Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.14.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94449	0.664
27DAP/17DAP	1.05175	0.932
39DAP/27DAP	0.93061	0.641
41DAP/39DAP	0.98914	0.967
42DAP/41DAP	1.25626	0.481
43DAP/42DAP	1.09434	0.937
47DAP/43DAP	0.89058	0.613
52DAP/47DAP	1.53863	0.308
57DAP/52DAP	1.23837	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74241	0.03
17DAP/reference	0.87943	0.169
27DAP/reference	0.9056	0.327
39DAP/reference	0.84171	0.114
41DAP/reference	0.73984	0.01
42DAP/reference	0.85307	0.01
43DAP/reference	0.92873	0.302
47DAP/reference	0.94985	0.207
52DAP/reference	0.91255	0.25
57DAP/reference	1.08585	0.159

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.52327	0.431
27DAP/17DAP	1.16522	0.909
39DAP/27DAP	0.93381	0.703
41DAP/39DAP	1.18367	0.417
42DAP/41DAP	0.99065	0.62
43DAP/42DAP	1.02294	1
47DAP/43DAP	1.15671	0.865
52DAP/47DAP	1.04218	0.899
57DAP/52DAP	1.49066	0.584
57DAP/7DAP	1.22256

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86858	0.138
17DAP/reference	0.85582	0.108
27DAP/reference	1.00157	0.8
39DAP/reference	0.80579	0.095
41DAP/reference	0.67685	0.058
42DAP/reference	0.71351	0.053
43DAP/reference	0.88737	0.22
47DAP/reference	0.83209	0.293
52DAP/reference	0.95075	0.332
57DAP/reference	0.88308	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.015	0.951
17DAP/reference	0.83551	0.083
27DAP/reference	0.88098	0.167
39DAP/reference	0.84519	0.189
41DAP/reference	0.84524	0.068
42DAP/reference	0.77187	0.016
43DAP/reference	0.88774	0.307
47DAP/reference	0.7914	0.014
52DAP/reference	0.86526	0.025
57DAP/reference	0.63553	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15677	0.287
17DAP/reference	0.85104	0.118
27DAP/reference	1.33364	0.271
39DAP/reference	0.85332	0.012
41DAP/reference	0.95577	0.512
42DAP/reference	0.91786	0.22
43DAP/reference	0.80056	0.024
47DAP/reference	0.84407	0.08
52DAP/reference	0.98828	0.718
57DAP/reference	0.99534	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94592	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.98964	0.945
51DAP/34DAP	1.12352	0.927
52DAP/51DAP	0.76468	1
53DAP/52DAP	0.91147	0.817
55DAP/53DAP	1.00473	0.951
57DAP/55DAP	0.53746	0.219
62DAP/57DAP	1.24215	0.868
68DAP/62DAP	1.24797	1
68DAP/14DAP	2.17624

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.816

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.41675
Immature Eggplant/Mature Eggplant	0.62525
Ripe Pepper/Ripe Tomato	0.3933
Mature Eggplant/Ripe Tomato	0.86969	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.36037
1-1-2/M82	1.0341	1
12-2/M82	0.98967	1
12-4/M82	0.99496
1-3/M82	N/A	N/A
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	1.03756
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.04617	1
5-3/M82	1.11018	1
6-2/M82	0.98001
6-3/M82	1.17554	1
7-1/M82	1.05323
7-2/M82	1.04285
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.73255	0.247
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.02426	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.95165	0.834
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	0.87207	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11706	0.692
DC3000/delta hrp 6h	1.01992	0.95
DC3000/delta hrp 12h	0.90362	1
DC3000/delta hrp 24h	0.88186	0.33

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96803	1
DC3000 delta B/DC3000 delta AB	0.76873	0.369

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84071	0.328
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03926	1
Var 0h	0.52615	1
Var 12h I row2-row1	0.90808	0.627
Var 12h NI row2-row1	0.64196	0.627
Var 36h I row2-row1	0.91845	1
Var 36h NI row2-row1	0.71527	0.549
Var 60h I row2-row1	1.0291	0.562
Var 60h NI row2-row1	1.08763	0.904
Time course 0hI-0hNI	1.04663	1
Time course 12hI-12hNI	0.99667	1
Time course 36hI-36hNI	1.05083	0.89
Time course 60hI-60hNI	0.54802	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)	1.02731	0.571
transgenic ySAMdc/azygous control (breaker)	0.92632	0.49
transgenic ySAMdc/azygous control (red)	0.90081	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.37238	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78911	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85957	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.05127	1