Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16113	0.671
27DAP/17DAP	0.9509	0.947
39DAP/27DAP	0.88242	0.573
41DAP/39DAP	0.76996	0.303
42DAP/41DAP	1.10586	0.978
43DAP/42DAP	1.20895	0.861
47DAP/43DAP	1.34453	0.42
52DAP/47DAP	1.28297	0.633
57DAP/52DAP	1.15787	0.843

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78091	0.063
17DAP/reference	0.93503	0.26
27DAP/reference	0.93733	0.385
39DAP/reference	0.89801	0.078
41DAP/reference	0.74954	0.009
42DAP/reference	0.86734	0.014
43DAP/reference	0.84595	0.015
47DAP/reference	0.93655	0.077
52DAP/reference	1.05965	0.272
57DAP/reference	0.93733	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84566	0.238
27DAP/17DAP	0.9637	0.878
39DAP/27DAP	1.55671	0.285
41DAP/39DAP	1.00079	1
42DAP/41DAP	1.00707	0.795
43DAP/42DAP	0.7283	0.093
47DAP/43DAP	0.97395	0.886
52DAP/47DAP	3.2075	0.036
57DAP/52DAP	2.6659	0.044
57DAP/7DAP	5.22977	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07975	0.705
17DAP/reference	1.17168	0.822
27DAP/reference	1.11259	0.974
39DAP/reference	1.38359	0.008
41DAP/reference	1.38506	0.207
42DAP/reference	1.3223	0.076
43DAP/reference	0.94098	0.22
47DAP/reference	0.95615	0.504
52DAP/reference	0.94694	0.477
57DAP/reference	1.16926	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71653	0.009
17DAP/reference	0.7218	0.005
27DAP/reference	0.78514	0.037
39DAP/reference	0.89177	0.189
41DAP/reference	0.91794	0.137
42DAP/reference	0.83638	0.023
43DAP/reference	0.74805	0.044
47DAP/reference	0.8362	0.011
52DAP/reference	0.87397	0.043
57DAP/reference	0.8945	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94191	0.362
17DAP/reference	0.80612	0.255
27DAP/reference	1.19944	0.408
39DAP/reference	1.21652	0.365
41DAP/reference	0.886	0.331
42DAP/reference	0.78	0.134
43DAP/reference	1.14354	0.599
47DAP/reference	1.01554	1
52DAP/reference	1.21088	0.674
57DAP/reference	0.9464	0.424

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92538	1
26DAP/20DAP	3.16851	0.421
34DAP/26DAP	3.50538	1
51DAP/34DAP	1.43642	0.993
52DAP/51DAP	5.35586	0.033
53DAP/52DAP	0.55722	0.063
55DAP/53DAP	1.63788	0.062
57DAP/55DAP	0.51082	0.046
62DAP/57DAP	1.09496	0.767
68DAP/62DAP	1.25823	1
68DAP/14DAP	1.80961	0.131

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.18878	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.28867
Mature Eggplant/Ripe Tomato	0.98677

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	0.95641
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.0863	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.93032	1
IL12-4/WTpooled	0.85206	0.71
IL1-4/WTpooled	1.10897
WT/WTpooled	1.05071	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	0.84822	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.27822	1
DC3000/delta hrp 12h	1.36306	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95232	0.691
DC3000 delta B/DC3000 delta AB	0.91041	0.183

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96802	1
Exp 36h	1.2714	1
Exp 60h	0.91543	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99899	1
Var 0h	0.92357	1
Var 12h I row2-row1	0.86059	0.514
Var 12h NI row2-row1	0.97882	0.906
Var 36h I row2-row1	1.06056	0.489
Var 36h NI row2-row1	1.32446	1
Var 60h I row2-row1	1.14029	0.562
Var 60h NI row2-row1	1.00991	1
Time course 0hI-0hNI	1.02487	0.852
Time course 12hI-12hNI	1.01657	0.833
Time course 36hI-36hNI	0.9938	0.718
Time course 60hI-60hNI	0.83268	0.011

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)	0.95054	0.338
transgenic ySAMdc/azygous control (breaker)	1.16314	0.178
transgenic ySAMdc/azygous control (red)	1.02885	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07127	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94339	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20307	0.307
Manapal/WT (break)	1.35394	0.183
Manapal/WT (red)	1.00378	1