Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.12.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84774	0.427
27DAP/17DAP	1.21235	0.793
39DAP/27DAP	1.18242	0.876
41DAP/39DAP	0.98154	0.839
42DAP/41DAP	1.44262	0.886
43DAP/42DAP	1.16528	0.799
47DAP/43DAP	0.52006	0.054
52DAP/47DAP	1.57325	0.351
57DAP/52DAP	0.9142	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14136	0.081
17DAP/reference	1.19455	0.059
27DAP/reference	1.07962	0.33
39DAP/reference	1.09675	0.083
41DAP/reference	1.13675	0.026
42DAP/reference	1.0097	1
43DAP/reference	1.08465	0.069
47DAP/reference	0.98247	0.473
52DAP/reference	0.81644	0.077
57DAP/reference	0.79625	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90473	0.484
27DAP/17DAP	0.98461	0.887
39DAP/27DAP	1.0259	1
41DAP/39DAP	1.5793	0.018
42DAP/41DAP	0.95014	0.62
43DAP/42DAP	0.91681	0.321
47DAP/43DAP	0.94226	0.637
52DAP/47DAP	1.58816	0.276
57DAP/52DAP	2.13936	0.065
57DAP/7DAP	0.95568	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83314	0.082
17DAP/reference	0.76437	0.021
27DAP/reference	0.64985	0.012
39DAP/reference	0.73595	0.011
41DAP/reference	0.71376	0.025
42DAP/reference	0.65486	0.01
43DAP/reference	0.54965	0.011
47DAP/reference	0.7855	0.222
52DAP/reference	0.72354	0.03
57DAP/reference	0.55379	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09367	0.319
17DAP/reference	1.14492	0.081
27DAP/reference	1.12802	0.345
39DAP/reference	1.05527	0.848
41DAP/reference	1.0407	1
42DAP/reference	0.9046	0.027
43DAP/reference	1.02321	0.899
47DAP/reference	0.97499	0.446
52DAP/reference	0.9422	0.259
57DAP/reference	1.2469	0.025

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9513	0.422
17DAP/reference	1.00412	1
27DAP/reference	0.75184	0.031
39DAP/reference	0.68636	0.01
41DAP/reference	0.81309	0.035
42DAP/reference	0.73563	0.025
43DAP/reference	0.77358	0.046
47DAP/reference	1.01055	1
52DAP/reference	0.72301	0.184
57DAP/reference	0.64278	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16425	0.678
26DAP/20DAP	0.93289	1
34DAP/26DAP	1.33771	1
51DAP/34DAP	0.94831	0.779
52DAP/51DAP	1.97658	0.033
53DAP/52DAP	0.77219	0.217
55DAP/53DAP	1.54097	0.134
57DAP/55DAP	0.93275	0.684
62DAP/57DAP	1.1697	0.569
68DAP/62DAP	0.77562	0.641
68DAP/14DAP	0.77508	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77715	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.57132	0.058
Mature Green Tomato/Ripe Tomato	1.48755	0.015
Immature Eggplant/Mature Eggplant	0.55953	0.117
Ripe Pepper/Ripe Tomato	1.2399
Mature Eggplant/Ripe Tomato	0.44573

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	0.82525
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.09621	0.447
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.91221
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.40877
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.3899	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.19617	0.758
DC3000/delta hrp 6h	1.16841	1
DC3000/delta hrp 12h	1.04729	1
DC3000/delta hrp 24h	1.90004	0.032

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.27781	0.102
DC3000 delta B/DC3000 delta AB	1.27036	0.146

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88927	0.328
Exp 36h	1.28106	0.693
Exp 60h	1.16872	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.89219	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.8781	0.315
transgenic ySAMdc/azygous control (breaker)	0.93095	0.49
transgenic ySAMdc/azygous control (red)	0.99849	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99699	0.806

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.37697	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71035	0.172
Manapal/WT (break)	1.09537	1
Manapal/WT (red)	1.25665	0.413