Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.17.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90996	0.503
27DAP/17DAP	1.27694	0.749
39DAP/27DAP	1.1928	0.631
41DAP/39DAP	0.83418	0.453
42DAP/41DAP	0.9964	1
43DAP/42DAP	0.95149	0.877
47DAP/43DAP	1.10315	0.873
52DAP/47DAP	0.77167	0.463
57DAP/52DAP	1.16602	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16174	0.5
17DAP/reference	0.95724	0.536
27DAP/reference	1.16354	0.106
39DAP/reference	0.98283	0.779
41DAP/reference	1.04135	1
42DAP/reference	0.99563	0.44
43DAP/reference	1.12386	0.471
47DAP/reference	1.21086	0.404
52DAP/reference	1.47983	0.045
57DAP/reference	1.42151	0.029

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00701	0.75
27DAP/17DAP	1.14473	0.943
39DAP/27DAP	0.89743	0.316
41DAP/39DAP	1.06118	0.827
42DAP/41DAP	0.78816	0.081
43DAP/42DAP	1.05834	1
47DAP/43DAP	0.91005	0.701
52DAP/47DAP	1.20205	0.598
57DAP/52DAP	1.41421	0.303
57DAP/7DAP	1.06982	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78784	0.082
17DAP/reference	0.6774	0.012
27DAP/reference	0.77969	0.037
39DAP/reference	0.79576	0.039
41DAP/reference	0.76098	0.047
42DAP/reference	0.78106	0.017
43DAP/reference	0.72356	0.03
47DAP/reference	0.99374	0.671
52DAP/reference	0.77616	0.028
57DAP/reference	0.81661	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70497	0.06
17DAP/reference	1.13871	0.874
27DAP/reference	1.02013	0.663
39DAP/reference	1.17446	0.529
41DAP/reference	1.31365	0.014
42DAP/reference	1.14235	0.207
43DAP/reference	1.01374	1
47DAP/reference	0.93011	0.277
52DAP/reference	0.97546	0.5
57DAP/reference	0.89348	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93151	0.214
17DAP/reference	0.88634	0.308
27DAP/reference	0.75465	0.032
39DAP/reference	0.92097	0.328
41DAP/reference	0.74936	0.031
42DAP/reference	1.02962	0.816
43DAP/reference	1.06198	0.767
47DAP/reference	1.20243	0.187
52DAP/reference	0.79547	0.118
57DAP/reference	1.61692	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.4641	0.966
26DAP/20DAP	1.18891	0.924
34DAP/26DAP	0.96547	0.92
51DAP/34DAP	1.24439	0.429
52DAP/51DAP	0.96941	1
53DAP/52DAP	0.9596	0.817
55DAP/53DAP	0.88227	0.169
57DAP/55DAP	1.45683	0.71
62DAP/57DAP	1.0494	1
68DAP/62DAP	1.71213	0.646
68DAP/14DAP	1.63609	0.384

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66683	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74455	0.213
Mature Green Tomato/Ripe Tomato	1.07559	1
Immature Eggplant/Mature Eggplant	0.88672	0.407
Ripe Pepper/Ripe Tomato	2.65833	0.258
Mature Eggplant/Ripe Tomato	2.0277	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02609
1-1-2/M82	1.12841	1
12-2/M82	0.9823
12-4/M82	0.87867	0.298
1-3/M82	1.14491	0.479
2-1-1/M82	0.75453
2-1/M82	1.00194	1
2-6/M82	0.90374	0.501
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.97605	1
4-3-2/M82	1.02169
4-3/M82	0.9644	1
5-3/M82	1.25963	0.572
6-2/M82	1.06038	0.253
6-3/M82	1.01978	1
7-1/M82	1.21598	0.598
7-2/M82	1.05344	1
9-3-2/M82	1.1026	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.80851	0.365
IL2-6/WTpooled	0.98026	1
IL7-5/WTpooled	1.42755	0.792
IL7-3/WTpooled	1.2559	0.362
IL12-4/WTpooled	1.32568	0.538
IL1-4/WTpooled	1.06678	1
WT/WTpooled	0.93256	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	1.0184	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16897	0.875
DC3000/delta hrp 6h	0.69211
DC3000/delta hrp 12h	1.60661	1
DC3000/delta hrp 24h	0.97982	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.54314	0.042
DC3000 delta B/DC3000 delta AB	1.74389	0.42

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.46118	1
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04118	1
Var 0h	1.14081	0.936
Var 12h I row2-row1	1.88534	0.58
Var 12h NI row2-row1	1.43515	1
Var 36h I row2-row1	1.00508	1
Var 36h NI row2-row1	1.01727
Var 60h I row2-row1	1.00395	1
Var 60h NI row2-row1	0.86176	0.977
Time course 0hI-0hNI	0.9416	0.711
Time course 12hI-12hNI	1.05855	0.816
Time course 36hI-36hNI	1.10936	0.166
Time course 60hI-60hNI	2.01264	0.042

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)	1.18985	0.268
transgenic ySAMdc/azygous control (breaker)	1.1995	0.172
transgenic ySAMdc/azygous control (red)	0.82095	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98035	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69274	0.172
Manapal/WT (break)	0.91734	1
Manapal/WT (red)	0.97421	0.728