Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22553	0.575
27DAP/17DAP	2.84195	0.109
39DAP/27DAP	2.02534	0.236
41DAP/39DAP	1.256	0.941
42DAP/41DAP	2.67001	0.028
43DAP/42DAP	0.98434	0.909
47DAP/43DAP	0.55894	0.057
52DAP/47DAP	0.72174	0.255
57DAP/52DAP	0.91072	0.869

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.059	0.522
17DAP/reference	1.10995	0.053
27DAP/reference	1.04319	0.672
39DAP/reference	1.017	0.816
41DAP/reference	1.18849	0.015
42DAP/reference	0.92039	0.054
43DAP/reference	0.98144	0.708
47DAP/reference	0.91811	0.106
52DAP/reference	0.87706	0.082
57DAP/reference	0.86189	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83833	0.26
27DAP/17DAP	1.15554	0.546
39DAP/27DAP	3.13037	0.043
41DAP/39DAP	2.70978	0.006
42DAP/41DAP	0.74124	0.01
43DAP/42DAP	0.52294	0.022
47DAP/43DAP	1.27749	0.024
52DAP/47DAP	1.0396	0.951
57DAP/52DAP	0.74028	0.339
57DAP/7DAP	1.26945	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10624	0.344
17DAP/reference	0.97138	0.447
27DAP/reference	1.05618	0.664
39DAP/reference	1.06402	0.46
41DAP/reference	1.01683	1
42DAP/reference	1.00403	0.641
43DAP/reference	0.9642	0.421
47DAP/reference	0.8437	0.05
52DAP/reference	0.76233	0.015
57DAP/reference	0.77899	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12953	0.203
17DAP/reference	1.13367	0.045
27DAP/reference	0.98362	0.576
39DAP/reference	0.98351	0.509
41DAP/reference	0.89248	0.089
42DAP/reference	0.87653	0.02
43DAP/reference	1.10013	0.347
47DAP/reference	0.93487	0.126
52DAP/reference	1.04789	0.24
57DAP/reference	1.26516	0.172

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.014	0.804
17DAP/reference	1.03292	0.876
27DAP/reference	0.86997	0.063
39DAP/reference	0.91373	0.031
41DAP/reference	0.91962	0.237
42DAP/reference	0.83919	0.108
43DAP/reference	0.92283	0.384
47DAP/reference	0.81903	0.12
52DAP/reference	0.85273	0.169
57DAP/reference	0.52596	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14455	0.966
26DAP/20DAP	0.89453	1
34DAP/26DAP	1.31537	0.304
51DAP/34DAP	0.99263	0.883
52DAP/51DAP	0.86027	1
53DAP/52DAP	1.57466	0.662
55DAP/53DAP	1.081	0.976
57DAP/55DAP	1.02638	0.78
62DAP/57DAP	0.92893	0.871
68DAP/62DAP	0.85094	0.378
68DAP/14DAP	0.84723	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.96368	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.19429	0.478
Immature Eggplant/Mature Eggplant	4.27926	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.21996
12-2/M82	N/A	N/A
12-4/M82	0.81771	0.358
1-3/M82	0.69464
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.96198
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	1.2847
4-3/M82	N/A	N/A
5-3/M82	1.19294
6-2/M82	2.48911
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	0.70118

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11244	0.277
IL2-6/WTpooled	1.16377	0.584
IL7-5/WTpooled	0.83819	1
IL7-3/WTpooled	1.17423	1
IL12-4/WTpooled	0.84675	0.581
IL1-4/WTpooled	1.07312	1
WT/WTpooled	0.92502	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	1.62819	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98804	1
DC3000/delta hrp 6h	1.11083	1
DC3000/delta hrp 12h	1.14137	1
DC3000/delta hrp 24h	0.93816	0.585

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	3.11766	0.061

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01593	1
Exp 36h	1.09349	1
Exp 60h	1.07941	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99183	1
Var 0h	1.04412	0.98
Var 12h I row2-row1	0.96487	0.948
Var 12h NI row2-row1	1.71612	0.266
Var 36h I row2-row1	1.53454	0.309
Var 36h NI row2-row1	0.53448	0.469
Var 60h I row2-row1	0.87	0.832
Var 60h NI row2-row1	0.82805	0.756
Time course 0hI-0hNI	1.40372	0.451
Time course 12hI-12hNI	0.93703	0.705
Time course 36hI-36hNI	3.50571	0.004
Time course 60hI-60hNI	20.0811	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)	0.91088	0.338
transgenic ySAMdc/azygous control (breaker)	1.096	1
transgenic ySAMdc/azygous control (red)	1.10871	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97393	0.393

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16741	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.2746	0.105
Manapal/WT (break)	0.74254	1
Manapal/WT (red)	1.24699	0.137