Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.6.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83533	0.405
27DAP/17DAP	0.86634	0.674
39DAP/27DAP	1.24289	0.546
41DAP/39DAP	1.23897	0.758
42DAP/41DAP	0.95254	1
43DAP/42DAP	1.0751	0.937
47DAP/43DAP	1.34711	0.173
52DAP/47DAP	0.83854	0.554
57DAP/52DAP	1.15642	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97751	0.55
17DAP/reference	0.90953	0.321
27DAP/reference	0.75415	0.027
39DAP/reference	0.94568	0.527
41DAP/reference	0.80605	0.039
42DAP/reference	1.4377	0.001
43DAP/reference	1.05654	0.403
47DAP/reference	1.12155	0.071
52DAP/reference	1.03225	0.84
57DAP/reference	1.19296	0.122

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92795	0.509
27DAP/17DAP	0.76723	0.446
39DAP/27DAP	1.00103	1
41DAP/39DAP	1.02604	1
42DAP/41DAP	0.83682	0.362
43DAP/42DAP	0.99942	0.902
47DAP/43DAP	0.90125	0.637
52DAP/47DAP	1.5123	0.249
57DAP/52DAP	1.114	0.992
57DAP/7DAP	1.00951	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84394	0.183
17DAP/reference	0.83911	0.167
27DAP/reference	0.84307	0.117
39DAP/reference	1.13174	0.133
41DAP/reference	0.88013	0.153
42DAP/reference	0.99101	0.506
43DAP/reference	0.94315	0.385
47DAP/reference	1.18296	0.525
52DAP/reference	0.94674	0.477
57DAP/reference	0.88083	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95918	0.592
17DAP/reference	0.99416	0.673
27DAP/reference	1.08177	0.427
39DAP/reference	1.21026	0.175
41DAP/reference	1.22528	0.007
42DAP/reference	1.27664	0.037
43DAP/reference	1.08496	0.875
47DAP/reference	1.4023	0.01
52DAP/reference	1.05627	1
57DAP/reference	1.20988	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8804	0.362
17DAP/reference	0.8548	0.313
27DAP/reference	0.74626	0.119
39DAP/reference	1.12927	0.245
41DAP/reference	0.98057	0.618
42DAP/reference	1.02909	0.789
43DAP/reference	0.96203	0.568
47DAP/reference	0.94285	0.421
52DAP/reference	0.8069	0.208
57DAP/reference	1.38887	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19292	0.966
26DAP/20DAP	0.86197	0.512
34DAP/26DAP	0.91448	0.857
51DAP/34DAP	0.90632	0.587
52DAP/51DAP	1.50321	0.288
53DAP/52DAP	0.93918	0.811
55DAP/53DAP	1.44769	0.415
57DAP/55DAP	0.92155	0.78
62DAP/57DAP	1.14941
68DAP/62DAP	0.76917	0.747
68DAP/14DAP	2.0557	0.074

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.62118	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.48526	0.058
Mature Green Tomato/Ripe Tomato	2.49866
Immature Eggplant/Mature Eggplant	0.87701	0.292
Ripe Pepper/Ripe Tomato	0.55259
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	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.86694	0.33
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	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	0.88306
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	1.19173	0.277
IL2-6/WTpooled	1.18609	0.584
IL7-5/WTpooled	0.8953	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.90843	1
IL1-4/WTpooled	1.0934	1
WT/WTpooled	1.10057	0.911

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	0.91084	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94719	1
DC3000/delta hrp 6h	0.91049	0.95
DC3000/delta hrp 12h	0.93535	1
DC3000/delta hrp 24h	0.90176	0.269

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88861	0.691
DC3000 delta B/DC3000 delta AB	0.84727	0.172

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00288	1
Exp 36h	1.12489	0.371
Exp 60h	1.18044	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98384	1
Var 0h	0.96449	1
Var 12h I row2-row1	0.92468	0.565
Var 12h NI row2-row1	1.07352	1
Var 36h I row2-row1	1.09739	1
Var 36h NI row2-row1	0.80064	1
Var 60h I row2-row1	1.07671	0.562
Var 60h NI row2-row1	1.02092	1
Time course 0hI-0hNI	0.84036	0.161
Time course 12hI-12hNI	0.9628	0.752
Time course 36hI-36hNI	0.96876	0.441
Time course 60hI-60hNI	0.40678	0.006

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)	1.03736	0.571
transgenic ySAMdc/azygous control (breaker)	1.01717	1
transgenic ySAMdc/azygous control (red)	0.94856	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01396	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12069	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79201	1
Manapal/WT (break)	0.91549	0.333
Manapal/WT (red)	0.89487	0.36