Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.6.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07544	0.838
27DAP/17DAP	1.32376	0.697
39DAP/27DAP	1.4725	0.692
41DAP/39DAP	0.8395	0.409
42DAP/41DAP	1.98461	0.223
43DAP/42DAP	1.25707	0.848
47DAP/43DAP	1.76207	0.246
52DAP/47DAP	0.43266	0.034
57DAP/52DAP	1.11596	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8115	0.06
17DAP/reference	0.81264	0.057
27DAP/reference	0.86032	0.147
39DAP/reference	1.20092	0.368
41DAP/reference	0.94909	0.542
42DAP/reference	1.62127	0.001
43DAP/reference	3.37014	0.007
47DAP/reference	2.31555	0.001
52DAP/reference	1.18207	0.43
57DAP/reference	2.23739	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77751	0.121
27DAP/17DAP	1.06697	0.775
39DAP/27DAP	1.82781	0.241
41DAP/39DAP	0.62391	0.034
42DAP/41DAP	1.50012	0.007
43DAP/42DAP	3.07613	0.013
47DAP/43DAP	1.69383	0.013
52DAP/47DAP	1.31737	0.367
57DAP/52DAP	0.588	0.08
57DAP/7DAP	3.95091	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68585	0.07
17DAP/reference	0.56558	0.017
27DAP/reference	0.72109	0.019
39DAP/reference	0.6329	0.012
41DAP/reference	0.8305	0.153
42DAP/reference	0.84773	0.07
43DAP/reference	1.13825	0.637
47DAP/reference	1.21712	0.173
52DAP/reference	0.80947	0.014
57DAP/reference	0.51472	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77531	0.069
17DAP/reference	0.96381	0.536
27DAP/reference	0.88852	0.22
39DAP/reference	0.76931	0.048
41DAP/reference	1.05133	1
42DAP/reference	1.03332	0.987
43DAP/reference	0.92813	0.394
47DAP/reference	1.19458	0.112
52DAP/reference	0.83323	0.086
57DAP/reference	0.97671	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58193	0.034
17DAP/reference	0.84156	0.305
27DAP/reference	0.54099	0.037
39DAP/reference	0.64414	0.025
41DAP/reference	0.76419	0.086
42DAP/reference	1.58107	0.008
43DAP/reference	1.6136	0.022
47DAP/reference	2.23048	0.005
52DAP/reference	2.26912	0.056
57DAP/reference	1.11831	0.511

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.48786	0.966
26DAP/20DAP	1.62151	0.099
34DAP/26DAP	0.78185	0.531
51DAP/34DAP	0.62205	0.058
52DAP/51DAP	1.05897	1
53DAP/52DAP	1.22657	0.662
55DAP/53DAP	0.82933	0.225
57DAP/55DAP	1.30065	0.393
62DAP/57DAP	0.67001	0.003
68DAP/62DAP	1.09126	1
68DAP/14DAP	0.69266	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	21.3045	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	18.2432	0.058
Mature Green Tomato/Ripe Tomato	0.40915	0.019
Immature Eggplant/Mature Eggplant	0.44187	0.064
Ripe Pepper/Ripe Tomato	0.08439	0.293
Mature Eggplant/Ripe Tomato	0.14108	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04048	0.742
1-1-2/M82	1.0205	1
12-2/M82	0.87591	0.955
12-4/M82	0.93274	0.319
1-3/M82	2.63318	0.248
2-1-1/M82	0.88133	0.683
2-1/M82	0.90132	0.74
2-6/M82	1.12817	0.395
3-2/M82	0.91629	1
4-1-1/M82	1.28147	1
4-1/M82	N/A	N/A
4-3-2/M82	2.34321
4-3/M82	1.03296	1
5-3/M82	1.05989	1
6-2/M82	1.55376	1
6-3/M82	1.1001	1
7-1/M82	1.04607	1
7-2/M82	1.00653	1
9-3-2/M82	1.64584	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.61239	0.243
IL2-6/WTpooled	1.06602	0.659
IL7-5/WTpooled	1.44969	0.75
IL7-3/WTpooled	0.88686	0.31
IL12-4/WTpooled	0.92329	0.581
IL1-4/WTpooled	0.9281	1
WT/WTpooled	0.98281	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	1.11666	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97801	1
DC3000/delta hrp 6h	1.10517	1
DC3000/delta hrp 12h	1.13199	1
DC3000/delta hrp 24h	0.90275	0.28

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.42224
DC3000 delta B/DC3000 delta AB	1.34087	0.234

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89992	1
Exp 36h	0.8637	0.471
Exp 60h	0.70938	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9866	1
Var 0h	0.50747	1
Var 12h I row2-row1	0.96031	0.856
Var 12h NI row2-row1	1.16618	1
Var 36h I row2-row1	1.02361	1
Var 36h NI row2-row1	1.45859	0.482
Var 60h I row2-row1	1.00101	1
Var 60h NI row2-row1	1.01397	1
Time course 0hI-0hNI	0.94965	0.595
Time course 12hI-12hNI	0.92867	0.458
Time course 36hI-36hNI	0.65419	0.023
Time course 60hI-60hNI	0.25924	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)	0.65049	0.324
transgenic ySAMdc/azygous control (breaker)	1.32668	0.248
transgenic ySAMdc/azygous control (red)	1.01959	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.956	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46685	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.31471	0.093
Manapal/WT (break)	1.04465	1
Manapal/WT (red)	0.86018	0.424