Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.3.2.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.67329	0.198
27DAP/17DAP	1.14068	0.859
39DAP/27DAP	1.50541	0.17
41DAP/39DAP	0.63411	0.066
42DAP/41DAP	1.42154	0.353
43DAP/42DAP	0.90997	0.813
47DAP/43DAP	0.88224	0.609
52DAP/47DAP	0.89499	0.675
57DAP/52DAP	1.08278	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91644	0.205
17DAP/reference	0.93763	0.111
27DAP/reference	0.96171	0.484
39DAP/reference	0.92641	0.267
41DAP/reference	1.05459	0.48
42DAP/reference	0.92084	0.026
43DAP/reference	1.00093	1
47DAP/reference	0.89788	0.06
52DAP/reference	0.89457	0.167
57DAP/reference	0.96236	0.415

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.49186	0.036
27DAP/17DAP	1.24483	0.383
39DAP/27DAP	0.96855	0.784
41DAP/39DAP	1.14648	1
42DAP/41DAP	1.00032	0.845
43DAP/42DAP	0.90711	0.482
47DAP/43DAP	0.97885	0.896
52DAP/47DAP	1.04407	0.987
57DAP/52DAP	1.35863	0.104
57DAP/7DAP	1.80679	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68241	0.296
17DAP/reference	1.1421	0.147
27DAP/reference	1.04469	0.804
39DAP/reference	1.3922	0.066
41DAP/reference	1.13417	0.117
42DAP/reference	1.53722	0.024
43DAP/reference	1.12014	0.746
47DAP/reference	1.19863	0.331
52DAP/reference	1.20806	0.149
57DAP/reference	1.21463	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95956	0.623
17DAP/reference	0.86597	0.086
27DAP/reference	0.9642	0.501
39DAP/reference	1.11105	0.424
41DAP/reference	0.90459	0.188
42DAP/reference	0.85786	0.081
43DAP/reference	1.22885	0.466
47DAP/reference	0.93813	0.253
52DAP/reference	0.94021	0.327
57DAP/reference	0.97593	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81384	0.092
17DAP/reference	0.86842	0.115
27DAP/reference	0.96178	0.516
39DAP/reference	0.89878	0.222
41DAP/reference	0.84508	0.031
42DAP/reference	0.84861	0.22
43DAP/reference	0.85439	0.052
47DAP/reference	0.94295	0.371
52DAP/reference	3.33418	0.278
57DAP/reference	0.92667	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0942	0.966
26DAP/20DAP	1.52872	0.18
34DAP/26DAP	1.18752	0.819
51DAP/34DAP	0.8244	0.143
52DAP/51DAP	0.86063	1
53DAP/52DAP	1.0703	0.738
55DAP/53DAP	0.97385	0.796
57DAP/55DAP	1.19096	0.793
62DAP/57DAP	0.66546	N/A
68DAP/62DAP	0.82068	0.668
68DAP/14DAP	0.91243	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.1279	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78619	N/A
Mature Green Tomato/Ripe Tomato	1.39648	0.331
Immature Eggplant/Mature Eggplant	N/A	N/A
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	1.70576	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	0.98575	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	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	1.18286	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	1.05173	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80794	0.418
IL12-4/WTpooled	0.95696	1
IL1-4/WTpooled	1.28826	N/A
WT/WTpooled	1.01267	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	0.95802	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12019	0.846
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.16407	1
DC3000/delta hrp 24h	0.95668	0.711

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31415	0.145
DC3000 delta B/DC3000 delta AB	1.14326	0.335

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88897	1
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	1.00296	1
Var 0h	0.97895	1
Var 12h I row2-row1	1.05567	0.692
Var 12h NI row2-row1	1.12688	0.34
Var 36h I row2-row1	1.07938	1
Var 36h NI row2-row1	1.49467	0.482
Var 60h I row2-row1	0.86959	0.439
Var 60h NI row2-row1	0.94238	1
Time course 0hI-0hNI	1.05497	0.764
Time course 12hI-12hNI	0.94742	0.606
Time course 36hI-36hNI	1.02425	0.975
Time course 60hI-60hNI	1.09166	0.216

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)	1.0913	0.921
transgenic ySAMdc/azygous control (breaker)	1.11912	1
transgenic ySAMdc/azygous control (red)	1.1827	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98314	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13141	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1752	0.14
Manapal/WT (break)	1.19697	0.183
Manapal/WT (red)	0.88237	0.229