Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99587	0.919
27DAP/17DAP	1.24434	0.842
39DAP/27DAP	0.86778	0.487
41DAP/39DAP	1.30989	0.252
42DAP/41DAP	1.02273	1
43DAP/42DAP	1.16547	0.954
47DAP/43DAP	0.89589	0.645
52DAP/47DAP	1.37392	0.525
57DAP/52DAP	0.94564	0.947

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00279	1
17DAP/reference	1.02502	0.427
27DAP/reference	1.0211	0.721
39DAP/reference	0.92731	0.391
41DAP/reference	0.94035	0.341
42DAP/reference	0.93228	0.006
43DAP/reference	1.01242	0.866
47DAP/reference	0.92436	0.025
52DAP/reference	0.96247	0.427
57DAP/reference	0.94017	0.078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00842	0.947
27DAP/17DAP	1.02677	0.909
39DAP/27DAP	1.02294	0.685
41DAP/39DAP	1.04387	0.817
42DAP/41DAP	1.03517	0.852
43DAP/42DAP	0.97402	0.558
47DAP/43DAP	0.98347	0.911
52DAP/47DAP	1.1025	0.639
57DAP/52DAP	1.05749	0.589
57DAP/7DAP	1.05813	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94718	0.138
17DAP/reference	0.99638	0.599
27DAP/reference	0.91857	0.062
39DAP/reference	0.90716	0.023
41DAP/reference	0.84909	0.054
42DAP/reference	0.75503	0.01
43DAP/reference	0.92671	0.091
47DAP/reference	0.91449	0.128
52DAP/reference	0.87309	0.04
57DAP/reference	0.95772	0.26

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02335	0.626
17DAP/reference	0.9713	0.434
27DAP/reference	0.94343	0.195
39DAP/reference	0.96815	0.281
41DAP/reference	0.97501	0.348
42DAP/reference	0.92308	0.067
43DAP/reference	1.09681	0.157
47DAP/reference	0.95695	0.173
52DAP/reference	0.94763	0.101
57DAP/reference	0.99343	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92969	0.068
17DAP/reference	1.01572	0.876
27DAP/reference	1.10299	0.037
39DAP/reference	1.02628	0.496
41DAP/reference	0.95022	0.293
42DAP/reference	0.93634	0.287
43DAP/reference	0.9826	0.59
47DAP/reference	0.91444	0.132
52DAP/reference	0.98311	0.747
57DAP/reference	0.77728	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03941	0.966
26DAP/20DAP	0.92339	0.512
34DAP/26DAP	0.96294	0.861
51DAP/34DAP	0.93815	0.555
52DAP/51DAP	0.974	1
53DAP/52DAP	0.94772	0.732
55DAP/53DAP	1.02146	0.948
57DAP/55DAP	1.10464	0.865
62DAP/57DAP	0.97612	0.994
68DAP/62DAP	0.98775	0.863
68DAP/14DAP	1.06479	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97726	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.7827	0.165
Immature Eggplant/Mature Eggplant	1.29554	0.05
Ripe Pepper/Ripe Tomato	0.49658	1
Mature Eggplant/Ripe Tomato	0.20207	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97646	0.961
1-1-2/M82	0.93219	0.804
12-2/M82	1.14745	1
12-4/M82	0.94339	1
1-3/M82	1.00779	1
2-1-1/M82	1.03533	1
2-1/M82	1.34398
2-6/M82	1.01699	1
3-2/M82	0.95969	1
4-1-1/M82	1.06689	1
4-1/M82	0.86636	1
4-3-2/M82	0.88015	0.698
4-3/M82	1.16447	1
5-3/M82	0.92507	0.49
6-2/M82	1.03569	1
6-3/M82	0.94999	1
7-1/M82	0.93124	0.408
7-2/M82	1.10528	1
9-3-2/M82	0.75603	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.09011	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89697	0.298
IL12-4/WTpooled	0.89421	0.71
IL1-4/WTpooled	0.88939	0.402
WT/WTpooled	1.01518	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	1.39452	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97105	1
DC3000/delta hrp 6h	0.90191	0.95
DC3000/delta hrp 12h	0.9983	1
DC3000/delta hrp 24h	1.12285	0.283

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0826	0.145
DC3000 delta B/DC3000 delta AB	0.94922	0.347

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99774	1
Exp 36h	1.54261	0.409
Exp 60h	1.22488	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03301	1
Var 0h	0.49988	1
Var 12h I row2-row1	1.12455	0.348
Var 12h NI row2-row1	1.05388	1
Var 36h I row2-row1	0.95774	0.805
Var 36h NI row2-row1	0.90211	0.584
Var 60h I row2-row1	1.31179	0.562
Var 60h NI row2-row1	0.9682	1
Time course 0hI-0hNI	1.20676	0.799
Time course 12hI-12hNI	1.06687	0.77
Time course 36hI-36hNI	1.65797	0.006
Time course 60hI-60hNI	1.56806	0.012

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)	1.26073	0.261
transgenic ySAMdc/azygous control (breaker)	0.47664	0.118
transgenic ySAMdc/azygous control (red)	1.15014	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97655	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.42481	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14393	0.307
Manapal/WT (break)	0.99612	1
Manapal/WT (red)	0.68216	0.181