Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.3.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02361	1
27DAP/17DAP	1.09442	1
39DAP/27DAP	1.54425	0.268
41DAP/39DAP	0.83169	0.362
42DAP/41DAP	1.2324	0.898
43DAP/42DAP	1.42655	0.894
47DAP/43DAP	0.51531	0.051
52DAP/47DAP	1.31952	0.601
57DAP/52DAP	1.20073	0.641

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04503	0.994
17DAP/reference	0.92994	0.448
27DAP/reference	1.02142	0.648
39DAP/reference	0.94554	0.6
41DAP/reference	0.93396	0.667
42DAP/reference	1.18212	0.004
43DAP/reference	0.99166
47DAP/reference	1.18646	0.031
52DAP/reference	1.00383	1
57DAP/reference	2.42342

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32456	0.284
27DAP/17DAP	1.09883	0.842
39DAP/27DAP	1.08767	0.698
41DAP/39DAP	1.0667	0.674
42DAP/41DAP	1.09904	0.893
43DAP/42DAP	N/A	N/A
47DAP/43DAP	0.86073	0.243
52DAP/47DAP	0.86057	0.433
57DAP/52DAP	1.00824	1
57DAP/7DAP	0.86886	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95001	0.104
17DAP/reference	0.96395	0.019
27DAP/reference	0.95973	0.058
39DAP/reference	0.9675	0.018
41DAP/reference	0.90522	0.025
42DAP/reference	0.96798	0.028
43DAP/reference	0.91626	0.027
47DAP/reference	1.05531	0.717
52DAP/reference	0.90971	0.027
57DAP/reference	0.96066	0.039

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04508	0.384
17DAP/reference	1.01816	0.557
27DAP/reference	1.03438	0.639
39DAP/reference	1.00764	1
41DAP/reference	0.96422	0.315
42DAP/reference	1.02789	0.73
43DAP/reference	0.94442	0.314
47DAP/reference	0.95353	0.049
52DAP/reference	1.11462	0.019
57DAP/reference	1.07902	0.131

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00537	1
17DAP/reference	1.00445	1
27DAP/reference	0.93989	0.218
39DAP/reference	0.97891	0.393
41DAP/reference	0.99325	0.682
42DAP/reference	1.06744	0.3
43DAP/reference	1.02645	0.688
47DAP/reference	1.10171	0.196
52DAP/reference	0.97476	0.675
57DAP/reference	1.00639	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83184	0.207
26DAP/20DAP	1.46796	0.379
34DAP/26DAP	0.89062	0.399
51DAP/34DAP	1.28721	0.105
52DAP/51DAP	0.99091	1
53DAP/52DAP	1.01022	0.944
55DAP/53DAP	0.83642	0.088
57DAP/55DAP	0.93603	0.715
62DAP/57DAP	1.12743	0.185
68DAP/62DAP	1.05525	0.808
68DAP/14DAP	1.01838	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.50761	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.55126	0.063
Mature Green Tomato/Ripe Tomato	1.65148	0.017
Immature Eggplant/Mature Eggplant	1.70723	0.05
Ripe Pepper/Ripe Tomato	0.21814	0.224
Mature Eggplant/Ripe Tomato	0.75357	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12687	0.591
1-1-2/M82	1.49571	1
12-2/M82	0.89586
12-4/M82	1.17628	1
1-3/M82	0.83488	0.378
2-1-1/M82	0.57128
2-1/M82	0.73182	0.322
2-6/M82	N/A	N/A
3-2/M82	1.16749	0.549
4-1-1/M82	0.89403
4-1/M82	3.88004	0.512
4-3-2/M82	2.00206	0.508
4-3/M82	1.123	1
5-3/M82	1.06905	1
6-2/M82	0.98339
6-3/M82	1.07673	1
7-1/M82	0.88733	1
7-2/M82	0.81183
9-3-2/M82	1.85973

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.47405	0.243
IL2-6/WTpooled	0.89086	1
IL7-5/WTpooled	0.90331	1
IL7-3/WTpooled	0.84727	0.31
IL12-4/WTpooled	0.70118	0.478
IL1-4/WTpooled	0.77733	0.476
WT/WTpooled	1.10651	0.87

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	1.08517	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93932	1
DC3000/delta hrp 6h	1.12886	1
DC3000/delta hrp 12h	1.03307	1
DC3000/delta hrp 24h	0.63343	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99733	1
DC3000 delta B/DC3000 delta AB	0.87354	0.203

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97727	1
Exp 36h	1.23424	0.693
Exp 60h	1.28153	0.399

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	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.9443	0.299
transgenic ySAMdc/azygous control (breaker)	0.89212	0.251
transgenic ySAMdc/azygous control (red)	1.44867	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07954	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.35442	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.22292	0.105
Manapal/WT (break)	1.01494	1
Manapal/WT (red)	1.04804	1