Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.3.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11043	0.755
27DAP/17DAP	1.00694	1
39DAP/27DAP	0.91282	0.529
41DAP/39DAP	1.39472	0.416
42DAP/41DAP	0.93086	1
43DAP/42DAP	1.13355	0.976
47DAP/43DAP	0.81291	0.36
52DAP/47DAP	1.1858	0.57
57DAP/52DAP	1.02619	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09653	0.278
17DAP/reference	1.09299	0.012
27DAP/reference	0.91462	0.359
39DAP/reference	0.73321	0.412
41DAP/reference	1.05048	0.338
42DAP/reference	1.4161	0.013
43DAP/reference	N/A	N/A
47DAP/reference	1.24912	0.001
52DAP/reference	1.11181	0.453
57DAP/reference	0.61338

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98296	0.697
27DAP/17DAP	0.977	0.887
39DAP/27DAP	0.9672	0.579
41DAP/39DAP	1.05487	0.781
42DAP/41DAP	0.98954	0.872
43DAP/42DAP	1.0078	0.699
47DAP/43DAP	0.89512	0.656
52DAP/47DAP	1.01374	0.956
57DAP/52DAP	1.01092	0.992
57DAP/7DAP	1.01309	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92031	0.086
17DAP/reference	0.89944	0.018
27DAP/reference	0.93361	0.031
39DAP/reference	0.9726	0.109
41DAP/reference	0.88576	0.023
42DAP/reference	0.91912	0.015
43DAP/reference	0.92343	0.069
47DAP/reference	0.90633	0.128
52DAP/reference	0.88435	0.072
57DAP/reference	0.92083	0.042

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29748	0.094
17DAP/reference	1.12301	0.061
27DAP/reference	1.14157	0.09
39DAP/reference	1.28569	0.141
41DAP/reference	1.28735	0.149
42DAP/reference	1.16302	0.18
43DAP/reference	1.18577	0.135
47DAP/reference	1.08674	0.169
52DAP/reference	1.10466	0.279
57DAP/reference	1.18542	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97369	0.29
17DAP/reference	1.0229	0.757
27DAP/reference	0.93426	0.195
39DAP/reference	0.96779	0.111
41DAP/reference	0.95583	0.037
42DAP/reference	1.07005	0.481
43DAP/reference	1.16367	0.308
47DAP/reference	0.94638	0.24
52DAP/reference	0.91801	0.262
57DAP/reference	0.96161	0.468

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94942	0.961
26DAP/20DAP	0.93193	0.512
34DAP/26DAP	0.93788	0.795
51DAP/34DAP	1.11671	0.339
52DAP/51DAP	0.96769	1
53DAP/52DAP	1.03414	0.783
55DAP/53DAP	0.92181	0.489
57DAP/55DAP	1.05657	0.643
62DAP/57DAP	0.95159	0.994
68DAP/62DAP	0.89946	0.722
68DAP/14DAP	0.84153	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99355	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.84697	0.666
Mature Green Tomato/Ripe Tomato	0.56452	0.028
Immature Eggplant/Mature Eggplant	1.60412	0.259
Ripe Pepper/Ripe Tomato	0.45333	0.224
Mature Eggplant/Ripe Tomato	0.4446	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0454	0.591
1-1-2/M82	1.04358	1
12-2/M82	1.04962
12-4/M82	1.04085	1
1-3/M82	0.85668	0.501
2-1-1/M82	1.23441	0.764
2-1/M82	N/A	N/A
2-6/M82	0.99808
3-2/M82	0.76917
4-1-1/M82	1.00711	1
4-1/M82	0.87595
4-3-2/M82	0.84607	1
4-3/M82	N/A	N/A
5-3/M82	0.97502	1
6-2/M82	0.98157
6-3/M82	N/A	N/A
7-1/M82	0.9773
7-2/M82	0.95649	0.599
9-3-2/M82	0.75525	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.28363	0.493
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.74744
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.0143	1
WT/WTpooled	N/A	N/A

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	1.09567	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05241	0.921
DC3000/delta hrp 6h	1.20566	1
DC3000/delta hrp 12h	1.1245	1
DC3000/delta hrp 24h	1.18779	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03695	0.29
DC3000 delta B/DC3000 delta AB	1.0056	0.748

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13738	1
Exp 36h	0.94667	0.82
Exp 60h	1.03163	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98962	1
Var 0h	0.73628	1
Var 12h I row2-row1	1.08252	0.544
Var 12h NI row2-row1	1.03769	1
Var 36h I row2-row1	0.94846	1
Var 36h NI row2-row1	0.97382	0.791
Var 60h I row2-row1	1.16976	0.562
Var 60h NI row2-row1	1.19201	0.904
Time course 0hI-0hNI	0.98877	0.973
Time course 12hI-12hNI	0.987	0.94
Time course 36hI-36hNI	0.96535	0.426
Time course 60hI-60hNI	1.01019	1

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)	1.06133	0.321
transgenic ySAMdc/azygous control (breaker)	2.83624	0.165
transgenic ySAMdc/azygous control (red)	1.76837	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99007	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90329	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89163	1
Manapal/WT (break)	0.68019	0.333
Manapal/WT (red)	1.34491	0.164