Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.2.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.38664	0.014
27DAP/17DAP	0.43818	0.029
39DAP/27DAP	1.05784	0.798
41DAP/39DAP	0.4033	0.041
42DAP/41DAP	0.91722	1
43DAP/42DAP	1.42642	0.629
47DAP/43DAP	0.77686	0.345
52DAP/47DAP	0.68123	0.137
57DAP/52DAP	1.11902	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.10684	0.011
17DAP/reference	1.65691	0.012
27DAP/reference	1.95286	0.021
39DAP/reference	0.66651	0.014
41DAP/reference	0.57728	0.008
42DAP/reference	0.82099	0.003
43DAP/reference	0.6594	0.015
47DAP/reference	0.63945	0.002
52DAP/reference	0.63342	0.047
57DAP/reference	0.90397	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.284	0.026
27DAP/17DAP	2.33948	0.021
39DAP/27DAP	0.3782	0.028
41DAP/39DAP	0.34837	0.018
42DAP/41DAP	0.96371	0.695
43DAP/42DAP	1.5951	0.015
47DAP/43DAP	0.64175	0.01
52DAP/47DAP	1.10869	0.71
57DAP/52DAP	0.85651	0.287
57DAP/7DAP	0.05846	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.33423	0.024
17DAP/reference	1.43714	0.102
27DAP/reference	0.97637	0.462
39DAP/reference	0.79415	0.011
41DAP/reference	0.98254	0.565
42DAP/reference	0.97481	0.482
43DAP/reference	0.85358	0.11
47DAP/reference	0.68099	0.03
52DAP/reference	0.73098	0.027
57DAP/reference	0.89486	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.86363	0.067
17DAP/reference	1.86859	0.024
27DAP/reference	1.47554	0.178
39DAP/reference	0.57965	0.014
41DAP/reference	0.64433	0.011
42DAP/reference	1.09188	0.987
43DAP/reference	0.53601	0.005
47DAP/reference	0.62724	0.012
52DAP/reference	0.45177	0.003
57DAP/reference	0.36175	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.46873	0.025
17DAP/reference	1.79775	0.117
27DAP/reference	1.77837	0.019
39DAP/reference	1.06619	0.483
41DAP/reference	1.13715	0.486
42DAP/reference	0.7755	0.087
43DAP/reference	0.82453	0.197
47DAP/reference	0.50634	0.005
52DAP/reference	0.72387	0.111
57DAP/reference	0.93482	0.359

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18658	0.966
26DAP/20DAP	1.13625	0.66
34DAP/26DAP	0.69831	0.152
51DAP/34DAP	0.51811	0.049
52DAP/51DAP	1.06608	0.481
53DAP/52DAP	0.71561	0.049
55DAP/53DAP	0.32763	0.016
57DAP/55DAP	0.62797	0.044
62DAP/57DAP	0.93188	0.871
68DAP/62DAP	1.7449	0.009
68DAP/14DAP	0.22213	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.07785	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.92865	0.058
Mature Green Tomato/Ripe Tomato	11.4474	0.015
Immature Eggplant/Mature Eggplant	0.39544	0.062
Ripe Pepper/Ripe Tomato	34.5475	0.256
Mature Eggplant/Ripe Tomato	75.7072	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.17274	1
1-1-2/M82	1.03831	1
12-2/M82	1.22115
12-4/M82	0.89107	1
1-3/M82	0.92084	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.97842
3-2/M82	0.82963	0.752
4-1-1/M82	0.93363	1
4-1/M82	1.84931
4-3-2/M82	N/A	N/A
4-3/M82	1.15292	1
5-3/M82	0.97117	1
6-2/M82	0.598
6-3/M82	0.98282
7-1/M82	0.86029	0.803
7-2/M82	0.89103	0.796
9-3-2/M82	0.90887

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71156
IL2-6/WTpooled	0.83209	1
IL7-5/WTpooled	1.50284
IL7-3/WTpooled	0.85306	0.418
IL12-4/WTpooled	1.0243	1
IL1-4/WTpooled	0.98482	1
WT/WTpooled	0.98624	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	0.92463	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00001	1
DC3000/delta hrp 6h	0.90981	0.95
DC3000/delta hrp 12h	0.89369	1
DC3000/delta hrp 24h	0.75574	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65848	0.023
DC3000 delta B/DC3000 delta AB	0.53327	0.035

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97353	1
Exp 36h	0.82707	0.434
Exp 60h	0.88639	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02121	1
Var 0h	1.05909	1
Var 12h I row2-row1	0.91975	0.77
Var 12h NI row2-row1	0.99328	1
Var 36h I row2-row1	0.96525	1
Var 36h NI row2-row1	1.11161	1
Var 60h I row2-row1	0.90379	0.439
Var 60h NI row2-row1	1.06377	0.904
Time course 0hI-0hNI	1.04722	0.764
Time course 12hI-12hNI	0.95647	0.769
Time course 36hI-36hNI	0.88131	0.136
Time course 60hI-60hNI	0.27969	0.006

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)	0.77933	0.315
transgenic ySAMdc/azygous control (breaker)	3.52953	0.248
transgenic ySAMdc/azygous control (red)	1.06185	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.74818	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.44788	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.2364	0.307
Manapal/WT (break)	1.90968	1
Manapal/WT (red)	0.92578	0.728