	1.16953	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01336	0.921
DC3000/delta hrp 6h	1.04493	0.95
DC3000/delta hrp 12h	1.08376	1
DC3000/delta hrp 24h	2.38923	0.022

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02717	1
DC3000 delta B/DC3000 delta AB	0.95063	0.589

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88212	1
Exp 36h	0.45868	0.165
Exp 60h	0.66081	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03151	1
Var 0h	0.93124	1
Var 12h I row2-row1	0.89829	0.344
Var 12h NI row2-row1	0.92788	0.82
Var 36h I row2-row1	1.01531	1
Var 36h NI row2-row1	1.12044	0.276
Var 60h I row2-row1	0.87879	0.832
Var 60h NI row2-row1	1.12242	0.904
Time course 0hI-0hNI	0.92915	0.373
Time course 12hI-12hNI	1.02558	0.818
Time course 36hI-36hNI	0.90692	0.187
Time course 60hI-60hNI	0.33923	0.005

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)	0.69194	0.272
transgenic ySAMdc/azygous control (breaker)	0.8432	0.49
transgenic ySAMdc/azygous control (red)	0.96944	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.85771	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.6128	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.57767	0.09
Manapal/WT (break)	1.26859	0.381
Manapal/WT (red)	0.92908	0.607