Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.9.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97741	0.811
27DAP/17DAP	1.14623	0.842
39DAP/27DAP	1.28127	0.833
41DAP/39DAP	1.3275	0.772
42DAP/41DAP	1.61328	0.877
43DAP/42DAP	0.91409	0.851
47DAP/43DAP	0.85013	0.517
52DAP/47DAP	1.55144	0.3
57DAP/52DAP	0.81257	0.71

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06331	1
17DAP/reference	1.05193	0.508
27DAP/reference	0.93702	0.314
39DAP/reference	1.03213	0.76
41DAP/reference	1.15598	0.241
42DAP/reference	0.97912	0.359
43DAP/reference	0.97284	0.653
47DAP/reference	0.90954	0.191
52DAP/reference	0.87312	0.089
57DAP/reference	0.91325	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91073	0.47
27DAP/17DAP	1.00608	1
39DAP/27DAP	0.89934	0.456
41DAP/39DAP	1.02381	1
42DAP/41DAP	1.09696	0.947
43DAP/42DAP	1.0689	0.699
47DAP/43DAP	1.10742	0.765
52DAP/47DAP	0.97017	0.902
57DAP/52DAP	1.03298	0.951
57DAP/7DAP	1.15177	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.76704	0.025
17DAP/reference	1.99939	0.006
27DAP/reference	1.69033	0.01
39DAP/reference	1.70107	0.005
41DAP/reference	1.71856	0.013
42DAP/reference	1.90285	0.006
43DAP/reference	2.09527	0.007
47DAP/reference	1.45186	0.458
52DAP/reference	1.93566	0.007
57DAP/reference	1.99558	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2717	0.103
17DAP/reference	1.25845	0.015
27DAP/reference	1.1725	0.373
39DAP/reference	1.05367	1
41DAP/reference	0.92011	0.16
42DAP/reference	1.11584	0.309
43DAP/reference	1.55144	0.059
47DAP/reference	1.18172	0.12
52DAP/reference	1.40477	0.038
57DAP/reference	1.46272	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.62523	0.021
17DAP/reference	1.42831	0.166
27DAP/reference	1.9123	0.017
39DAP/reference	1.80627	0.016
41DAP/reference	1.73828	0.007
42DAP/reference	1.83806	0.016
43DAP/reference	1.4003	0.128
47DAP/reference	0.95814	0.306
52DAP/reference	1.66979	0.11
57DAP/reference	1.02351	0.801

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97443	1
26DAP/20DAP	1.48181	0.262
34DAP/26DAP	1.66222	1
51DAP/34DAP	0.82415	0.333
52DAP/51DAP	1.1353
53DAP/52DAP	0.90351	0.803
55DAP/53DAP	1.10671	0.848
57DAP/55DAP	1.10655	0.826
62DAP/57DAP	1.05106	1
68DAP/62DAP	1.09595	0.945
68DAP/14DAP	0.88395	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16281	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.96983	0.745
Mature Green Tomato/Ripe Tomato	1.31699	0.948
Immature Eggplant/Mature Eggplant	1.04009	1
Ripe Pepper/Ripe Tomato	1.19197	1
Mature Eggplant/Ripe Tomato	1.20089	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98369	0.961
1-1-2/M82	0.97166	1
12-2/M82	0.98267	1
12-4/M82	0.98694	1
1-3/M82	0.91009	0.501
2-1-1/M82	0.98393	1
2-1/M82	1.05202	1
2-6/M82	0.94195	1
3-2/M82	0.93738
4-1-1/M82	1.00139	1
4-1/M82	0.6584	1
4-3-2/M82	0.94381	1
4-3/M82	0.95355	0.72
5-3/M82	1.00723	1
6-2/M82	0.98958	1
6-3/M82	1.02722	1
7-1/M82	0.93837	0.803
7-2/M82	0.9641	0.796
9-3-2/M82	0.90783

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	2.02015
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	1.62985	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00016	1
DC3000/delta hrp 6h	1.27207	0.777
DC3000/delta hrp 12h	1.07236	1
DC3000/delta hrp 24h	1.00374	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	6.94856

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82292	1
Exp 36h	1.17892	1
Exp 60h	1.11089	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97387	1
Var 0h	1.27061	0.936
Var 12h I row2-row1	1.07628	0.506
Var 12h NI row2-row1	0.81418	0.546
Var 36h I row2-row1	1.00855	1
Var 36h NI row2-row1	0.93703	0.522
Var 60h I row2-row1	0.95889	0.285
Var 60h NI row2-row1	0.9878	1
Time course 0hI-0hNI	0.88663	0.15
Time course 12hI-12hNI	0.97757	0.882
Time course 36hI-36hNI	1.07589	0.355
Time course 60hI-60hNI	1.24786	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)	1.08415	0.292
transgenic ySAMdc/azygous control (breaker)	1.25578	0.248
transgenic ySAMdc/azygous control (red)	0.92524	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03508	0.163

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88079	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85347	0.172
Manapal/WT (break)	1.08367	1
Manapal/WT (red)	0.96189	0.503