Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.6.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9226	0.568
27DAP/17DAP	1.1053	0.849
39DAP/27DAP	3.06244	0.094
41DAP/39DAP	2.36883	0.193
42DAP/41DAP	2.7686	0.016
43DAP/42DAP	2.4217	0.724
47DAP/43DAP	0.88523	0.613
52DAP/47DAP	0.63491	0.149
57DAP/52DAP	1.70504	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55049	0.025
17DAP/reference	0.69289	0.007
27DAP/reference	0.71419	0.012
39DAP/reference	1.17349	0.734
41DAP/reference	0.90644	0.267
42DAP/reference	2.13099	0.001
43DAP/reference	2.74854	0.006
47DAP/reference	2.03514	0.002
52DAP/reference	1.04155	0.453
57DAP/reference	1.66153	0.097

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03923	1
27DAP/17DAP	1.27866	0.274
39DAP/27DAP	1.06333	0.751
41DAP/39DAP	0.8931	0.793
42DAP/41DAP	1.29336	0.795
43DAP/42DAP	1.62313	0.038
47DAP/43DAP	0.97262	0.877
52DAP/47DAP	1.03462	0.907
57DAP/52DAP	0.78478	0.213
57DAP/7DAP	0.95898	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70064	0.138
17DAP/reference	0.98318	0.599
27DAP/reference	1.22081	0.974
39DAP/reference	1.04066	1
41DAP/reference	1.15576	0.891
42DAP/reference	1.05313	1
43DAP/reference	1.17717	0.178
47DAP/reference	1.81009	0.021
52DAP/reference	0.9667	0.571
57DAP/reference	1.07425	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62021	0.012
17DAP/reference	0.54093	0.005
27DAP/reference	0.58042	0.01
39DAP/reference	0.61453	0.015
41DAP/reference	0.62795	0.024
42DAP/reference	0.57565	0.01
43DAP/reference	0.5383	0.004
47DAP/reference	0.7537	0.027
52DAP/reference	0.56179	0.003
57DAP/reference	0.76116	0.02

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00128	0.75
17DAP/reference	0.47773	0.045
27DAP/reference	1.07192	0.843
39DAP/reference	0.72717	0.271
41DAP/reference	1.02936	1
42DAP/reference	1.54424	0.424
43DAP/reference	2.02855	0.04
47DAP/reference	2.29843	0.006
52DAP/reference	2.12703	0.039
57DAP/reference	1.14075	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12076	0.966
26DAP/20DAP	0.89591	1
34DAP/26DAP	0.78345	0.606
51DAP/34DAP	1.03194	1
52DAP/51DAP	0.86297	1
53DAP/52DAP	1.16733	0.662
55DAP/53DAP	1.07285	0.982
57DAP/55DAP	1.35287	0.543
62DAP/57DAP	1.79642	0.303
68DAP/62DAP	0.95318	0.769
68DAP/14DAP	1.19724	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.78876	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.74297
Mature Green Tomato/Ripe Tomato	0.18305	0.02
Immature Eggplant/Mature Eggplant	3.30368
Ripe Pepper/Ripe Tomato	0.07326	0.224
Mature Eggplant/Ripe Tomato	0.02365

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.76486
12-2/M82	N/A	N/A
12-4/M82	1.9554	1
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	0.96036
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.55001
4-3-2/M82	1.33642
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
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	1.84337	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16232	0.277
IL2-6/WTpooled	1.29479	0.788
IL7-5/WTpooled	0.60676
IL7-3/WTpooled	0.83118	0.31
IL12-4/WTpooled	1.23592	0.891
IL1-4/WTpooled	0.76018	0.415
WT/WTpooled	1.0862	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02558	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.07655	1
DC3000/delta hrp 24h	0.63194	0.069

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	1.28954

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
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	N/A	N/A
Var 0h	1.10571	1
Var 12h I row2-row1	0.70088
Var 12h NI row2-row1	1.31036
Var 36h I row2-row1	1.02141	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	1.00923
Var 60h NI row2-row1	1.13294	0.904
Time course 0hI-0hNI	0.73046	0.352
Time course 12hI-12hNI	0.91435	0.39
Time course 36hI-36hNI	0.83931	0.148
Time course 60hI-60hNI	0.66627	0.009

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)	0.44031	0.213
transgenic ySAMdc/azygous control (breaker)	1.39032	0.248
transgenic ySAMdc/azygous control (red)	1.24763	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09971	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.38833	0.307
Manapal/WT (break)	0.55848	0.285
Manapal/WT (red)	0.50669	0.188