Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.3.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68556	0.131
27DAP/17DAP	0.86236	0.67
39DAP/27DAP	1.37553	0.558
41DAP/39DAP	0.86846	0.586
42DAP/41DAP	0.91109	1
43DAP/42DAP	1.02365	1
47DAP/43DAP	0.84729	0.487
52DAP/47DAP	1.27196	0.976
57DAP/52DAP	0.97709	0.966

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09084	0.132
17DAP/reference	0.98423	0.737
27DAP/reference	0.92908	0.201
39DAP/reference	0.95076	0.37
41DAP/reference	0.93252	0.267
42DAP/reference	0.97282	0.188
43DAP/reference	1.09041	0.053
47DAP/reference	0.96411	0.207
52DAP/reference	0.95829	0.33
57DAP/reference	1.12952	0.076

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.56984	0.056
27DAP/17DAP	1.13232	0.863
39DAP/27DAP	1.03257	1
41DAP/39DAP	0.9627	0.986
42DAP/41DAP	0.99558	0.801
43DAP/42DAP	1.03703	0.699
47DAP/43DAP	0.8951	0.506
52DAP/47DAP	0.88574	0.603
57DAP/52DAP	1.094	0.858
57DAP/7DAP	1.22784	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23986	0.185
17DAP/reference	1.69465	0.006
27DAP/reference	1.25392	0.16
39DAP/reference	1.37533	0.011
41DAP/reference	1.42141	0.021
42DAP/reference	1.35199	0.046
43DAP/reference	1.36466	0.032
47DAP/reference	1.5751	0.015
52DAP/reference	1.14971	0.081
57DAP/reference	1.24014	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21493	0.213
17DAP/reference	0.96852	0.523
27DAP/reference	1.36776	0.114
39DAP/reference	1.37013	0.021
41DAP/reference	1.14452	0.737
42DAP/reference	1.0846	0.324
43DAP/reference	0.91765	0.344
47DAP/reference	1.08248	0.603
52DAP/reference	0.91722	0.101
57DAP/reference	0.8959	0.243

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26964	0.882
17DAP/reference	1.12831	0.522
27DAP/reference	1.62415	0.023
39DAP/reference	1.46032	0.013
41DAP/reference	1.27578	0.156
42DAP/reference	1.13417	0.258
43DAP/reference	1.24829	0.157
47DAP/reference	0.93975	0.325
52DAP/reference	1.46345	0.03
57DAP/reference	1.64716	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.999	1
26DAP/20DAP	1.08181	0.974
34DAP/26DAP	0.93627	0.861
51DAP/34DAP	1.1743	0.925
52DAP/51DAP	1.22232	0.413
53DAP/52DAP	1.16241	0.797
55DAP/53DAP	1.36697	0.225
57DAP/55DAP	0.95514	0.795
62DAP/57DAP	0.94174	0.466
68DAP/62DAP	1.29469	0.214
68DAP/14DAP	2.0622	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.28422	0.326

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87012	0.364
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.22976	0.058
Ripe Pepper/Ripe Tomato	1.21392	1
Mature Eggplant/Ripe Tomato	1.34162	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.91383	0.619
1-3/M82	0.95355
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.92913
5-3/M82	1.01268	1
6-2/M82	N/A	N/A
6-3/M82	1.12225
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06884	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.8445	1
IL7-3/WTpooled	0.84391
IL12-4/WTpooled	1.04331	0.839
IL1-4/WTpooled	0.94358	0.699
WT/WTpooled	1.0234	0.785

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	0.92781	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05329	0.758
DC3000/delta hrp 6h	0.83895	0.95
DC3000/delta hrp 12h	0.90406	1
DC3000/delta hrp 24h	1.01094	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87568	0.92
DC3000 delta B/DC3000 delta AB	1.05509	0.677

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84175	1
Exp 36h	2.96699	0.693
Exp 60h	2.15458	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95168
Var 0h	1.07745	1
Var 12h I row2-row1	1.14988	0.324
Var 12h NI row2-row1	1.16484
Var 36h I row2-row1	1.05331
Var 36h NI row2-row1	0.91706	0.61
Var 60h I row2-row1	2.45917
Var 60h NI row2-row1	0.9831	1
Time course 0hI-0hNI	0.93321	0.495
Time course 12hI-12hNI	1.13644	0.714
Time course 36hI-36hNI	1.13536	0.017
Time course 60hI-60hNI	1.81207	0.012

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)	1.17757	0.339
transgenic ySAMdc/azygous control (breaker)	0.74905	0.49
transgenic ySAMdc/azygous control (red)	1.07141	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0962	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.45977	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05145	1
Manapal/WT (break)	1.58462	0.183
Manapal/WT (red)	0.89831	0.274