Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.13.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81129	0.395
27DAP/17DAP	0.70061	0.182
39DAP/27DAP	0.98052	0.733
41DAP/39DAP	0.78648	0.252
42DAP/41DAP	1.12406	1
43DAP/42DAP	0.78014	0.522
47DAP/43DAP	1.19354	0.555
52DAP/47DAP	0.67217	0.218
57DAP/52DAP	2.18423	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.108	0.814
17DAP/reference	1.02315	0.787
27DAP/reference	0.9785	0.567
39DAP/reference	1.07182	0.76
41DAP/reference	0.91485	0.341
42DAP/reference	0.74343	0.001
43DAP/reference	0.83442	0.093
47DAP/reference	0.77115	0.001
52DAP/reference	0.83066	0.064
57DAP/reference	0.86387	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68408	0.05
27DAP/17DAP	1.47906	0.075
39DAP/27DAP	0.66555	0.07
41DAP/39DAP	1.15148	0.861
42DAP/41DAP	1.13412	0.708
43DAP/42DAP	0.52458	0.023
47DAP/43DAP	1.25202	0.027
52DAP/47DAP	0.99196	0.93
57DAP/52DAP	1.375	0.352
57DAP/7DAP	0.73164	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19103	0.377
17DAP/reference	0.89129	0.02
27DAP/reference	0.90501	0.037
39DAP/reference	0.92939	0.014
41DAP/reference	0.90869	0.038
42DAP/reference	0.95274	0.222
43DAP/reference	1.01844	0.923
47DAP/reference	1.1473	0.285
52DAP/reference	0.91827	0.115
57DAP/reference	0.90896	0.045

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0477	0.577
17DAP/reference	0.8089	0.014
27DAP/reference	0.90695	0.212
39DAP/reference	0.7181	0.038
41DAP/reference	0.68779	0.007
42DAP/reference	0.70126	0.018
43DAP/reference	0.79819	0.092
47DAP/reference	0.85172	0.025
52DAP/reference	0.70215	0.006
57DAP/reference	0.72612	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95176	0.092
17DAP/reference	0.93467	0.268
27DAP/reference	0.88467	0.05
39DAP/reference	0.90476	0.019
41DAP/reference	0.91943	0.096
42DAP/reference	0.85325	0.087
43DAP/reference	0.80047	0.088
47DAP/reference	0.67473	0.007
52DAP/reference	0.71906	0.084
57DAP/reference	0.69038	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09186	0.966
26DAP/20DAP	0.9404	1
34DAP/26DAP	0.68651	0.399
51DAP/34DAP	1.18285	0.524
52DAP/51DAP	0.78896	1
53DAP/52DAP	1.36928	0.06
55DAP/53DAP	1.23755	0.301
57DAP/55DAP	0.99312	0.909
62DAP/57DAP	0.55875	0.004
68DAP/62DAP	1.20765	0.899
68DAP/14DAP	1.15644	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00303	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.99977	0.886
Mature Green Tomato/Ripe Tomato	3.91922	0.015
Immature Eggplant/Mature Eggplant	1.21631	0.065
Ripe Pepper/Ripe Tomato	4.21587	0.256
Mature Eggplant/Ripe Tomato	4.46698	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87023	0.605
1-1-2/M82	0.96815	1
12-2/M82	1.0548	1
12-4/M82	1.00491
1-3/M82	0.82502	0.376
2-1-1/M82	1.14706
2-1/M82	N/A	N/A
2-6/M82	1.02937
3-2/M82	0.78915	0.414
4-1-1/M82	1.01484	1
4-1/M82	1.20824
4-3-2/M82	1.10596	1
4-3/M82	1.17275	1
5-3/M82	0.94085	1
6-2/M82	1.10435
6-3/M82	0.95712
7-1/M82	1.19269	1
7-2/M82	1.12906	0.385
9-3-2/M82	1.23873	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.54405	0.243
IL2-6/WTpooled	0.2769	0.348
IL7-5/WTpooled	2.56919	1
IL7-3/WTpooled	0.87571	1
IL12-4/WTpooled	0.5494	0.581
IL1-4/WTpooled	0.56034	0.415
WT/WTpooled	0.97922	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	0.93993	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06667	0.921
DC3000/delta hrp 6h	1.28891	1
DC3000/delta hrp 12h	0.40064
DC3000/delta hrp 24h	3.33893	0.024

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12918	0.333
DC3000 delta B/DC3000 delta AB	0.95082	0.674

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00389	1
Exp 36h	0.76003	0.366
Exp 60h	0.72115	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03222	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.42159	0.406
Var 12h NI row2-row1	0.85635	0.443
Var 36h I row2-row1	0.91249	1
Var 36h NI row2-row1	1.14825	0.276
Var 60h I row2-row1	0.73168	0.285
Var 60h NI row2-row1	1.06498	0.904
Time course 0hI-0hNI	0.89242	0.174
Time course 12hI-12hNI	0.83273	0.089
Time course 36hI-36hNI	0.73428	0.023
Time course 60hI-60hNI	0.52597	0.007

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)	0.98228	0.789
transgenic ySAMdc/azygous control (breaker)	0.77313	0.173
transgenic ySAMdc/azygous control (red)	0.89443	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05853	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96711	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05863	1
Manapal/WT (break)	0.83329	1
Manapal/WT (red)	0.8435	0.274