Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.11.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.17123	0.014
27DAP/17DAP	0.60956	0.123
39DAP/27DAP	0.81011	0.549
41DAP/39DAP	1.36756	0.569
42DAP/41DAP	1.51584	0.73
43DAP/42DAP	0.96042	0.9
47DAP/43DAP	1.11462	0.926
52DAP/47DAP	1.0104	0.927
57DAP/52DAP	0.90764	0.86

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57992	0.008
17DAP/reference	0.9637	0.536
27DAP/reference	0.89935	0.055
39DAP/reference	1.01403	0.816
41DAP/reference	1.00427	1
42DAP/reference	0.88911	0.054
43DAP/reference	0.90076	0.061
47DAP/reference	0.86164	0.011
52DAP/reference	0.75725	0.015
57DAP/reference	0.70566	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.15818	0.017
27DAP/17DAP	0.99937	0.943
39DAP/27DAP	0.91537	0.52
41DAP/39DAP	1.23401	0.801
42DAP/41DAP	0.94193	0.641
43DAP/42DAP	0.94437	0.709
47DAP/43DAP	1.08667	0.865
52DAP/47DAP	1.21884	0.498
57DAP/52DAP	1.17374	0.567
57DAP/7DAP	0.44699	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19666	0.055
17DAP/reference	1.12623	0.221
27DAP/reference	1.1321	0.088
39DAP/reference	1.23194	0.018
41DAP/reference	1.11105	0.291
42DAP/reference	1.13993	0.037
43DAP/reference	1.12876	0.063
47DAP/reference	0.84843	0.128
52DAP/reference	1.09445	0.247
57DAP/reference	1.0237	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57411	0.038
17DAP/reference	0.91325	0.201
27DAP/reference	0.79219	0.053
39DAP/reference	0.81035	0.012
41DAP/reference	0.85725	0.094
42DAP/reference	0.81875	0.046
43DAP/reference	1.13376	0.308
47DAP/reference	1.01514	0.916
52DAP/reference	0.7889	0.005
57DAP/reference	1.01562	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42762	0.142
17DAP/reference	0.95212	0.47
27DAP/reference	1.20281	0.034
39DAP/reference	1.18584	0.018
41DAP/reference	1.08381	0.439
42DAP/reference	0.92731	0.445
43DAP/reference	0.84431	0.125
47DAP/reference	0.71883	0.008
52DAP/reference	1.00237	0.871
57DAP/reference	0.82114	0.158

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9514	1
26DAP/20DAP	1.13346	0.524
34DAP/26DAP	0.66231	0.05
51DAP/34DAP	0.52498	0.056
52DAP/51DAP	1.07481	0.86
53DAP/52DAP	1.39802	0.261
55DAP/53DAP	0.71999	0.016
57DAP/55DAP	1.19049	0.805
62DAP/57DAP	0.76924	0.162
68DAP/62DAP	0.98985	0.863
68DAP/14DAP	0.40919	0.08

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.30156	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.10091	1
Mature Green Tomato/Ripe Tomato	0.69919
Immature Eggplant/Mature Eggplant	0.93223	0.407
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	47.5392	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92092	0.944
1-1-2/M82	1.27085
12-2/M82	1.18798
12-4/M82	1.51011
1-3/M82	0.77396
2-1-1/M82	0.73132
2-1/M82	N/A	N/A
2-6/M82	1.07319	1
3-2/M82	0.70612
4-1-1/M82	0.84179
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.7171	0.578
5-3/M82	1.05139	1
6-2/M82	0.57013
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.84203	0.796
9-3-2/M82	0.85045

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.54908	0.493
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.43821
IL7-3/WTpooled	0.99808	1
IL12-4/WTpooled	0.85003	0.71
IL1-4/WTpooled	1.322	1
WT/WTpooled	1.00718	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	1.23044	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05498	0.921
DC3000/delta hrp 6h	0.87473	0.95
DC3000/delta hrp 12h	1.08284	1
DC3000/delta hrp 24h	1.04824	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10371	0.408
DC3000 delta B/DC3000 delta AB	1.31429	0.279

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85876	1
Exp 36h	3.08998	0.693
Exp 60h	1.7698	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05938	1
Var 0h	1.26579	0.98
Var 12h I row2-row1	1.64182	0.443
Var 12h NI row2-row1	0.95985	0.906
Var 36h I row2-row1	0.80434	0.805
Var 36h NI row2-row1	0.56893	0.225
Var 60h I row2-row1	0.99037	1
Var 60h NI row2-row1	1.2178	0.904
Time course 0hI-0hNI	0.89951	0.235
Time course 12hI-12hNI	1.02746	0.818
Time course 36hI-36hNI	0.92777	0.344
Time course 60hI-60hNI	1.81324	0.008

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)	0.99988	1
transgenic ySAMdc/azygous control (breaker)	0.76964	0.132
transgenic ySAMdc/azygous control (red)	0.94398	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00955	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.46995	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.52768	1
Manapal/WT (break)	0.99398	1
Manapal/WT (red)	1.08967	1