Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.2.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0034	1
27DAP/17DAP	0.96804	0.967
39DAP/27DAP	0.83941	0.474
41DAP/39DAP	1.19638	0.58
42DAP/41DAP	0.95425	1
43DAP/42DAP	0.99684	0.937
47DAP/43DAP	1.0059	0.444
52DAP/47DAP	1.30673	0.538
57DAP/52DAP	1.04247	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98018	0.539
17DAP/reference	0.99959	1
27DAP/reference	0.97886	0.471
39DAP/reference	0.98443	0.638
41DAP/reference	0.92702	0.267
42DAP/reference	0.89677	0.019
43DAP/reference	0.9708	0.594
47DAP/reference	0.88891	0.032
52DAP/reference	0.81871	0.027
57DAP/reference	0.78248	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04185	0.65
27DAP/17DAP	1.03956	0.848
39DAP/27DAP	0.97329	0.747
41DAP/39DAP	1.03951	0.861
42DAP/41DAP	0.97553	0.743
43DAP/42DAP	1.02008	0.513
47DAP/43DAP	1.02313	0.865
52DAP/47DAP	1.02784	0.883
57DAP/52DAP	0.98913	0.813
57DAP/7DAP	0.99039	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9991	1
17DAP/reference	0.87487	0.124
27DAP/reference	0.85459	0.033
39DAP/reference	0.90666	0.264
41DAP/reference	0.91407	0.062
42DAP/reference	0.89242	0.035
43DAP/reference	0.81854	0.024
47DAP/reference	0.86915	0.168
52DAP/reference	0.81705	0.022
57DAP/reference	0.85841	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06322	0.404
17DAP/reference	1.04309	0.396
27DAP/reference	0.9595	0.381
39DAP/reference	0.98757	0.554
41DAP/reference	0.90804	0.014
42DAP/reference	0.87759	0.011
43DAP/reference	0.98182	0.633
47DAP/reference	0.90662	0.015
52DAP/reference	1.05569	0.343
57DAP/reference	1.06486	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88975	0.169
17DAP/reference	0.98361	0.709
27DAP/reference	0.87708
39DAP/reference	0.81276	0.04
41DAP/reference	0.89769	0.077
42DAP/reference	0.82132	0.041
43DAP/reference	0.84976	0.035
47DAP/reference	0.87082	0.125
52DAP/reference	0.77805	0.132
57DAP/reference	0.69098	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91902	0.541
26DAP/20DAP	0.91686	0.512
34DAP/26DAP	0.92991	0.479
51DAP/34DAP	0.94491	0.449
52DAP/51DAP	0.96007	1
53DAP/52DAP	1.05298	0.608
55DAP/53DAP	0.88439	0.336
57DAP/55DAP	1.10635	0.865
62DAP/57DAP	1.11168	0.35
68DAP/62DAP	1.03094	1
68DAP/14DAP	1.28296	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96976	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.53549
Mature Green Tomato/Ripe Tomato	0.97033	0.66
Immature Eggplant/Mature Eggplant	1.24254	0.165
Ripe Pepper/Ripe Tomato	1.11203	1
Mature Eggplant/Ripe Tomato	0.97117	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05555	0.877
1-1-2/M82	0.96601	1
12-2/M82	1.12879	1
12-4/M82	0.96644	1
1-3/M82	0.97991	0.501
2-1-1/M82	1.05291	0.422
2-1/M82	1.24204	0.32
2-6/M82	0.94926	1
3-2/M82	1.07316
4-1-1/M82	0.97034	1
4-1/M82	1.06984
4-3-2/M82	0.96272	1
4-3/M82	1.05149	1
5-3/M82	1.04889	1
6-2/M82	1.03193	1
6-3/M82	1.009	1
7-1/M82	0.94452	0.452
7-2/M82	0.98153	1
9-3-2/M82	0.71564

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94964	0.321
IL2-6/WTpooled	0.96829	1
IL7-5/WTpooled	0.97075	1
IL7-3/WTpooled	1.0673	1
IL12-4/WTpooled	1.16242	0.532
IL1-4/WTpooled	0.94687	0.476
WT/WTpooled	1.00388	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	0.92758	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01522	0.921
DC3000/delta hrp 6h	1.06884	1
DC3000/delta hrp 12h	1.03829	1
DC3000/delta hrp 24h	1.0432	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02516	0.515
DC3000 delta B/DC3000 delta AB	1.00962	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9479	1
Exp 36h	1.02032	1
Exp 60h	0.90054	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96772	1
Var 0h	0.9704	1
Var 12h I row2-row1	1.04577	0.654
Var 12h NI row2-row1	1.11593	1
Var 36h I row2-row1	0.85468	1
Var 36h NI row2-row1	0.83812	0.469
Var 60h I row2-row1	1.39078	0.562
Var 60h NI row2-row1	1.11181	0.904
Time course 0hI-0hNI	1.00415	1
Time course 12hI-12hNI	1.01472	0.849
Time course 36hI-36hNI	1.02186	0.401
Time course 60hI-60hNI	1.04612	0.115

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)	0.95825	0.377
transgenic ySAMdc/azygous control (breaker)	1.87357	0.162
transgenic ySAMdc/azygous control (red)	0.82767	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00295	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18236	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.36644	0.083
Manapal/WT (break)	1.35668	0.183
Manapal/WT (red)	1.52249	0.413