Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.7.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07625	0.838
27DAP/17DAP	1.11858	0.849
39DAP/27DAP	1.01701	0.876
41DAP/39DAP	0.90457	0.602
42DAP/41DAP	0.94965	1
43DAP/42DAP	1.08196	0.982
47DAP/43DAP	1.10385	0.756
52DAP/47DAP	0.84498	0.574
57DAP/52DAP	1.00833	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84783	0.039
17DAP/reference	0.9414	0.448
27DAP/reference	0.89258	0.073
39DAP/reference	0.94143	0.475
41DAP/reference	0.83212	0.049
42DAP/reference	0.95179	0.176
43DAP/reference	0.9431	0.464
47DAP/reference	1.03839	0.728
52DAP/reference	0.9786	0.515
57DAP/reference	1.22826	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.53008	0.105
27DAP/17DAP	1.21643	0.65
39DAP/27DAP	1.0208	1
41DAP/39DAP	1.25355	0.096
42DAP/41DAP	1.04665	0.853
43DAP/42DAP	0.83779	0.206
47DAP/43DAP	1.39956	0.376
52DAP/47DAP	0.93736	0.729
57DAP/52DAP	1.33404	0.895
57DAP/7DAP	2.31414	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73999	0.108
17DAP/reference	0.87498	0.167
27DAP/reference	0.93758	0.325
39DAP/reference	0.94717	0.354
41DAP/reference	0.90176	0.213
42DAP/reference	0.80972	0.013
43DAP/reference	1.06654	1
47DAP/reference	0.99811	1
52DAP/reference	1.12634	0.159
57DAP/reference	1.05074	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87511	0.19
17DAP/reference	0.93508	0.269
27DAP/reference	1.06468	0.847
39DAP/reference	1.10428	0.213
41DAP/reference	1.03573	0.814
42DAP/reference	0.89966	0.189
43DAP/reference	0.93556	0.32
47DAP/reference	0.84726	0.033
52DAP/reference	1.07329	0.444
57DAP/reference	0.84436	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86789	0.158
17DAP/reference	0.94261	0.488
27DAP/reference	1.08552	0.531
39DAP/reference	1.55676	0.406
41DAP/reference	0.87853	0.027
42DAP/reference	0.9674	0.552
43DAP/reference	0.76523	0.035
47DAP/reference	0.96302	0.434
52DAP/reference	1.52709	0.631
57DAP/reference	0.89696	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01131	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.94511
51DAP/34DAP	0.85401	0.618
52DAP/51DAP	0.84392	0.151
53DAP/52DAP	0.9171	0.732
55DAP/53DAP	0.93889	0.735
57DAP/55DAP	0.59551	0.046
62DAP/57DAP	1.73438	0.833
68DAP/62DAP	1.03245
68DAP/14DAP	1.49096	0.223

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16087	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.83831	0.317
Immature Eggplant/Mature Eggplant	0.65762
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	1.14653
12-2/M82	N/A	N/A
12-4/M82	0.8315
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	0.96412
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.72688	0.698
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	0.86435	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.74635	0.321
IL2-6/WTpooled	0.91433	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89141	1
IL12-4/WTpooled	0.92928	1
IL1-4/WTpooled	0.94283	0.834
WT/WTpooled	0.96378	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	0.94764	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17404	0.921
DC3000/delta hrp 6h	1.34446	1
DC3000/delta hrp 12h	1.11359	1
DC3000/delta hrp 24h	0.79128	0.065

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.693	1
Exp 36h	0.88249	0.943
Exp 60h	0.7134	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.20456	1
Var 0h	1.51025	0.421
Var 12h I row2-row1	1.10135	0.692
Var 12h NI row2-row1	1.05857	0.649
Var 36h I row2-row1	0.91522	0.805
Var 36h NI row2-row1	1.23458	1
Var 60h I row2-row1	0.83935	0.582
Var 60h NI row2-row1	1.04101	1
Time course 0hI-0hNI	0.86097	0.256
Time course 12hI-12hNI	1.05605	0.876
Time course 36hI-36hNI	0.72093	0.023
Time course 60hI-60hNI	0.63738	0.026

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)	1.00297	1
transgenic ySAMdc/azygous control (breaker)	0.80118	0.15
transgenic ySAMdc/azygous control (red)	1.27488	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09141	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0961	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7777	0.172
Manapal/WT (break)	1.04379	1
Manapal/WT (red)	1.15528	0.222