Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.13.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96631	0.728
27DAP/17DAP	0.98409	0.964
39DAP/27DAP	0.92857	0.631
41DAP/39DAP	1.2161	0.619
42DAP/41DAP	1.0635	0.994
43DAP/42DAP	1.00913	0.937
47DAP/43DAP	0.98288	0.847
52DAP/47DAP	1.18947	0.718
57DAP/52DAP	1.04223	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9734	0.432
17DAP/reference	1.0372	0.201
27DAP/reference	1.01561	0.806
39DAP/reference	0.98779	0.779
41DAP/reference	1.02178	0.516
42DAP/reference	0.95552	0.115
43DAP/reference	1.00032	1
47DAP/reference	0.9406	0.127
52DAP/reference	0.90434	0.064
57DAP/reference	0.98267	0.503

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01505	0.899
27DAP/17DAP	0.99942	1
39DAP/27DAP	0.98632	0.881
41DAP/39DAP	1.01352	0.868
42DAP/41DAP	1.00364	1
43DAP/42DAP	0.98899	0.774
47DAP/43DAP	0.97088	0.787
52DAP/47DAP	0.95932	0.801
57DAP/52DAP	1.01082	1
57DAP/7DAP	0.99625	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91814	0.122
17DAP/reference	0.94007	0.011
27DAP/reference	0.96577	0.146
39DAP/reference	0.93871	0.014
41DAP/reference	0.90472	0.02
42DAP/reference	0.85165	0.01
43DAP/reference	0.93866	0.21
47DAP/reference	0.883	0.128
52DAP/reference	0.92625	0.163
57DAP/reference	0.91832	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99297	0.869
17DAP/reference	0.98405	0.576
27DAP/reference	0.98101	0.537
39DAP/reference	0.98611	0.539
41DAP/reference	0.95932	0.364
42DAP/reference	1.0333	0.863
43DAP/reference	1.01554	0.793
47DAP/reference	1.04743	0.282
52DAP/reference	0.91954	0.037
57DAP/reference	0.91534	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97852	0.087
17DAP/reference	0.99897	0.886
27DAP/reference	0.98154	0.516
39DAP/reference	0.96181	0.222
41DAP/reference	0.95042	0.264
42DAP/reference	0.93377	0.134
43DAP/reference	0.94596	0.171
47DAP/reference	0.93997	0.072
52DAP/reference	1.05363	0.623
57DAP/reference	0.87833	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9741	1
26DAP/20DAP	0.92507	0.512
34DAP/26DAP	0.98106	0.988
51DAP/34DAP	0.93623	0.394
52DAP/51DAP	0.99964	1
53DAP/52DAP	1.06037	0.723
55DAP/53DAP	0.9704	0.864
57DAP/55DAP	1.13633	0.056
62DAP/57DAP	1.07203	0.445
68DAP/62DAP	0.92352	0.787
68DAP/14DAP	1.1016	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94074	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.91487
Mature Green Tomato/Ripe Tomato	0.82756	0.096
Immature Eggplant/Mature Eggplant	1.37536
Ripe Pepper/Ripe Tomato	1.63114	1
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01227	1
1-1-2/M82	0.96378	1
12-2/M82	0.98416	0.955
12-4/M82	1.02171	1
1-3/M82	0.93406	1
2-1-1/M82	1.09247	0.764
2-1/M82	1.42978
2-6/M82	1.00127	1
3-2/M82	0.97671	1
4-1-1/M82	0.98424	1
4-1/M82	0.76708	0.737
4-3-2/M82	0.86543	1
4-3/M82	0.93017	1
5-3/M82	1.00351	1
6-2/M82	1.04926	1
6-3/M82	1.02305	1
7-1/M82	0.90607	0.803
7-2/M82	1.00427
9-3-2/M82	0.88716	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8025	0.243
IL2-6/WTpooled	0.67165	0.473
IL7-5/WTpooled	0.87424	0.559
IL7-3/WTpooled	1.01862	1
IL12-4/WTpooled	0.7259	0.581
IL1-4/WTpooled	0.91968	0.834
WT/WTpooled	0.97833	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11176	0.724
DC3000/delta hrp 6h	1.10707	1
DC3000/delta hrp 12h	0.96203	1
DC3000/delta hrp 24h	0.9822	0.966

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2087	0.355
DC3000 delta B/DC3000 delta AB	1.05214	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01826	1
Exp 36h	1.01638	1
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01399	1
Var 0h	2.04527	0.782
Var 12h I row2-row1	1.21196	0.199
Var 12h NI row2-row1	0.92994	0.627
Var 36h I row2-row1	0.93425	1
Var 36h NI row2-row1	0.8516	0.549
Var 60h I row2-row1	1.11071	0.562
Var 60h NI row2-row1	1.12705	0.904
Time course 0hI-0hNI	1.05621	0.852
Time course 12hI-12hNI	1.00339	1
Time course 36hI-36hNI	1.01398	0.799
Time course 60hI-60hNI	1.35715	0.011

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)	0.881	0.614
transgenic ySAMdc/azygous control (breaker)	1.38831	1
transgenic ySAMdc/azygous control (red)	1.41604	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00762	0.656

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12132	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.34689	0.172
Manapal/WT (break)	0.7437	0.333
Manapal/WT (red)	0.7674	0.242