Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.12.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72146	0.044
27DAP/17DAP	0.99343	0.947
39DAP/27DAP	1.57148	0.236
41DAP/39DAP	0.58518	0.045
42DAP/41DAP	2.49234	0.681
43DAP/42DAP	1.1166	1
47DAP/43DAP	0.70557	0.175
52DAP/47DAP	0.83341	0.564
57DAP/52DAP	1.05731	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49428	0.024
17DAP/reference	0.93209	0.448
27DAP/reference	0.58909	0.013
39DAP/reference	0.65931	0.041
41DAP/reference	0.65903	0.011
42DAP/reference	1.20168	0.001
43DAP/reference	0.8379	0.022
47DAP/reference	1.07946	0.318
52DAP/reference	0.67918	0.03
57DAP/reference	0.82326	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82165	0.09
27DAP/17DAP	1.09916	0.569
39DAP/27DAP	0.93933	0.356
41DAP/39DAP	0.98845	0.973
42DAP/41DAP	1.00462	0.892
43DAP/42DAP	0.93545	0.235
47DAP/43DAP	1.00541	1
52DAP/47DAP	0.86956	0.382
57DAP/52DAP	0.95432	0.598
57DAP/7DAP	0.42717	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.42964	0.024
17DAP/reference	1.59106	0.009
27DAP/reference	1.18792	0.041
39DAP/reference	1.04431	0.237
41DAP/reference	1.2665	0.011
42DAP/reference	1.18236	0.174
43DAP/reference	1.04486	0.707
47DAP/reference	1.12677	0.075
52DAP/reference	0.97136	0.477
57DAP/reference	0.77261	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12032	0.66
17DAP/reference	1.4109	0.027
27DAP/reference	1.36452	0.057
39DAP/reference	0.87999	0.168
41DAP/reference	1.08265	0.688
42DAP/reference	1.49617	0.023
43DAP/reference	0.71554	0.036
47DAP/reference	1.03368	0.965
52DAP/reference	0.56315	0.004
57DAP/reference	0.64041	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59527	0.017
17DAP/reference	1.22777	0.436
27DAP/reference	1.16948	0.131
39DAP/reference	1.23738	0.018
41DAP/reference	0.94219	0.037
42DAP/reference	1.34151	0.015
43DAP/reference	1.46517	0.022
47DAP/reference	0.72569	0.005
52DAP/reference	1.52716	0.079
57DAP/reference	0.9664	0.475

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97293	1
26DAP/20DAP	1.8763	0.149
34DAP/26DAP	0.73764	0.301
51DAP/34DAP	0.86897	0.252
52DAP/51DAP	0.91059	1
53DAP/52DAP	1.07605	0.935
55DAP/53DAP	0.9618	0.807
57DAP/55DAP	0.98566	0.867
62DAP/57DAP	1.18571	0.723
68DAP/62DAP	0.80215	0.211
68DAP/14DAP	1.12306	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	9.02903	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03271	0.287
Mature Green Tomato/Ripe Tomato	0.88866	0.377
Immature Eggplant/Mature Eggplant	0.91901	0.292
Ripe Pepper/Ripe Tomato	1.07456	1
Mature Eggplant/Ripe Tomato	1.47644	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99745	1
1-1-2/M82	1.41825	1
12-2/M82	0.55623	0.727
12-4/M82	1.57037	1
1-3/M82	1.37401
2-1-1/M82	1.03925	1
2-1/M82	0.94762
2-6/M82	1.38259	0.594
3-2/M82	1.02259	0.84
4-1-1/M82	1.88221	0.739
4-1/M82	0.71255
4-3-2/M82	1.96315	0.284
4-3/M82	1.57923	1
5-3/M82	1.25113	0.572
6-2/M82	N/A	N/A
6-3/M82	0.64442	0.916
7-1/M82	0.97298	1
7-2/M82	1.89473	0.324
9-3-2/M82	1.77555

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.07967	0.584
IL7-5/WTpooled	1.23723	0.792
IL7-3/WTpooled	0.9829	1
IL12-4/WTpooled	1.05303	0.595
IL1-4/WTpooled	0.91046	0.444
WT/WTpooled	0.99184	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	1.16218	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99502	1
DC3000/delta hrp 6h	1.09238	1
DC3000/delta hrp 12h	1.36383	1
DC3000/delta hrp 24h	1.23149	0.283

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.30405	0.042
DC3000 delta B/DC3000 delta AB	1.39978	0.096

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23836	1
Exp 36h	1.02595	1
Exp 60h	1.17875	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02645	1
Var 0h	0.71457	1
Var 12h I row2-row1	0.87454	0.338
Var 12h NI row2-row1	1.15701	0.235
Var 36h I row2-row1	1.19539	0.601
Var 36h NI row2-row1	0.90943	0.549
Var 60h I row2-row1	0.88218	0.374
Var 60h NI row2-row1	0.82781	0.866
Time course 0hI-0hNI	1.08975	0.603
Time course 12hI-12hNI	1.01456	0.867
Time course 36hI-36hNI	1.39201	0.009
Time course 60hI-60hNI	1.47704	0.01

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)	1.06349	0.571
transgenic ySAMdc/azygous control (breaker)	1.12914	0.178
transgenic ySAMdc/azygous control (red)	1.19752	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.40506	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91977	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13304	0.307
Manapal/WT (break)	1.00778	1
Manapal/WT (red)	1.01232	1