Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.18.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03693	0.858
27DAP/17DAP	1.04236	0.9
39DAP/27DAP	0.91438	0.62
41DAP/39DAP	1.30089	0.344
42DAP/41DAP	0.88443	1
43DAP/42DAP	0.97384	0.912
47DAP/43DAP	0.96967	0.868
52DAP/47DAP	1.18953	0.593
57DAP/52DAP	1.11073	0.652

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39293	0.055
17DAP/reference	1.50927	0.013
27DAP/reference	1.20971	0.285
39DAP/reference	1.04809	0.885
41DAP/reference	2.1257	0.017
42DAP/reference	1.28977	0.001
43DAP/reference	1.05295	0.982
47DAP/reference	1.19361	0.003
52DAP/reference	0.96917	0.449
57DAP/reference	0.83052	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98292	0.75
27DAP/17DAP	0.98121	0.919
39DAP/27DAP	1.08311	0.465
41DAP/39DAP	0.97155	0.893
42DAP/41DAP	0.93218	0.589
43DAP/42DAP	0.9813	0.801
47DAP/43DAP	0.99778	0.998
52DAP/47DAP	1.03623	0.883
57DAP/52DAP	1.02017	0.906
57DAP/7DAP	0.99286	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97356	0.495
17DAP/reference	0.91468	0.031
27DAP/reference	0.8792	0.011
39DAP/reference	0.99612	0.745
41DAP/reference	0.97703	0.469
42DAP/reference	0.92366	0.058
43DAP/reference	0.96781	0.072
47DAP/reference	1.02574	0.98
52DAP/reference	0.96204	0.213
57DAP/reference	0.96832	0.26

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3737	0.049
17DAP/reference	1.48575	0.065
27DAP/reference	1.43867	0.023
39DAP/reference	1.32683	0.015
41DAP/reference	1.26602	0.072
42DAP/reference	1.21662	0.011
43DAP/reference	1.16974	0.368
47DAP/reference	1.37282	0.008
52DAP/reference	1.37008	0.074
57DAP/reference	1.76009	0.02

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00258	0.699
17DAP/reference	1.03547	0.775
27DAP/reference	0.99734	0.805
39DAP/reference	0.90894	0.063
41DAP/reference	0.9737	0.417
42DAP/reference	0.94209	0.361
43DAP/reference	0.94224	0.398
47DAP/reference	1.15319	0.543
52DAP/reference	0.95789	0.65
57DAP/reference	0.60585	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09196	1
26DAP/20DAP	0.96613	0.512
34DAP/26DAP	0.97736	0.94
51DAP/34DAP	0.9606	0.674
52DAP/51DAP	1.00352	0.965
53DAP/52DAP	1.00819	0.935
55DAP/53DAP	N/A	N/A
57DAP/55DAP	1.13306	0.626
62DAP/57DAP	1.0737	1
68DAP/62DAP	0.84166	0.543
68DAP/14DAP	0.68755	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94358	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.92721	0.522
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.89349	1
Mature Eggplant/Ripe Tomato	0.73169	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01779	1
1-1-2/M82	1.06119	1
12-2/M82	1.19294	1
12-4/M82	1.02538	1
1-3/M82	0.92765	0.378
2-1-1/M82	0.95377	0.92
2-1/M82	1.48473	1
2-6/M82	0.8732	0.501
3-2/M82	1.00988	1
4-1-1/M82	0.9028	1
4-1/M82	0.82864	1
4-3-2/M82	0.86993	1
4-3/M82	0.85932	0.72
5-3/M82	0.96931	1
6-2/M82	1.03879	1
6-3/M82	0.97386	1
7-1/M82	0.8543
7-2/M82	0.98377	1
9-3-2/M82	0.96068	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.83391	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13106	1
IL12-4/WTpooled	1.13963	0.538
IL1-4/WTpooled	0.90803	0.402
WT/WTpooled	1.01157	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	1.14597	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99533	1
DC3000/delta hrp 6h	0.88395	0.95
DC3000/delta hrp 12h	1.14405	1
DC3000/delta hrp 24h	1.12349	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1461	0.183
DC3000 delta B/DC3000 delta AB	1.04256	0.565

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11742	1
Exp 36h	1.05216	1
Exp 60h	1.17613	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99819	1
Var 0h	0.9301	1
Var 12h I row2-row1	1.0592	0.379
Var 12h NI row2-row1	0.98924	1
Var 36h I row2-row1	0.78718	0.805
Var 36h NI row2-row1	0.69994	0.549
Var 60h I row2-row1	1.11257	1
Var 60h NI row2-row1	1.12409	0.904
Time course 0hI-0hNI	1.02947	0.867
Time course 12hI-12hNI	1.05328	0.663
Time course 36hI-36hNI	0.9533	0.418
Time course 60hI-60hNI	1.28483	0.01

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)	1.00763	0.789
transgenic ySAMdc/azygous control (breaker)	0.56966	0.142
transgenic ySAMdc/azygous control (red)	0.77361	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94417	0.248

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76538	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82781	1
Manapal/WT (break)	1.05709	1
Manapal/WT (red)	0.93472	0.607