Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04295	0.878
27DAP/17DAP	1.16663	0.804
39DAP/27DAP	1.01611	0.876
41DAP/39DAP	0.945	0.771
42DAP/41DAP	1.1665	0.852
43DAP/42DAP	0.98784	0.934
47DAP/43DAP	1.28307	0.555
52DAP/47DAP	0.83925	0.579
57DAP/52DAP	1.09512	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05456	0.5
17DAP/reference	1.10302	0.015
27DAP/reference	1.03667	0.405
39DAP/reference	0.99718	0.975
41DAP/reference	1.01335	0.759
42DAP/reference	0.98514	0.372
43DAP/reference	1.06467	0.111
47DAP/reference	0.88957	0.035
52DAP/reference	0.83279	0.089
57DAP/reference	0.97053	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99864	0.847
27DAP/17DAP	1.04962	0.885
39DAP/27DAP	1.00747	0.874
41DAP/39DAP	1.08482	0.484
42DAP/41DAP	1.0377	0.74
43DAP/42DAP	0.92888	0.157
47DAP/43DAP	0.95873	0.815
52DAP/47DAP	1.67479	0.209
57DAP/52DAP	1.67326	0.056
57DAP/7DAP	2.51869	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79526	0.086
17DAP/reference	0.72816	0.011
27DAP/reference	0.78805	0.01
39DAP/reference	0.83298	0.013
41DAP/reference	0.869	0.046
42DAP/reference	0.78017	0.014
43DAP/reference	0.74046	0.013
47DAP/reference	0.85435	0.222
52DAP/reference	0.80387	0.043
57DAP/reference	0.94619	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93473	0.457
17DAP/reference	1.04773	0.32
27DAP/reference	0.92788	0.119
39DAP/reference	0.99826	0.702
41DAP/reference	0.89943	0.042
42DAP/reference	0.98346	0.594
43DAP/reference	0.96599	0.527
47DAP/reference	1.01572	0.795
52DAP/reference	0.97328	0.28
57DAP/reference	1.04891	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92227	0.29
17DAP/reference	1.01099	1
27DAP/reference	0.77254	0.031
39DAP/reference	0.78097	0.018
41DAP/reference	0.85989	0.05
42DAP/reference	0.81893	0.059
43DAP/reference	0.81795	0.071
47DAP/reference	0.97482	0.434
52DAP/reference	0.7937	0.169
57DAP/reference	0.91635	0.247

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01481	0.966
26DAP/20DAP	1.32451	0.558
34DAP/26DAP	1.49115	1
51DAP/34DAP	1.16573	0.949
52DAP/51DAP	2.01853	0.035
53DAP/52DAP	0.68095	0.086
55DAP/53DAP	1.45753	0.042
57DAP/55DAP	0.55255	0.068
62DAP/57DAP	0.96562	0.994
68DAP/62DAP	0.80546	0.406
68DAP/14DAP	0.85497	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.42534	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07272	0.666
Mature Green Tomato/Ripe Tomato	1.09349	0.814
Immature Eggplant/Mature Eggplant	1.14886	0.198
Ripe Pepper/Ripe Tomato	1.16116
Mature Eggplant/Ripe Tomato	1.45089	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85579
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.98411	1
1-3/M82	0.88448	0.501
2-1-1/M82	N/A	N/A
2-1/M82	1.13297
2-6/M82	1.07844	0.452
3-2/M82	1.00891	1
4-1-1/M82	N/A	N/A
4-1/M82	0.96889
4-3-2/M82	0.8465	0.487
4-3/M82	0.72783	0.72
5-3/M82	1.04474	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.23321
7-2/M82	0.92265	0.796
9-3-2/M82	0.97592	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98535	1
IL2-6/WTpooled	1.05915	0.788
IL7-5/WTpooled	1.16053	0.792
IL7-3/WTpooled	0.92561	1
IL12-4/WTpooled	1.00981	0.737
IL1-4/WTpooled	1.0368	0.426
WT/WTpooled	1.04211	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	0.79947	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94725	1
DC3000/delta hrp 6h	1.10754	1
DC3000/delta hrp 12h	0.99846	1
DC3000/delta hrp 24h	0.93692	0.607

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03167	0.476
DC3000 delta B/DC3000 delta AB	0.93778	0.483

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	0.98443	1
Var 0h	1.07333	0.98
Var 12h I row2-row1	0.67684	0.39
Var 12h NI row2-row1	0.91985	0.546
Var 36h I row2-row1	0.94778	1
Var 36h NI row2-row1	1.06271	1
Var 60h I row2-row1	0.83881	0.285
Var 60h NI row2-row1	1.07112	0.904
Time course 0hI-0hNI	0.95395	0.734
Time course 12hI-12hNI	0.99839	1
Time course 36hI-36hNI	0.80144	0.055
Time course 60hI-60hNI	0.41032	0.005

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)	0.98697	0.862
transgenic ySAMdc/azygous control (breaker)	1.41478	0.178
transgenic ySAMdc/azygous control (red)	1.10221	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02814	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.44667	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.00035	0.083
Manapal/WT (break)	1.64919	0.14
Manapal/WT (red)	1.68857	0.137