Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.18.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32892	0.085
27DAP/17DAP	1.76763	0.597
39DAP/27DAP	0.84456	0.338
41DAP/39DAP	1.39527	0.822
42DAP/41DAP	1.60225	0.632
43DAP/42DAP	1.24688	0.671
47DAP/43DAP	1.32673	0.733
52DAP/47DAP	0.77596	0.598
57DAP/52DAP	0.95666	0.936

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00103	0.771
17DAP/reference	1.03733	0.22
27DAP/reference	1.04285	0.587
39DAP/reference	1.05935	0.021
41DAP/reference	0.94668	0.154
42DAP/reference	0.88726	0.017
43DAP/reference	1.0433	0.36
47DAP/reference	0.84413	0.006
52DAP/reference	0.9193	0.202
57DAP/reference	0.86705	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96715	0.644
27DAP/17DAP	0.99418	0.943
39DAP/27DAP	1.01493	0.779
41DAP/39DAP	1.03962	0.883
42DAP/41DAP	0.93676	0.591
43DAP/42DAP	1.00847	0.788
47DAP/43DAP	0.96537	0.774
52DAP/47DAP	0.98348	0.93
57DAP/52DAP	1.02985	0.813
57DAP/7DAP	1.05553	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86857	0.168
17DAP/reference	1.04319	1
27DAP/reference	0.8269	0.109
39DAP/reference	1.12557	0.222
41DAP/reference	1.18236	0.232
42DAP/reference	0.77658	0.111
43DAP/reference	0.98718	0.608
47DAP/reference	0.82324	0.034
52DAP/reference	1.02356	0.886
57DAP/reference	1.13394	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97725	0.706
17DAP/reference	0.93517	0.208
27DAP/reference	0.9036	0.203
39DAP/reference	0.88471	0.087
41DAP/reference	0.80195	0.024
42DAP/reference	0.85919	0.012
43DAP/reference	0.99371	0.736
47DAP/reference	0.97181	0.434
52DAP/reference	0.90635	0.037
57DAP/reference	1.00125	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99882	0.75
17DAP/reference	0.94007	0.508
27DAP/reference	1.24537	0.447
39DAP/reference	0.91357	0.464
41DAP/reference	0.82115	0.132
42DAP/reference	0.84731	0.361
43DAP/reference	1.06252	0.894
47DAP/reference	0.91071	0.224
52DAP/reference	0.84758	0.395
57DAP/reference	0.62512	0.027

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98156	1
26DAP/20DAP	0.85778	0.512
34DAP/26DAP	0.91608	0.619
51DAP/34DAP	0.91719	0.402
52DAP/51DAP	1.00318	1
53DAP/52DAP	1.06349	0.643
55DAP/53DAP	0.99033	0.876
57DAP/55DAP	1.09009	0.805
62DAP/57DAP	1.23519	0.034
68DAP/62DAP	0.85139	0.429
68DAP/14DAP	0.96233	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80632	0.059

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04553	1
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.96896	0.912
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	9.49432	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97393	0.961
1-1-2/M82	0.94801	1
12-2/M82	1.10002	1
12-4/M82	1.14163	1
1-3/M82	0.69185	0.378
2-1-1/M82	1.0298	0.764
2-1/M82	N/A	N/A
2-6/M82	1.17089	0.594
3-2/M82	1.01362
4-1-1/M82	1.01536	1
4-1/M82	1.30487
4-3-2/M82	N/A	N/A
4-3/M82	0.60847	0.388
5-3/M82	0.93429	1
6-2/M82	0.95459	1
6-3/M82	1.17836	1
7-1/M82	N/A	N/A
7-2/M82	1.14136
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94296	1
IL2-6/WTpooled	1.22682	0.419
IL7-5/WTpooled	0.61827	1
IL7-3/WTpooled	1.02036	1
IL12-4/WTpooled	1.08333	0.737
IL1-4/WTpooled	1.0841	1
WT/WTpooled	1.03296	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	0.98708	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02637	0.921
DC3000/delta hrp 6h	0.93381	0.95
DC3000/delta hrp 12h	1.18676	1
DC3000/delta hrp 24h	0.97774	0.924

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0735	0.408
DC3000 delta B/DC3000 delta AB	1.02053	0.687

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	1.11785	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99754	1
Var 0h	1.32907	0.339
Var 12h I row2-row1	1.15998	0.202
Var 12h NI row2-row1	0.91635	0.488
Var 36h I row2-row1	1.00365	1
Var 36h NI row2-row1	0.79407	0.522
Var 60h I row2-row1	1.3292	0.562
Var 60h NI row2-row1	1.35078	0.904
Time course 0hI-0hNI	1.07257	0.799
Time course 12hI-12hNI	1.01235	0.9
Time course 36hI-36hNI	1.00529	1
Time course 60hI-60hNI	1.13885	0.16

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)	0.86413	0.299
transgenic ySAMdc/azygous control (breaker)	1.03038	1
transgenic ySAMdc/azygous control (red)	1.02945	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05787	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95223	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96832	1
Manapal/WT (break)	1.55966	0.381
Manapal/WT (red)	1.10422	1