Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.3.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7011	0.144
27DAP/17DAP	1.07829	0.902
39DAP/27DAP	0.66771	0.382
41DAP/39DAP	0.90783	0.701
42DAP/41DAP	1.07881	0.999
43DAP/42DAP	0.97839	0.93
47DAP/43DAP	1.0675	0.756
52DAP/47DAP	1.28342	0.63
57DAP/52DAP	1.36658	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85422	0.154
17DAP/reference	1.01543	0.764
27DAP/reference	1.02554	1
39DAP/reference	1.19801	0.301
41DAP/reference	0.9108	0.434
42DAP/reference	1.16707	0.963
43DAP/reference	0.87895
47DAP/reference	0.56966	0.027
52DAP/reference	1.05531	0.709
57DAP/reference	0.82097	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83464	0.238
27DAP/17DAP	0.90925	0.684
39DAP/27DAP	0.80717	0.243
41DAP/39DAP	1.00814	1
42DAP/41DAP	1.10703	0.879
43DAP/42DAP	0.97016	0.751
47DAP/43DAP	1.15972	0.066
52DAP/47DAP	1.4091	0.334
57DAP/52DAP	0.96784	0.726
57DAP/7DAP	1.30542

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82196	0.07
17DAP/reference	1.02005	1
27DAP/reference	0.9786	0.571
39DAP/reference	1.05938	1
41DAP/reference	0.88339	0.082
42DAP/reference	1.00268	0.828
43DAP/reference	0.9068	0.013
47DAP/reference	0.95562	0.504
52DAP/reference	0.91572	0.232
57DAP/reference	0.94256	0.26

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97888	0.72
17DAP/reference	0.98726	0.728
27DAP/reference	1.08039	0.573
39DAP/reference	0.87875	0.257
41DAP/reference	1.05672	1
42DAP/reference	1.18753	0.351
43DAP/reference	1.15843	0.396
47DAP/reference	0.98756	0.609
52DAP/reference	1.36225	0.259
57DAP/reference	1.15593	0.177

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01776	1
17DAP/reference	1.1822	0.269
27DAP/reference	1.11194	0.164
39DAP/reference	1.20033	0.196
41DAP/reference	1.12238	0.754
42DAP/reference	1.02552	0.775
43DAP/reference	0.98839	0.712
47DAP/reference	0.8751	0.409
52DAP/reference	1.00538	0.838
57DAP/reference	1.47902	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.84816	0.961
26DAP/20DAP	1.02166	1
34DAP/26DAP	0.86505	0.816
51DAP/34DAP	1.25977	0.869
52DAP/51DAP	1.31606	0.396
53DAP/52DAP	0.92853	0.758
55DAP/53DAP	1.04377	0.994
57DAP/55DAP	0.94626	0.825
62DAP/57DAP	1.04081	1
68DAP/62DAP	1.38845	0.253
68DAP/14DAP	2.01797	0.02

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.22205	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.78223
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	4.35536	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.17734	0.877
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.18256
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.66371
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.92386	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.76086	0.243
IL2-6/WTpooled	1.09332	0.788
IL7-5/WTpooled	0.74858	1
IL7-3/WTpooled	0.82744	0.31
IL12-4/WTpooled	1.03947	0.695
IL1-4/WTpooled	0.98213	1
WT/WTpooled	1.16588	0.855

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	0.92636	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02321	0.921
DC3000/delta hrp 6h	0.94523	0.95
DC3000/delta hrp 12h	1.26954	1
DC3000/delta hrp 24h	0.83189	0.053

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53622
DC3000 delta B/DC3000 delta AB	0.66909	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07781	1
Exp 36h	1.11679	1
Exp 60h	1.20353	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.98999	1
Var 12h I row2-row1	0.81223	0.363
Var 12h NI row2-row1	1.19696	0.34
Var 36h I row2-row1	0.82448	0.438
Var 36h NI row2-row1	1.03836	1
Var 60h I row2-row1	0.95683	0.952
Var 60h NI row2-row1	1.0939	0.904
Time course 0hI-0hNI	0.99562	1
Time course 12hI-12hNI	0.90531	0.586
Time course 36hI-36hNI	1.09705	0.101
Time course 60hI-60hNI	0.92149	0.161

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.95029	1
transgenic ySAMdc/azygous control (red)	0.76695	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95005	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7817	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.37876	0.14
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.88137	0.229