Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.2.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93639	0.486
27DAP/17DAP	1.02494	0.916
39DAP/27DAP	1.18619	0.677
41DAP/39DAP	1.21566	0.338
42DAP/41DAP	1.04727	0.997
43DAP/42DAP	1.02665	1
47DAP/43DAP	0.87543	0.584
52DAP/47DAP	1.0339	0.989
57DAP/52DAP	1.04737	0.873

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91836	0.078
17DAP/reference	0.97759	0.63
27DAP/reference	1.00439	1
39DAP/reference	0.97087	0.565
41DAP/reference	0.96565	0.434
42DAP/reference	0.88739	0.004
43DAP/reference	0.97131	0.594
47DAP/reference	0.94426	0.224
52DAP/reference	1.12318	0.128
57DAP/reference	0.90405	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05868	0.762
27DAP/17DAP	1.0601	0.831
39DAP/27DAP	0.98009	0.887
41DAP/39DAP	1.06295	0.853
42DAP/41DAP	0.95068	0.565
43DAP/42DAP	1.11329	0.032
47DAP/43DAP	1.01641	0.897
52DAP/47DAP	0.98993	0.935
57DAP/52DAP	1.02655	0.877
57DAP/7DAP	1.29443	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3156	0.056
17DAP/reference	1.06586	0.399
27DAP/reference	0.99147	0.656
39DAP/reference	1.23445	0.007
41DAP/reference	0.958	0.431
42DAP/reference	0.99138	0.641
43DAP/reference	1.1625	0.178
47DAP/reference	1.46119	0.027
52DAP/reference	1.15843	0.021
57DAP/reference	1.41055	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97739	0.72
17DAP/reference	0.94134	0.245
27DAP/reference	0.97718	0.501
39DAP/reference	0.98508	0.539
41DAP/reference	0.98416	0.472
42DAP/reference	0.94314	0.212
43DAP/reference	0.85406	0.09
47DAP/reference	0.93893	0.149
52DAP/reference	0.96972	0.38
57DAP/reference	0.93318	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20157	0.036
17DAP/reference	1.10211	0.531
27DAP/reference	0.93616	0.27
39DAP/reference	1.01827	0.912
41DAP/reference	0.97746	0.293
42DAP/reference	0.96793	0.552
43DAP/reference	1.03717	0.961
47DAP/reference	1.06389	0.73
52DAP/reference	0.96596	0.65
57DAP/reference	1.25642	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16786	0.43
26DAP/20DAP	0.93867	1
34DAP/26DAP	0.97279	0.988
51DAP/34DAP	1.04925	0.814
52DAP/51DAP	1.03767	0.776
53DAP/52DAP	0.90124	0.553
55DAP/53DAP	0.95996	0.735
57DAP/55DAP	0.97652	0.863
62DAP/57DAP	1.36049	0.185
68DAP/62DAP	1.10948	1
68DAP/14DAP	1.12233	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.74117	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.0795	0.287
Mature Green Tomato/Ripe Tomato	0.82819	0.038
Immature Eggplant/Mature Eggplant	0.89824	0.448
Ripe Pepper/Ripe Tomato	0.45326	0.224
Mature Eggplant/Ripe Tomato	0.74632	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.47157	0.877
1-1-2/M82	N/A	N/A
12-2/M82	0.81448
12-4/M82	0.93482	1
1-3/M82	0.85207	0.378
2-1-1/M82	0.82846	0.683
2-1/M82	0.83226
2-6/M82	1.15546	0.329
3-2/M82	N/A	N/A
4-1-1/M82	1.14819
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.99858	1
5-3/M82	0.89324	1
6-2/M82	0.97436	1
6-3/M82	1.06181	1
7-1/M82	1.36356
7-2/M82	1.02664	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99219	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.38242	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.45002
IL1-4/WTpooled	1.22785	1
WT/WTpooled	0.89441	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	1.23168	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9566	1
DC3000/delta hrp 6h	0.87711	0.95
DC3000/delta hrp 12h	0.94863	1
DC3000/delta hrp 24h	0.86246	0.246

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.64202	0.023
DC3000 delta B/DC3000 delta AB	0.8401	0.026

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02532	1
Exp 36h	1.27655	1
Exp 60h	1.1581	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98709	1
Var 0h	1.12499	1
Var 12h I row2-row1	0.96324	0.856
Var 12h NI row2-row1	1.05763	1
Var 36h I row2-row1	0.94439	1
Var 36h NI row2-row1	1.08669	1
Var 60h I row2-row1	0.91733	0.374
Var 60h NI row2-row1	0.86967	0.932
Time course 0hI-0hNI	1.00156	1
Time course 12hI-12hNI	0.98062	0.827
Time course 36hI-36hNI	1.04495	0.248
Time course 60hI-60hNI	0.80987	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)	0.88952	0.391
transgenic ySAMdc/azygous control (breaker)	1.12202	0.248
transgenic ySAMdc/azygous control (red)	0.93992	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0573	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89859	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94163	1
Manapal/WT (break)	0.72025	0.262
Manapal/WT (red)	1.16103	1