Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.11.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09724	0.947
27DAP/17DAP	1.15411	0.852
39DAP/27DAP	0.7362	0.286
41DAP/39DAP	0.75846	0.225
42DAP/41DAP	0.9674	1
43DAP/42DAP	0.8079	0.598
47DAP/43DAP	1.3799	0.442
52DAP/47DAP	1.12003	0.819
57DAP/52DAP	0.87582	0.879

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07322	0.46
17DAP/reference	1.31682	0.026
27DAP/reference	1.27521	0.025
39DAP/reference	1.18357	0.058
41DAP/reference	1.20194	0.393
42DAP/reference	0.82233	0.015
43DAP/reference	0.98676	0.763
47DAP/reference	0.92388	0.224
52DAP/reference	0.78427	0.015
57DAP/reference	0.85841	0.036

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9555	0.644
27DAP/17DAP	0.76386	0.363
39DAP/27DAP	0.67215	0.037
41DAP/39DAP	1.0394	1
42DAP/41DAP	1.12841	0.763
43DAP/42DAP	0.52348	0.024
47DAP/43DAP	0.92633	0.75
52DAP/47DAP	1.72087	0.091
57DAP/52DAP	0.83365	0.313
57DAP/7DAP	0.7165	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29867	0.037
17DAP/reference	1.72829	0.006
27DAP/reference	1.29801	0.015
39DAP/reference	1.58936	0.021
41DAP/reference	1.27536	0.184
42DAP/reference	1.52373	0.008
43DAP/reference	1.41581	0.021
47DAP/reference	1.00893	0.671
52DAP/reference	1.27402	0.016
57DAP/reference	1.42413	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23814	0.117
17DAP/reference	1.31172	0.191
27DAP/reference	0.98182	0.554
39DAP/reference	0.90714	0.235
41DAP/reference	0.88752	0.205
42DAP/reference	0.78477	0.05
43DAP/reference	1.01139	0.721
47DAP/reference	0.81262	0.021
52DAP/reference	0.99984	0.666
57DAP/reference	1.38496	0.083

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58379	0.022
17DAP/reference	1.20951	0.427
27DAP/reference	1.76716	0.033
39DAP/reference	1.50449	0.021
41DAP/reference	1.43891	0.016
42DAP/reference	1.34786	0.106
43DAP/reference	1.00314	0.66
47DAP/reference	1.00349	0.667
52DAP/reference	1.86549	0.074
57DAP/reference	0.75351	0.084

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98383	1
26DAP/20DAP	1.05232	1
34DAP/26DAP	0.86784	0.811
51DAP/34DAP	0.91412	0.674
52DAP/51DAP	1.09906	0.86
53DAP/52DAP	1.17751	0.882
55DAP/53DAP	1.14416	0.527
57DAP/55DAP	1.04676	0.975
62DAP/57DAP	1.30332	0.767
68DAP/62DAP	0.97051	0.885
68DAP/14DAP	0.65657	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88741	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	6.93379
Mature Green Tomato/Ripe Tomato	10.2946	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.10308	1
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.94555	0.761
12-2/M82	0.98322
12-4/M82	0.82293
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.10503
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.27711	0.572
6-2/M82	N/A	N/A
6-3/M82	1.31227
7-1/M82	N/A	N/A
7-2/M82	1.21018
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.39162
IL2-6/WTpooled	1.26925	0.395
IL7-5/WTpooled	0.85923	1
IL7-3/WTpooled	0.93463	1
IL12-4/WTpooled	1.09577	0.483
IL1-4/WTpooled	1.18157	1
WT/WTpooled	0.91696	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05927	0.774
DC3000/delta hrp 6h	0.70842
DC3000/delta hrp 12h	1.07658	1
DC3000/delta hrp 24h	0.87787	0.225

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.93606
DC3000 delta B/DC3000 delta AB	1.88746

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89392	0.328
Exp 36h	0.67348	0.406
Exp 60h	0.73511	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04996	1
Var 0h	0.9097	0.332
Var 12h I row2-row1	0.85196	0.338
Var 12h NI row2-row1	0.85448	0.906
Var 36h I row2-row1	1.20242
Var 36h NI row2-row1	0.77347
Var 60h I row2-row1	0.56403
Var 60h NI row2-row1	1.22806	0.904
Time course 0hI-0hNI	1.13979	0.852
Time course 12hI-12hNI	1.00672	1
Time course 36hI-36hNI	1.17048	0.453
Time course 60hI-60hNI	0.86735	0.319

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)	1.012	0.921
transgenic ySAMdc/azygous control (breaker)	0.59626	0.15
transgenic ySAMdc/azygous control (red)	0.95787	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02568	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7851	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9704	1
Manapal/WT (break)	1.20444	1
Manapal/WT (red)	0.65514	0.181