Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.20.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99002	0.867
27DAP/17DAP	1.19435	0.849
39DAP/27DAP	1.02545	1
41DAP/39DAP	1.17066	0.715
42DAP/41DAP	0.97444	1
43DAP/42DAP	1.0266	1
47DAP/43DAP	0.97137	0.859
52DAP/47DAP	1.08151	0.957
57DAP/52DAP	1.09866	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9751	0.476
17DAP/reference	0.92533	0.278
27DAP/reference	1.01329	0.909
39DAP/reference	0.98239	0.704
41DAP/reference	0.91149	0.201
42DAP/reference	0.96201	0.115
43DAP/reference	0.93711	0.316
47DAP/reference	0.97044	0.242
52DAP/reference	0.80039	0.064
57DAP/reference	0.86013	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99674	0.871
27DAP/17DAP	1.01421	0.954
39DAP/27DAP	0.98798	0.898
41DAP/39DAP	1.03669	0.807
42DAP/41DAP	0.98153	0.801
43DAP/42DAP	1.02349	0.513
47DAP/43DAP	0.99812	1
52DAP/47DAP	0.96106	0.686
57DAP/52DAP	1.03279	0.798
57DAP/7DAP	0.94718	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05128	0.491
17DAP/reference	0.97801	0.253
27DAP/reference	0.89268	0.019
39DAP/reference	1.04703	0.222
41DAP/reference	1.02913	0.655
42DAP/reference	0.93057	0.01
43DAP/reference	0.98986	0.608
47DAP/reference	1.04194	1
52DAP/reference	1.1551	0.352
57DAP/reference	1.16432	0.147

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96805	0.518
17DAP/reference	0.95331	0.116
27DAP/reference	0.91491	0.257
39DAP/reference	0.96446	0.404
41DAP/reference	0.92602	0.237
42DAP/reference	0.91848	0.03
43DAP/reference	0.91975	0.181
47DAP/reference	0.99808	0.749
52DAP/reference	0.91206	0.009
57DAP/reference	0.91863	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96052	0.214
17DAP/reference	0.96127	0.389
27DAP/reference	1.01855	0.805
39DAP/reference	1.00662	0.836
41DAP/reference	0.97012	0.264
42DAP/reference	0.88062	0.059
43DAP/reference	0.90445	0.092
47DAP/reference	1.02505	0.934
52DAP/reference	0.92611	0.368
57DAP/reference	0.85504	0.118

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99326	1
26DAP/20DAP	1.09782	0.598
34DAP/26DAP	0.97118	0.741
51DAP/34DAP	1.00798	0.962
52DAP/51DAP	0.9908	1
53DAP/52DAP	1.02025	0.819
55DAP/53DAP	0.99726	0.925
57DAP/55DAP	1.04496	0.841
62DAP/57DAP	0.96794	0.994
68DAP/62DAP	1.02961	1
68DAP/14DAP	1.35224	0.065

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00495	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14129	0.068
Mature Green Tomato/Ripe Tomato	0.93983	0.569
Immature Eggplant/Mature Eggplant	1.03907	0.507
Ripe Pepper/Ripe Tomato	0.95705	1
Mature Eggplant/Ripe Tomato	1.18244	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99513	1
1-1-2/M82	0.89986	1
12-2/M82	0.9685	0.955
12-4/M82	0.91655	1
1-3/M82	0.97804	1
2-1-1/M82	1.01313	0.422
2-1/M82	1.04008	1
2-6/M82	0.98316	1
3-2/M82	0.99698	1
4-1-1/M82	0.84067	0.847
4-1/M82	1.10167	1
4-3-2/M82	0.85167	1
4-3/M82	0.95023	1
5-3/M82	0.99816	1
6-2/M82	0.95324	1
6-3/M82	1.02675	1
7-1/M82	0.96249	0.476
7-2/M82	1.01694	1
9-3-2/M82	0.95179

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.41261	0.277
IL2-6/WTpooled	0.83895	0.383
IL7-5/WTpooled	0.97864	1
IL7-3/WTpooled	1.30257	1
IL12-4/WTpooled	1.07143	0.546
IL1-4/WTpooled	1.10129	1
WT/WTpooled	0.91043	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	1.03006	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11633	0.75
DC3000/delta hrp 6h	0.69549	0.95
DC3000/delta hrp 12h	0.96492	1
DC3000/delta hrp 24h	1.02396	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14458	0.081
DC3000 delta B/DC3000 delta AB	1.0909	0.335

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04088	1
Exp 36h	1.27526	0.693
Exp 60h	1.2803	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9958	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.23857	0.283
Var 12h NI row2-row1	1.02923	1
Var 36h I row2-row1	1.06405	1
Var 36h NI row2-row1	0.83235	0.478
Var 60h I row2-row1	0.95545	0.306
Var 60h NI row2-row1	1.06881	1
Time course 0hI-0hNI	0.98915	0.994
Time course 12hI-12hNI	1.01922	0.824
Time course 36hI-36hNI	1.0377	0.355
Time course 60hI-60hNI	1.7312	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)	1.09901	0.286
transgenic ySAMdc/azygous control (breaker)	0.66371	0.173
transgenic ySAMdc/azygous control (red)	1.07547	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00365	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68632	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75896	1
Manapal/WT (break)	1.05332	1
Manapal/WT (red)	0.89692	0.424