Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.10.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98914	0.876
27DAP/17DAP	0.95255	0.928
39DAP/27DAP	0.76193	0.392
41DAP/39DAP	1.36232	0.268
42DAP/41DAP	1.02586	1
43DAP/42DAP	0.86843	0.713
47DAP/43DAP	1.00023	0.972
52DAP/47DAP	1.18821	0.645
57DAP/52DAP	0.96707	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89157	0.145
17DAP/reference	1.04483	0.476
27DAP/reference	1.04488	0.735
39DAP/reference	1.10211	0.153
41DAP/reference	1.04757	0.552
42DAP/reference	0.86846	0.006
43DAP/reference	0.97398	0.675
47DAP/reference	0.95315	0.161
52DAP/reference	0.76786	0.115
57DAP/reference	0.8494	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96397	0.542
27DAP/17DAP	0.98684	0.919
39DAP/27DAP	1.09315	0.394
41DAP/39DAP	1.04168	0.861
42DAP/41DAP	1.00796	1
43DAP/42DAP	1.03405	0.585
47DAP/43DAP	0.98816	0.928
52DAP/47DAP	1.08138	0.789
57DAP/52DAP	1.03812	0.768
57DAP/7DAP	1.13467	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86075	0.073
17DAP/reference	0.90754	0.011
27DAP/reference	0.92186	0.011
39DAP/reference	0.9777	0.354
41DAP/reference	0.98531	0.449
42DAP/reference	0.95652	0.211
43DAP/reference	0.97017	0.403
47DAP/reference	0.85157	0.168
52DAP/reference	1.08359	0.459
57DAP/reference	1.04895	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99856	0.93
17DAP/reference	0.97549	0.499
27DAP/reference	0.78137	0.081
39DAP/reference	0.84221	0.173
41DAP/reference	0.74494	0.04
42DAP/reference	0.88493	0.237
43DAP/reference	0.91664	0.157
47DAP/reference	1.02017	0.833
52DAP/reference	0.90846	0.037
57DAP/reference	1.10666	0.193

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88917	0.038
17DAP/reference	0.93153	0.407
27DAP/reference	0.94139	0.089
39DAP/reference	0.90947	0.012
41DAP/reference	0.90368	0.167
42DAP/reference	0.73833	0.087
43DAP/reference	0.79222	0.137
47DAP/reference	0.88437	0.199
52DAP/reference	0.84372	0.116
57DAP/reference	0.54184	0.036

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99589	1
26DAP/20DAP	0.91288	0.113
34DAP/26DAP	1.01141	1
51DAP/34DAP	0.93468	0.522
52DAP/51DAP	1.00563	0.939
53DAP/52DAP	1.05099	0.783
55DAP/53DAP	1.00509	1
57DAP/55DAP	1.12899	0.666
62DAP/57DAP	1.11195	0.833
68DAP/62DAP	1.15431	0.912
68DAP/14DAP	0.94365	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02808	0.782

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.06416	0.948
Immature Eggplant/Mature Eggplant	0.96584
Ripe Pepper/Ripe Tomato	1.34539
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05773	1
1-1-2/M82	1.02857	1
12-2/M82	1.0557	1
12-4/M82	0.9568	1
1-3/M82	0.81288	0.441
2-1-1/M82	1.08313	0.764
2-1/M82	1.00462
2-6/M82	1.01097	1
3-2/M82	1.01218	1
4-1-1/M82	1.11097	1
4-1/M82	0.97866	1
4-3-2/M82	0.94029	1
4-3/M82	0.97554	1
5-3/M82	0.95179	1
6-2/M82	1.13101	1
6-3/M82	1.00526	1
7-1/M82	1.01407	1
7-2/M82	1.01243	1
9-3-2/M82	0.89944	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.57981
IL2-6/WTpooled	1.2776	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.77395	0.31
IL12-4/WTpooled	1.12817	0.695
IL1-4/WTpooled	1.12729	1
WT/WTpooled	0.94832	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	0.7006	0.216

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00413	1
DC3000/delta hrp 6h	1.00416	1
DC3000/delta hrp 12h	1.00306	1
DC3000/delta hrp 24h	0.97965	0.897

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9725	0.66
DC3000 delta B/DC3000 delta AB	1.06543	0.412

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81652	0.328
Exp 36h	0.81997	0.623
Exp 60h	1.18727	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99888	1
Var 0h	1.11778	1
Var 12h I row2-row1	0.98188	0.948
Var 12h NI row2-row1	0.98943	1
Var 36h I row2-row1	1.05748	0.908
Var 36h NI row2-row1	1.1136	0.276
Var 60h I row2-row1	1.2617	1
Var 60h NI row2-row1	1.06186	0.904
Time course 0hI-0hNI	1.001	1
Time course 12hI-12hNI	1.00295	0.892
Time course 36hI-36hNI	0.90227	0.081
Time course 60hI-60hNI	0.85347	0.081

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)	1.07729	0.654
transgenic ySAMdc/azygous control (breaker)	1.49431	0.161
transgenic ySAMdc/azygous control (red)	0.99886	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95568	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.54235	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.73768	0.083
Manapal/WT (break)	3.06626	0.123
Manapal/WT (red)	2.30563	0.222