Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.16.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15034	0.709
27DAP/17DAP	1.05385	1
39DAP/27DAP	1.5533	0.176
41DAP/39DAP	1.0147	0.69
42DAP/41DAP	0.99555	1
43DAP/42DAP	1.1314	1
47DAP/43DAP	1.40065	0.442
52DAP/47DAP	1.05281	0.916
57DAP/52DAP	1.26527	0.904

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93198	0.224
17DAP/reference	0.93168	0.097
27DAP/reference	0.98192	0.623
39DAP/reference	0.97528	0.704
41DAP/reference	0.95663	0.341
42DAP/reference	0.99492	0.531
43DAP/reference	1.02786	0.758
47DAP/reference	1.01858	0.817
52DAP/reference	0.98698	0.58
57DAP/reference	1.10647	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06724	1
27DAP/17DAP	0.91613	0.684
39DAP/27DAP	0.92635	0.536
41DAP/39DAP	0.95858	0.923
42DAP/41DAP	1.07782	0.719
43DAP/42DAP	1.04955	0.554
47DAP/43DAP	1.00959	1
52DAP/47DAP	1.11944	0.681
57DAP/52DAP	1.06498	0.662
57DAP/7DAP	1.03469	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17417	0.173
17DAP/reference	1.53419	0.025
27DAP/reference	1.41464	0.007
39DAP/reference	1.45998	0.044
41DAP/reference	1.34537	0.104
42DAP/reference	1.52355	0.009
43DAP/reference	1.44979	0.035
47DAP/reference	1.37859	0.037
52DAP/reference	1.5717	0.007
57DAP/reference	1.70129	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90282	0.231
17DAP/reference	0.94793	0.214
27DAP/reference	1.12954	0.192
39DAP/reference	0.97629	0.485
41DAP/reference	1.02818	0.944
42DAP/reference	1.02928	0.969
43DAP/reference	0.85076	0.201
47DAP/reference	0.9883	0.487
52DAP/reference	0.92159	0.012
57DAP/reference	0.82515	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52439	0.019
17DAP/reference	1.2062	0.17
27DAP/reference	1.55091	0.016
39DAP/reference	1.45634	0.007
41DAP/reference	1.57214	0.016
42DAP/reference	1.33375	0.038
43DAP/reference	1.63548	0.022
47DAP/reference	1.16741	0.085
52DAP/reference	1.63741	0.086
57DAP/reference	1.46062	0.038

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18742	0.735
26DAP/20DAP	0.96634	1
34DAP/26DAP	1.23434	0.542
51DAP/34DAP	1.12692	0.627
52DAP/51DAP	1.25464	0.253
53DAP/52DAP	0.93837	0.79
55DAP/53DAP	1.39127	0.16
57DAP/55DAP	0.92829	0.698
62DAP/57DAP	1.15141	1
68DAP/62DAP	1.08021	0.897
68DAP/14DAP	0.78835	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08052	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14757	0.113
Mature Green Tomato/Ripe Tomato	0.6613	0.086
Immature Eggplant/Mature Eggplant	1.55743	0.05
Ripe Pepper/Ripe Tomato	0.5589	0.224
Mature Eggplant/Ripe Tomato	0.86157	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.10046
12-2/M82	N/A	N/A
12-4/M82	1.75989
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.31921
4-3-2/M82	1.19938	1
4-3/M82	N/A	N/A
5-3/M82	0.88505
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.33083	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.64019
IL2-6/WTpooled	1.14209	0.659
IL7-5/WTpooled	0.91734
IL7-3/WTpooled	1.1592	1
IL12-4/WTpooled	1.24929	0.532
IL1-4/WTpooled	0.88331	0.834
WT/WTpooled	0.97135	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	1.07969	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.86144	1
DC3000/delta hrp 6h	1.06805	1
DC3000/delta hrp 12h	0.99833	1
DC3000/delta hrp 24h	0.93836	0.607

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44293	0.229
DC3000 delta B/DC3000 delta AB	1.18841	0.256

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02722	1
Exp 36h	0.94601	0.749
Exp 60h	1.02394	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00773	1
Var 0h	0.49357	1
Var 12h I row2-row1	0.92778	0.565
Var 12h NI row2-row1	1.00735	1
Var 36h I row2-row1	1.1167	0.601
Var 36h NI row2-row1	0.95524	0.61
Var 60h I row2-row1	0.84294	0.439
Var 60h NI row2-row1	0.91666	0.756
Time course 0hI-0hNI	1.00426	0.867
Time course 12hI-12hNI	1.02026	0.811
Time course 36hI-36hNI	1.16939	0.007
Time course 60hI-60hNI	1.13892	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)	0.90079	0.3
transgenic ySAMdc/azygous control (breaker)	1.44651	1
transgenic ySAMdc/azygous control (red)	1.02541	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02344	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38712	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02604	1
Manapal/WT (break)	0.8573	1
Manapal/WT (red)	1.50281	0.222