Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.3.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73924	0.169
27DAP/17DAP	1.37728	0.703
39DAP/27DAP	1.15521	0.768
41DAP/39DAP	0.94176	0.655
42DAP/41DAP	0.7733	0.774
43DAP/42DAP	0.84078	0.705
47DAP/43DAP	1.04443	0.889
52DAP/47DAP	2.37146	0.078
57DAP/52DAP	0.96799	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86965	0.326
17DAP/reference	0.87215	0.129
27DAP/reference	1.01681	0.925
39DAP/reference	0.82761	0.284
41DAP/reference	3.25569	0.516
42DAP/reference	0.97748	0.469
43DAP/reference	0.97921
47DAP/reference	0.9749	0.445
52DAP/reference	1.05337	0.766
57DAP/reference	0.41148	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06263	0.774
27DAP/17DAP	1.04939	0.909
39DAP/27DAP	1.04837	0.672
41DAP/39DAP	1.16504	0.157
42DAP/41DAP	0.87026	0.218
43DAP/42DAP	1.016	0.83
47DAP/43DAP	0.93636	0.677
52DAP/47DAP	1.13793	0.552
57DAP/52DAP	1.02619	1
57DAP/7DAP	1.18748	0.153

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96278	0.445
17DAP/reference	0.95567	0.389
27DAP/reference	1.04383	0.804
39DAP/reference	1.1819	0.282
41DAP/reference	1.11625	0.56
42DAP/reference	1.14639	0.308
43DAP/reference	1.24279	0.031
47DAP/reference	1.32979	0.023
52DAP/reference	1.38935	0.021
57DAP/reference	1.38804	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02024	0.874
17DAP/reference	1.04773	0.859
27DAP/reference	0.93851	0.366
39DAP/reference	1.18448	0.783
41DAP/reference	1.10836	0.536
42DAP/reference	1.13642	0.247
43DAP/reference	1.05109	1
47DAP/reference	1.20509	0.074
52DAP/reference	0.98362	0.5
57DAP/reference	0.95277	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10536	0.676
17DAP/reference	0.86613	0.234
27DAP/reference	1.08346	0.487
39DAP/reference	1.13668	0.108
41DAP/reference	1.02676	1
42DAP/reference	1.00866	1
43DAP/reference	1.07151	0.768
47DAP/reference	1.04589	0.994
52DAP/reference	0.88021	0.277
57DAP/reference	1.04403	0.66

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11167	0.966
26DAP/20DAP	0.72514	0.244
34DAP/26DAP	0.9318	0.741
51DAP/34DAP	1.17342	0.496
52DAP/51DAP	0.79743	0.151
53DAP/52DAP	1.25317	0.723
55DAP/53DAP	0.89617	0.619
57DAP/55DAP	1.16991	0.841
62DAP/57DAP	1.16601	0.569
68DAP/62DAP	1.21171	0.405
68DAP/14DAP	1.23055	0.223

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.75732	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.45549	0.025
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.3291	0.224
Mature Eggplant/Ripe Tomato	0.21973	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20283	0.742
1-1-2/M82	1.2564	1
12-2/M82	2.29824	0.281
12-4/M82	0.78613	0.282
1-3/M82	1.05544
2-1-1/M82	0.94491	1
2-1/M82	1.08802
2-6/M82	1.03754	1
3-2/M82	0.90989
4-1-1/M82	1.09157	1
4-1/M82	N/A	N/A
4-3-2/M82	1.17516	0.508
4-3/M82	1.05219	1
5-3/M82	0.66969	0.49
6-2/M82	1.28946
6-3/M82	1.01982	1
7-1/M82	N/A	N/A
7-2/M82	1.14452	1
9-3-2/M82	0.93206

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.36753	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.93919
IL7-3/WTpooled	1.25916
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.95664	1
WT/WTpooled	0.85436	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	1.22401	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04353	0.875
DC3000/delta hrp 6h	1.04999	1
DC3000/delta hrp 12h	1.132	1
DC3000/delta hrp 24h	0.86572	0.207

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91242	0.841
DC3000 delta B/DC3000 delta AB	1.07334	0.655

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97505	1
Exp 36h	0.88957	0.589
Exp 60h	1.10502	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99671	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.00654	1
Var 12h NI row2-row1	0.88156	0.349
Var 36h I row2-row1	0.85658	0.805
Var 36h NI row2-row1	1.39849	0.276
Var 60h I row2-row1	1.57904	0.562
Var 60h NI row2-row1	1.4001	0.281
Time course 0hI-0hNI	0.92801	0.522
Time course 12hI-12hNI	0.94914	0.606
Time course 36hI-36hNI	0.7542	0.028
Time course 60hI-60hNI	0.23373	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)	1.12966	0.212
transgenic ySAMdc/azygous control (breaker)	0.74438	0.142
transgenic ySAMdc/azygous control (red)	0.96202	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.16029	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88545	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95043	1
Manapal/WT (break)	0.76938	0.297
Manapal/WT (red)	0.70298	0.181