Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05466	0.838
27DAP/17DAP	1.0077	1
39DAP/27DAP	0.79516	0.443
41DAP/39DAP	1.06273	0.63
42DAP/41DAP	0.99131	1
43DAP/42DAP	1.11177	0.985
47DAP/43DAP	1.0346	0.965
52DAP/47DAP	0.81371	0.545
57DAP/52DAP	1.02853	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00173	1
17DAP/reference	1.02347	0.528
27DAP/reference	1.03833	0.599
39DAP/reference	1.03856	0.524
41DAP/reference	1.09425	0.073
42DAP/reference	0.9756	0.25
43DAP/reference	1.04864	0.252
47DAP/reference	1.03875	0.478
52DAP/reference	0.95382	0.35
57DAP/reference	1.08245	0.195

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97071	0.526
27DAP/17DAP	0.99819	0.969
39DAP/27DAP	1.03834	0.677
41DAP/39DAP	0.99819	1
42DAP/41DAP	0.97822	0.759
43DAP/42DAP	1.0288	0.273
47DAP/43DAP	1.03472	0.853
52DAP/47DAP	0.99457	0.962
57DAP/52DAP	0.96878	0.566
57DAP/7DAP	1.00133	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70119	0.038
17DAP/reference	2.2753	0.006
27DAP/reference	1.77618	0.007
39DAP/reference	2.3474	0.006
41DAP/reference	2.4798	0.011
42DAP/reference	2.51314	0.01
43DAP/reference	3.24729	0.007
47DAP/reference	1.23351	0.761
52DAP/reference	2.74552	0.007
57DAP/reference	2.33541	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92021	0.152
17DAP/reference	0.98787	0.642
27DAP/reference	0.84419	0.047
39DAP/reference	0.94425	0.265
41DAP/reference	0.96128	0.34
42DAP/reference	1.03558	0.794
43DAP/reference	0.85244	0.224
47DAP/reference	1.07267	0.159
52DAP/reference	1.00742	1
57DAP/reference	0.9896	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43884	0.06
17DAP/reference	1.39227	0.394
27DAP/reference	2.94036	0.012
39DAP/reference	2.66669	0.008
41DAP/reference	1.85637	0.027
42DAP/reference	1.86306	0.239
43DAP/reference	1.71698	0.056
47DAP/reference	0.98484	0.558
52DAP/reference	1.64612	0.289
57DAP/reference	1.50201	0.758

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99122	1
26DAP/20DAP	1.01659	1
34DAP/26DAP	1.01929	1
51DAP/34DAP	1.05464	0.565
52DAP/51DAP	0.95779	1
53DAP/52DAP	1.04945	0.712
55DAP/53DAP	0.97699	0.709
57DAP/55DAP	1.03455	0.898
62DAP/57DAP	0.96749	0.681
68DAP/62DAP	0.99808	0.914
68DAP/14DAP	0.8922	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87966	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86416
Mature Green Tomato/Ripe Tomato	1.28485	0.267
Immature Eggplant/Mature Eggplant	1.15949	0.181
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.04599

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06551	0.526
1-1-2/M82	0.94064	0.958
12-2/M82	0.92499	0.955
12-4/M82	0.96122	1
1-3/M82	0.95848	0.501
2-1-1/M82	0.96774	1
2-1/M82	1.15352	1
2-6/M82	0.95117	1
3-2/M82	1.04801
4-1-1/M82	0.98383	1
4-1/M82	0.92911	1
4-3-2/M82	0.94002	1
4-3/M82	0.92285	0.509
5-3/M82	1.03209	1
6-2/M82	0.98862	1
6-3/M82	1.04209	1
7-1/M82	1.06991	0.992
7-2/M82	0.97213	0.881
9-3-2/M82	0.77588	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02619	0.46
IL7-5/WTpooled	0.73596
IL7-3/WTpooled	1.01728	1
IL12-4/WTpooled	0.99758	1
IL1-4/WTpooled	1.03486	1
WT/WTpooled	0.93779	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	0.64228	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04716	0.875
DC3000/delta hrp 6h	1.27817	1
DC3000/delta hrp 12h	1.04403	1
DC3000/delta hrp 24h	0.98247	0.934

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00682	1
DC3000 delta B/DC3000 delta AB	0.98822	0.983

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.14135	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	1.00917	1
Var 0h	0.89158	0.933
Var 12h I row2-row1	1.19075	0.163
Var 12h NI row2-row1	0.99128	1
Var 36h I row2-row1	0.95783	1
Var 36h NI row2-row1	0.88619	0.61
Var 60h I row2-row1	1.25038	0.562
Var 60h NI row2-row1	0.99386	1
Time course 0hI-0hNI	1.0484	0.867
Time course 12hI-12hNI	1.03638	0.773
Time course 36hI-36hNI	1.00522	1
Time course 60hI-60hNI	1.07427	0.096

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)	1.23154	0.541
transgenic ySAMdc/azygous control (breaker)	1.62244	0.248
transgenic ySAMdc/azygous control (red)	1.32549	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95604	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8473	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.67667	1
Manapal/WT (break)	0.90755	1
Manapal/WT (red)	0.86243	0.503