Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91204	0.586
27DAP/17DAP	1.12192	0.86
39DAP/27DAP	1.04421	1
41DAP/39DAP	1.11034	0.584
42DAP/41DAP	0.91938	1
43DAP/42DAP	0.9692	0.906
47DAP/43DAP	0.89698	0.568
52DAP/47DAP	1.02655	0.898
57DAP/52DAP	0.93501	0.936

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87274	0.115
17DAP/reference	0.95301	0.368
27DAP/reference	0.87098	0.07
39DAP/reference	0.97412	0.651
41DAP/reference	0.84921	0.267
42DAP/reference	0.87615	0.134
43DAP/reference	1.02145	0.957
47DAP/reference	0.90529	0.077
52DAP/reference	0.87774	0.139
57DAP/reference	0.97254	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93325	0.663
27DAP/17DAP	1.16727	0.836
39DAP/27DAP	0.96029	0.833
41DAP/39DAP	1.01783	1
42DAP/41DAP	1.30005	0.651
43DAP/42DAP	0.93428	0.538
47DAP/43DAP	0.98426	0.947
52DAP/47DAP	0.90551	0.655
57DAP/52DAP	1.24333	0.35
57DAP/7DAP	1.74209	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94641	0.326
17DAP/reference	1.09119	0.627
27DAP/reference	0.95458	0.43
39DAP/reference	0.87713	0.073
41DAP/reference	0.82452	0.046
42DAP/reference	0.88947	0.111
43DAP/reference	0.85393	0.038
47DAP/reference	0.82802	0.04
52DAP/reference	0.92082	0.213
57DAP/reference	0.95988	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09266	0.787
17DAP/reference	1.08343	0.613
27DAP/reference	0.98401	0.598
39DAP/reference	0.89407	0.227
41DAP/reference	0.9081	0.169
42DAP/reference	0.9983	0.723
43DAP/reference	1.05243	0.949
47DAP/reference	0.92864	0.087
52DAP/reference	0.74278	0.037
57DAP/reference	0.79242	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97692	0.489
17DAP/reference	0.95744	0.508
27DAP/reference	0.95791	0.465
39DAP/reference	1.01028	0.819
41DAP/reference	0.88916	0.167
42DAP/reference	0.91265	0.172
43DAP/reference	0.93603	0.294
47DAP/reference	0.8462	0.024
52DAP/reference	0.76887	0.172
57DAP/reference	1.00025	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1309	0.678
26DAP/20DAP	0.9008	1
34DAP/26DAP	1.52801	0.819
51DAP/34DAP	0.72094
52DAP/51DAP	0.85956	1
53DAP/52DAP	1.03928	0.797
55DAP/53DAP	1.12451	0.861
57DAP/55DAP	0.97422	0.839
62DAP/57DAP	1.20613	0.217
68DAP/62DAP	0.70342	0.152
68DAP/14DAP	1.10407	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74798	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77384	0.251
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.72636	0.05
Ripe Pepper/Ripe Tomato	6.37245	0.256
Mature Eggplant/Ripe Tomato	3.67723	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92189
1-1-2/M82	1.1563
12-2/M82	N/A	N/A
12-4/M82	0.85387	1
1-3/M82	1.17768
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	0.94698	1
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	1.26057
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.76166
IL7-3/WTpooled	1.13569
IL12-4/WTpooled	0.61371
IL1-4/WTpooled	1.32788	1
WT/WTpooled	0.68372	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	1.5924	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01177	1
DC3000/delta hrp 6h	0.85726	0.95
DC3000/delta hrp 12h	0.99741	1
DC3000/delta hrp 24h	2.36379	0.023

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.44017	0.151

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88627	1
Exp 36h	0.97045	0.943
Exp 60h	0.87157	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02417	1
Var 0h	0.71982	0.782
Var 12h I row2-row1	1.04506	1
Var 12h NI row2-row1	0.67662
Var 36h I row2-row1	0.98613	1
Var 36h NI row2-row1	1.47907	1
Var 60h I row2-row1	0.74008	0.285
Var 60h NI row2-row1	0.97401	1
Time course 0hI-0hNI	1.03764	0.719
Time course 12hI-12hNI	1.00154	1
Time course 36hI-36hNI	1.07143	0.799
Time course 60hI-60hNI	4.86956	0.008

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)	0.9597	0.485
transgenic ySAMdc/azygous control (breaker)	1.57738	0.162
transgenic ySAMdc/azygous control (red)	1.20711	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11519	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17168	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.58892	0.096
Manapal/WT (break)	2.32255	0.381
Manapal/WT (red)	1.15589	1