Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.3.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25566	0.315
27DAP/17DAP	1.57385	0.353
39DAP/27DAP	2.34757	0.449
41DAP/39DAP	2.43206	0.321
42DAP/41DAP	0.9683	1
43DAP/42DAP	0.96508	0.909
47DAP/43DAP	0.53068	0.049
52DAP/47DAP	0.75325	0.41
57DAP/52DAP	1.13689	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83037	0.06
17DAP/reference	0.9964	0.904
27DAP/reference	1.29812	0.096
39DAP/reference	0.99616	0.901
41DAP/reference	1.17798	0.05
42DAP/reference	1.94118	0.029
43DAP/reference	1.03861	1
47DAP/reference	2.75344	0.001
52DAP/reference	2.56132	0.007
57DAP/reference	1.10623	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73696	0.27
27DAP/17DAP	0.98596	0.919
39DAP/27DAP	2.32587	0.046
41DAP/39DAP	3.66197	0.017
42DAP/41DAP	0.65557	0.016
43DAP/42DAP	0.51627	0.02
47DAP/43DAP	1.09329	0.552
52DAP/47DAP	1.08687	0.831
57DAP/52DAP	0.69807	0.289
57DAP/7DAP	0.86536	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74061	0.067
17DAP/reference	0.71952	0.021
27DAP/reference	0.94238	0.283
39DAP/reference	0.69974	0.034
41DAP/reference	0.81121	0.111
42DAP/reference	1.0421	0.889
43DAP/reference	0.8111	0.012
47DAP/reference	1.99984	0.292
52DAP/reference	0.86846	0.057
57DAP/reference	0.93037	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5888	0.013
17DAP/reference	1.08018	0.979
27DAP/reference	2.78088	0.013
39DAP/reference	2.62634	0.011
41DAP/reference	2.2426	0.005
42DAP/reference	2.57359	0.007
43DAP/reference	1.30191	1
47DAP/reference	2.23715	0.008
52DAP/reference	1.614	0.007
57DAP/reference	1.18692	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85327	0.214
17DAP/reference	0.76499	0.121
27DAP/reference	0.98708	0.566
39DAP/reference	1.09646	0.935
41DAP/reference	0.96027	0.459
42DAP/reference	1.74451	0.279
43DAP/reference	2.65998	0.241
47DAP/reference	2.12989	0.037
52DAP/reference	1.22711	0.583
57DAP/reference	6.1316	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2486	0.966
26DAP/20DAP	1.3561	0.297
34DAP/26DAP	1.53481	0.304
51DAP/34DAP	1.53925	0.039
52DAP/51DAP	0.96094	1
53DAP/52DAP	1.65625	0.027
55DAP/53DAP	1.11931	0.487
57DAP/55DAP	2.18615	0.461
62DAP/57DAP	0.91002	0.994
68DAP/62DAP	1.2962	0.367
68DAP/14DAP	2.86262	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89746	0.048

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.7814	0.232
Mature Green Tomato/Ripe Tomato	2.88656	0.016
Immature Eggplant/Mature Eggplant	1.53299	0.05
Ripe Pepper/Ripe Tomato	1.85228	1
Mature Eggplant/Ripe Tomato	0.73941	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11352	0.574
1-1-2/M82	1.84493	1
12-2/M82	0.69856	0.862
12-4/M82	1.28484	1
1-3/M82	1.70938	0.277
2-1-1/M82	0.92435	N/A
2-1/M82	1.58651	1
2-6/M82	1.46523	0.395
3-2/M82	2.05394	0.388
4-1-1/M82	1.65628	0.938
4-1/M82	0.80587	N/A
4-3-2/M82	2.39955	0.508
4-3/M82	1.04571	N/A
5-3/M82	1.66807	0.496
6-2/M82	5.17085	0.235
6-3/M82	1.264	1
7-1/M82	N/A	N/A
7-2/M82	1.3188	N/A
9-3-2/M82	2.22024	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.66037	0.243
IL2-6/WTpooled	1.00792	N/A
IL7-5/WTpooled	0.91881	1
IL7-3/WTpooled	1.54345	N/A
IL12-4/WTpooled	1.10902	0.891
IL1-4/WTpooled	0.9435	0.699
WT/WTpooled	0.96305	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	1.93544	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97385	1
DC3000/delta hrp 6h	1.02993	1
DC3000/delta hrp 12h	1.35236	1
DC3000/delta hrp 24h	0.92477	0.534

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.05398	0.042
DC3000 delta B/DC3000 delta AB	3.8541	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07449	1
Exp 36h	1.13102	1
Exp 60h	1.24269	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98616	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.09751	N/A
Var 12h NI row2-row1	1.55376	N/A
Var 36h I row2-row1	1.94447	0.283
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.26938	0.63
Time course 12hI-12hNI	1.24208	0.774
Time course 36hI-36hNI	6.28981	0.004
Time course 60hI-60hNI	63.95	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)	0.95796	0.614
transgenic ySAMdc/azygous control (breaker)	0.81037	0.173
transgenic ySAMdc/azygous control (red)	1.28915	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.5708	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92292	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.64389	1
Manapal/WT (break)	0.90909	1
Manapal/WT (red)	1.31191	1