Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91788	0.568
27DAP/17DAP	1.01349	1
39DAP/27DAP	1.13767	0.774
41DAP/39DAP	1.0709	0.822
42DAP/41DAP	1.20143	0.92
43DAP/42DAP	0.9887	0.925
47DAP/43DAP	0.95092	0.746
52DAP/47DAP	1.17614	0.983
57DAP/52DAP	1.0806	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9515	0.336
17DAP/reference	0.96736	0.448
27DAP/reference	0.96892	0.444
39DAP/reference	0.94281	0.541
41DAP/reference	0.95699	0.434
42DAP/reference	0.94609	0.05
43DAP/reference	0.98707	0.763
47DAP/reference	0.89816	0.009
52DAP/reference	0.84091	0.025
57DAP/reference	0.88815	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0398	0.63
27DAP/17DAP	0.95423	0.446
39DAP/27DAP	1.01761	0.707
41DAP/39DAP	1.07729	0.663
42DAP/41DAP	0.95671	0.612
43DAP/42DAP	0.964	0.522
47DAP/43DAP	0.99584	0.99
52DAP/47DAP	1.00695	0.979
57DAP/52DAP	1.05639	0.674
57DAP/7DAP	1.12662	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03587	0.676
17DAP/reference	1.01865	0.525
27DAP/reference	1.03043	0.453
39DAP/reference	1.04958	0.096
41DAP/reference	1.04337	0.491
42DAP/reference	1.02839	0.686
43DAP/reference	0.98833	0.502
47DAP/reference	0.99852	1
52DAP/reference	1.15563	0.352
57DAP/reference	1.0626	0.082

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99904	0.97
17DAP/reference	0.97398	0.347
27DAP/reference	0.9918	0.619
39DAP/reference	0.9196	0.147
41DAP/reference	0.94112	0.068
42DAP/reference	0.91362	0.042
43DAP/reference	0.98502	0.67
47DAP/reference	0.93805	0.116
52DAP/reference	0.92434	0.066
57DAP/reference	0.92846	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01508	0.846
17DAP/reference	0.95988	0.407
27DAP/reference	0.94678	0.119
39DAP/reference	1.03572	0.33
41DAP/reference	0.9521	0.512
42DAP/reference	0.96914	0.552
43DAP/reference	0.97397	0.449
47DAP/reference	0.98985	0.61
52DAP/reference	1.00519	0.99
57DAP/reference	0.857	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06222	0.966
26DAP/20DAP	1.11546	0.555
34DAP/26DAP	0.94568	0.848
51DAP/34DAP	1.00356	1
52DAP/51DAP	1.07299	0.431
53DAP/52DAP	1.00191	1
55DAP/53DAP	0.99093	0.894
57DAP/55DAP	0.9778	0.88
62DAP/57DAP	1.04361	1
68DAP/62DAP	1.0503	0.926
68DAP/14DAP	1.07029	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.11376	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.08189	0.113
Mature Green Tomato/Ripe Tomato	1.3873
Immature Eggplant/Mature Eggplant	0.87599	0.159
Ripe Pepper/Ripe Tomato	1.10466	1
Mature Eggplant/Ripe Tomato	0.78088	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92589	0.934
1-1-2/M82	0.78559	1
12-2/M82	0.92396	0.74
12-4/M82	0.93653	1
1-3/M82	1.08008	1
2-1-1/M82	0.99434	1
2-1/M82	1.00663	1
2-6/M82	0.95296	1
3-2/M82	1.02233	0.967
4-1-1/M82	1.13847	0.977
4-1/M82	0.98491	1
4-3-2/M82	1.07293	0.508
4-3/M82	0.93604	0.72
5-3/M82	1.00177	1
6-2/M82	1.06117	1
6-3/M82	0.99909	1
7-1/M82	0.8995	1
7-2/M82	0.97468	1
9-3-2/M82	1.05698	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01204
IL2-6/WTpooled	0.88147	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.14955	1
IL12-4/WTpooled	0.96565	0.71
IL1-4/WTpooled	1.07314	1
WT/WTpooled	0.94702	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	1.20522	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00102	1
DC3000/delta hrp 6h	1.01455	1
DC3000/delta hrp 12h	1.13954	1
DC3000/delta hrp 24h	0.95774	0.682

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03597	0.333
DC3000 delta B/DC3000 delta AB	1.00425	0.771

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86057	1
Exp 36h	1.29488	1
Exp 60h	1.13691	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99626	1
Var 0h	0.97122	1
Var 12h I row2-row1	1.14587	0.272
Var 12h NI row2-row1	1.1457	1
Var 36h I row2-row1	1.06336	1
Var 36h NI row2-row1	0.80742	0.347
Var 60h I row2-row1	1.03662	1
Var 60h NI row2-row1	0.99152	1
Time course 0hI-0hNI	0.9824	0.943
Time course 12hI-12hNI	1.03608	0.756
Time course 36hI-36hNI	1.21716	0.044
Time course 60hI-60hNI	1.58277	0.012

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)	1.02953	1
transgenic ySAMdc/azygous control (breaker)	1.78446	0.178
transgenic ySAMdc/azygous control (red)	1.28245	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03807	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89381	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7059	1
Manapal/WT (break)	0.74182	1
Manapal/WT (red)	1.71119	0.164