Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.3.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94219	0.617
27DAP/17DAP	0.84432	0.583
39DAP/27DAP	2.33276	0.046
41DAP/39DAP	0.91676	0.568
42DAP/41DAP	1.14339	1
43DAP/42DAP	1.06254	1
47DAP/43DAP	0.68879	0.19
52DAP/47DAP	1.23105	0.902
57DAP/52DAP	1.6451	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19651	0.23
17DAP/reference	0.88456	0.368
27DAP/reference	0.91072	0.187
39DAP/reference	0.82959
41DAP/reference	0.91379	0.667
42DAP/reference	1.03816	0.812
43DAP/reference	N/A	N/A
47DAP/reference	1.51658	0.057
52DAP/reference	N/A	N/A
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42946	0.04
27DAP/17DAP	1.09489	0.751
39DAP/27DAP	0.91033	0.45
41DAP/39DAP	1.60857	0.837
42DAP/41DAP	1.17457	0.694
43DAP/42DAP	0.85127	0.336
47DAP/43DAP	1.03077	0.951
52DAP/47DAP	1.1651	0.619
57DAP/52DAP	1.25029	0.385
57DAP/7DAP	1.13352	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6038	0.025
17DAP/reference	1.14285	0.045
27DAP/reference	1.27661	0.026
39DAP/reference	1.39053	0.008
41DAP/reference	1.3727	0.028
42DAP/reference	1.70053	0.016
43DAP/reference	1.48282	0.009
47DAP/reference	1.89144	0.018
52DAP/reference	1.92707	0.009
57DAP/reference	1.44935	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99819	0.77
17DAP/reference	0.81871	0.159
27DAP/reference	1.35596	0.156
39DAP/reference	0.95331	0.442
41DAP/reference	0.96043	0.422
42DAP/reference	1.11674	0.214
43DAP/reference	0.8585	0.314
47DAP/reference	1.04856	0.775
52DAP/reference	0.76681	0.014
57DAP/reference	0.64032	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32296	0.122
17DAP/reference	0.95528	0.537
27DAP/reference	1.09617	0.325
39DAP/reference	1.44379	0.03
41DAP/reference	1.15593	0.188
42DAP/reference	1.43201	0.022
43DAP/reference	1.37366	0.06
47DAP/reference	0.8474	0.125
52DAP/reference	1.41032	0.088
57DAP/reference	2.83861	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82392	1
26DAP/20DAP	1.85039	0.308
34DAP/26DAP	0.94433	0.874
51DAP/34DAP	3.61808	0.021
52DAP/51DAP	0.95336	1
53DAP/52DAP	1.47991	0.171
55DAP/53DAP	0.62421	0.049
57DAP/55DAP	0.71941	0.118
62DAP/57DAP	0.64612	0.005
68DAP/62DAP	1.34851	0.22
68DAP/14DAP	2.6029	0.042

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.5574	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89831	0.436
Mature Green Tomato/Ripe Tomato	0.85188	0.411
Immature Eggplant/Mature Eggplant	2.21528	0.05
Ripe Pepper/Ripe Tomato	1.23386	1
Mature Eggplant/Ripe Tomato	0.75343	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.81949	0.69
1-1-2/M82	1.04151	1
12-2/M82	1.13051	1
12-4/M82	0.66621
1-3/M82	2.24747	0.248
2-1-1/M82	0.86258	0.784
2-1/M82	0.84559
2-6/M82	0.74762	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.85845	1
4-1/M82	0.80588
4-3-2/M82	1.07217	0.508
4-3/M82	0.87748
5-3/M82	1.17755	1
6-2/M82	0.94129
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.98247
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96292	1
IL2-6/WTpooled	1.84898
IL7-5/WTpooled	0.92573	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.12988
IL1-4/WTpooled	0.85307	0.699
WT/WTpooled	1.00197

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	1.17398	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18194	0.692
DC3000/delta hrp 6h	0.97394	0.95
DC3000/delta hrp 12h	1.05608	1
DC3000/delta hrp 24h	0.90843	0.403

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23228	0.042
DC3000 delta B/DC3000 delta AB	1.37327	0.149

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14437	1
Exp 36h	1.40779	0.693
Exp 60h	1.39648	0.399

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	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	1.22586
Var 36h NI row2-row1	0.9678
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	1.20136	0.19
Time course 60hI-60hNI	0.49463

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)	0.81716	0.315
transgenic ySAMdc/azygous control (breaker)	0.67701	0.173
transgenic ySAMdc/azygous control (red)	1.10674	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0976	0.142

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78143	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0554	1
Manapal/WT (break)	1.70783	0.183
Manapal/WT (red)	0.81512	0.181