Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.2.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09224	0.904
27DAP/17DAP	0.94944	0.934
39DAP/27DAP	1.88336	0.057
41DAP/39DAP	0.51361	0.045
42DAP/41DAP	1.12602	0.873
43DAP/42DAP	1.09239	1
47DAP/43DAP	1.1843	0.584
52DAP/47DAP	0.94397	0.816
57DAP/52DAP	1.30541	0.477

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91466	0.238
17DAP/reference	0.801	0.024
27DAP/reference	0.86292	0.04
39DAP/reference	0.97309	0.68
41DAP/reference	0.79453	0.014
42DAP/reference	1.19949	0.043
43DAP/reference	1.05904	0.217
47DAP/reference	1.09761	0.284
52DAP/reference	1.39004	0.011
57DAP/reference	1.32393	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00475	0.899
27DAP/17DAP	1.08242	0.836
39DAP/27DAP	1.03003	0.845
41DAP/39DAP	1.01686	0.921
42DAP/41DAP	1.02105	1
43DAP/42DAP	0.82634	0.025
47DAP/43DAP	0.99184	0.977
52DAP/47DAP	0.81257	0.071
57DAP/52DAP	0.90058	0.436
57DAP/7DAP	1.09943	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.74247	0.034
17DAP/reference	1.0948	0.574
27DAP/reference	1.24825	0.107
39DAP/reference	1.6393	0.011
41DAP/reference	1.8759	0.008
42DAP/reference	1.41083	0.174
43DAP/reference	1.25359	0.07
47DAP/reference	1.45366	0.027
52DAP/reference	2.18731	0.008
57DAP/reference	2.12353	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91654	0.412
17DAP/reference	1.17596	0.101
27DAP/reference	1.28418	0.039
39DAP/reference	1.26381	0.093
41DAP/reference	1.4552	0.007
42DAP/reference	1.54417	0.014
43DAP/reference	0.97593	0.607
47DAP/reference	1.39826	0.013
52DAP/reference	1.10855	0.069
57DAP/reference	1.00246	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32745	0.044
17DAP/reference	0.96077	0.537
27DAP/reference	1.18129	0.131
39DAP/reference	1.53542	0.017
41DAP/reference	1.29451	0.065
42DAP/reference	1.16129	0.204
43DAP/reference	1.09752	0.617
47DAP/reference	1.30176	0.02
52DAP/reference	1.71973	0.041
57DAP/reference	1.99834	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22911	1
26DAP/20DAP	1.70363	0.308
34DAP/26DAP	1.16444	1
51DAP/34DAP	0.73107	0.125
52DAP/51DAP	0.888	1
53DAP/52DAP	1.06801	0.819
55DAP/53DAP	0.60384	0.016
57DAP/55DAP	1.17579	0.694
62DAP/57DAP	1.06468
68DAP/62DAP	1.0081	0.939
68DAP/14DAP	1.26401	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.64305	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.12666	0.417
Mature Green Tomato/Ripe Tomato	1.54785	0.016
Immature Eggplant/Mature Eggplant	0.4854
Ripe Pepper/Ripe Tomato	0.63425	0.224
Mature Eggplant/Ripe Tomato	0.18182	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95161	0.944
1-1-2/M82	1.15435	1
12-2/M82	N/A	N/A
12-4/M82	1.08419	1
1-3/M82	0.8508
2-1-1/M82	0.97093	1
2-1/M82	N/A	N/A
2-6/M82	1.03303	1
3-2/M82	0.74128	0.752
4-1-1/M82	N/A	N/A
4-1/M82	1.69973
4-3-2/M82	1.32412
4-3/M82	0.95281	1
5-3/M82	1.0679	0.572
6-2/M82	0.78289	1
6-3/M82	0.92628	1
7-1/M82	0.98821
7-2/M82	1.05868	1
9-3-2/M82	1.16659	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.48904	0.337
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.65921	0.362
IL12-4/WTpooled	1.1065	1
IL1-4/WTpooled	0.77432
WT/WTpooled	0.93442	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	1.16537	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98091	1
DC3000/delta hrp 6h	0.63602
DC3000/delta hrp 12h	0.92265	1
DC3000/delta hrp 24h	1.46547	0.077

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8056	0.293
DC3000 delta B/DC3000 delta AB	1.08474	0.601

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.11714	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98385	1
Var 0h	1.17615	0.421
Var 12h I row2-row1	0.96906	0.948
Var 12h NI row2-row1	1.20616	1
Var 36h I row2-row1	1.17136	0.309
Var 36h NI row2-row1	1.68424	1
Var 60h I row2-row1	0.97209	0.952
Var 60h NI row2-row1	0.80365	0.359
Time course 0hI-0hNI	0.86945	0.169
Time course 12hI-12hNI	1.04351	0.56
Time course 36hI-36hNI	1.32222	0.128
Time course 60hI-60hNI	1.2664	0.033

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)	0.94378	0.289
transgenic ySAMdc/azygous control (breaker)	0.82171	0.15
transgenic ySAMdc/azygous control (red)	1.01261	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00062	0.94

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93095	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90691	1
Manapal/WT (break)	1.12704	1
Manapal/WT (red)	0.89861	0.503