Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.13.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98917	0.839
27DAP/17DAP	1	0.967
39DAP/27DAP	0.83817	0.487
41DAP/39DAP	1.67257	0.202
42DAP/41DAP	0.95116	1
43DAP/42DAP	0.95758	0.9
47DAP/43DAP	0.93956	0.768
52DAP/47DAP	1.40227	0.641
57DAP/52DAP	1.0148	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93843	0.269
17DAP/reference	0.97889	0.474
27DAP/reference	1.01301	0.759
39DAP/reference	1.2768	0.504
41DAP/reference	0.95986	0.434
42DAP/reference	0.90492	0.004
43DAP/reference	0.88591	0.259
47DAP/reference	0.9258	0.032
52DAP/reference	0.82914	0.033
57DAP/reference	0.90815	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96903	0.644
27DAP/17DAP	1.00826	0.973
39DAP/27DAP	1.0571	0.558
41DAP/39DAP	0.98323	1
42DAP/41DAP	0.95528	0.568
43DAP/42DAP	0.99979	1
47DAP/43DAP	1.00721	0.956
52DAP/47DAP	0.98567	0.913
57DAP/52DAP	1.02988	0.851
57DAP/7DAP	1.07298	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86729	0.078
17DAP/reference	0.92078	0.044
27DAP/reference	0.90014	0.011
39DAP/reference	0.917	0.014
41DAP/reference	0.91304	0.044
42DAP/reference	0.89321	0.015
43DAP/reference	0.89929	0.019
47DAP/reference	0.83747	0.05
52DAP/reference	0.88653	0.057
57DAP/reference	0.95667	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96523	0.503
17DAP/reference	0.94613	0.26
27DAP/reference	1.0511	0.917
39DAP/reference	0.96234	0.33
41DAP/reference	0.84903	0.038
42DAP/reference	0.87255	0.039
43DAP/reference	0.91598	0.17
47DAP/reference	0.94057	0.253
52DAP/reference	0.91483	0.04
57DAP/reference	0.96739	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93136	0.047
17DAP/reference	0.92056	0.239
27DAP/reference	0.96266	0.195
39DAP/reference	0.92944	0.054
41DAP/reference	0.94967	0.371
42DAP/reference	0.99535	0.816
43DAP/reference	0.9028	0.088
47DAP/reference	0.90884	0.132
52DAP/reference	0.89298	0.368
57DAP/reference	0.63679	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01972	0.966
26DAP/20DAP	0.98407	1
34DAP/26DAP	1.14191	0.819
51DAP/34DAP	1.01523	0.925
52DAP/51DAP	1.01711	0.836
53DAP/52DAP	1.04825	0.58
55DAP/53DAP	0.95535	0.325
57DAP/55DAP	1.01441	0.997
62DAP/57DAP	1.0156	1
68DAP/62DAP	1.07421	1
68DAP/14DAP	0.71685	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03163	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82524	0.41
Mature Green Tomato/Ripe Tomato	0.93675	0.522
Immature Eggplant/Mature Eggplant	1.39331	0.05
Ripe Pepper/Ripe Tomato	6.29599
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9597	0.944
1-1-2/M82	0.99028	1
12-2/M82	0.9804	1
12-4/M82	0.98292	1
1-3/M82	0.95643	1
2-1-1/M82	1.08475	0.764
2-1/M82	1.15512	0.289
2-6/M82	0.97484	1
3-2/M82	0.98938	1
4-1-1/M82	1.01315	1
4-1/M82	0.9442	1
4-3-2/M82	1.01286	1
4-3/M82	1.00488	1
5-3/M82	0.95282	1
6-2/M82	1.00037	1
6-3/M82	1.01216	1
7-1/M82	1.02967	1
7-2/M82	1.0108	1
9-3-2/M82	0.83239	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.16241	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.82443	0.418
IL12-4/WTpooled	0.88032	0.484
IL1-4/WTpooled	0.89869
WT/WTpooled	1.13869	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	1.19892

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11128	0.656
DC3000/delta hrp 6h	1.9487	1
DC3000/delta hrp 12h	0.98331	1
DC3000/delta hrp 24h	0.98364	0.957

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11112	0.044
DC3000 delta B/DC3000 delta AB	1.13334	0.292

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.65267	0.749
Exp 60h	0.66807	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00056	1
Var 0h	0.79685	1
Var 12h I row2-row1	1.12417	0.189
Var 12h NI row2-row1	0.94357	0.627
Var 36h I row2-row1	0.80787	0.805
Var 36h NI row2-row1	1.0436	1
Var 60h I row2-row1	1.17769	1
Var 60h NI row2-row1	1.28796	0.904
Time course 0hI-0hNI	1.07408	0.833
Time course 12hI-12hNI	1.01386	0.867
Time course 36hI-36hNI	0.93114	0.202
Time course 60hI-60hNI	1.17503	0.009

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)	1.37814	0.455
transgenic ySAMdc/azygous control (breaker)	1.18594	1
transgenic ySAMdc/azygous control (red)	1.47083	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96683	0.112

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06585	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77186	1
Manapal/WT (break)	0.84538	0.333
Manapal/WT (red)	N/A	N/A