Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.8.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09669	0.912
27DAP/17DAP	0.9849	1
39DAP/27DAP	0.88561	0.544
41DAP/39DAP	1.23239	0.339
42DAP/41DAP	0.89171	1
43DAP/42DAP	1.11509	1
47DAP/43DAP	1.11565	0.873
52DAP/47DAP	1.13804	0.897
57DAP/52DAP	0.96617	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9855	0.562
17DAP/reference	1.09124	0.033
27DAP/reference	1.00532	0.996
39DAP/reference	0.99904	1
41DAP/reference	1.08449	0.122
42DAP/reference	0.92324	0.004
43DAP/reference	1.03909	0.518
47DAP/reference	0.94464	0.055
52DAP/reference	0.9455	0.292
57DAP/reference	0.86119	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09487	0.264
27DAP/17DAP	0.88947	0.58
39DAP/27DAP	0.95258	0.668
41DAP/39DAP	1.01662	0.921
42DAP/41DAP	1.05943	0.893
43DAP/42DAP	0.83274	0.048
47DAP/43DAP	1.04205	0.812
52DAP/47DAP	1.16939	0.444
57DAP/52DAP	0.94279	0.608
57DAP/7DAP	1.19069	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2521	0.154
17DAP/reference	1.2782	0.023
27DAP/reference	1.21833	0.009
39DAP/reference	1.44267	0.006
41DAP/reference	1.36018	0.026
42DAP/reference	1.34093	0.024
43DAP/reference	1.26209	0.014
47DAP/reference	1.2604	0.272
52DAP/reference	1.36079	0.013
57DAP/reference	1.38652	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05001	0.569
17DAP/reference	1.03231	0.338
27DAP/reference	0.87372	0.097
39DAP/reference	0.86098	0.077
41DAP/reference	0.93558	0.34
42DAP/reference	0.87428	0.089
43DAP/reference	0.98319	0.67
47DAP/reference	0.90501	0.018
52DAP/reference	1.00159	1
57DAP/reference	1.23003	0.075

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05665	0.28
17DAP/reference	0.94161	0.407
27DAP/reference	1.05523	0.408
39DAP/reference	1.10392	0.125
41DAP/reference	0.88928	0.237
42DAP/reference	0.95331	0.552
43DAP/reference	1.06794	0.91
47DAP/reference	0.95937	0.452
52DAP/reference	1.22241	0.324
57DAP/reference	0.64198	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05963	0.966
26DAP/20DAP	0.82088	0.512
34DAP/26DAP	0.9484	0.874
51DAP/34DAP	1.21863	0.445
52DAP/51DAP	1.02779	0.954
53DAP/52DAP	0.87881	0.677
55DAP/53DAP	1.15067	0.576
57DAP/55DAP	1.02283	0.975
62DAP/57DAP	0.96115	0.681
68DAP/62DAP	1.06104	0.899
68DAP/14DAP	0.98689	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97998	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.35174	0.077
Mature Green Tomato/Ripe Tomato	0.70611	0.051
Immature Eggplant/Mature Eggplant	4.63794	0.05
Ripe Pepper/Ripe Tomato	0.86973	1
Mature Eggplant/Ripe Tomato	0.56089	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99313	1
1-1-2/M82	0.92771	0.754
12-2/M82	1.08542
12-4/M82	0.92268	1
1-3/M82	0.95332	0.501
2-1-1/M82	1.32121
2-1/M82	1.28369
2-6/M82	1.01908
3-2/M82	0.9287	1
4-1-1/M82	1.04466
4-1/M82	1.08945	1
4-3-2/M82	1.04163	1
4-3/M82	1.18422	0.268
5-3/M82	1.00698	1
6-2/M82	N/A	N/A
6-3/M82	0.92612	0.982
7-1/M82	1.02519
7-2/M82	1.11315	1
9-3-2/M82	0.93553	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02091	0.493
IL2-6/WTpooled	0.94132	1
IL7-5/WTpooled	1.03886	1
IL7-3/WTpooled	1.07329	1
IL12-4/WTpooled	0.95494	1
IL1-4/WTpooled	1.05513	0.426
WT/WTpooled	1.04414	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	1.03581	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96482	1
DC3000/delta hrp 6h	1.35627	1
DC3000/delta hrp 12h	1.15005	1
DC3000/delta hrp 24h	1.15584	0.088

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.74194	0.045
DC3000 delta B/DC3000 delta AB	0.75184	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.35836	1
Exp 36h	1.35137	0.693
Exp 60h	1.23673	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00265	1
Var 0h	0.98759	1
Var 12h I row2-row1	0.91058	0.363
Var 12h NI row2-row1	0.91541	0.627
Var 36h I row2-row1	1.02702	1
Var 36h NI row2-row1	1.18483	0.482
Var 60h I row2-row1	0.99631	1
Var 60h NI row2-row1	0.93371	1
Time course 0hI-0hNI	1.00004	1
Time course 12hI-12hNI	0.97942	0.847
Time course 36hI-36hNI	0.96773	0.389
Time course 60hI-60hNI	0.60116	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)	0.90462	0.314
transgenic ySAMdc/azygous control (breaker)	0.68452	0.142
transgenic ySAMdc/azygous control (red)	0.92883	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03604	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10011	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69543	1
Manapal/WT (break)	0.99034	1
Manapal/WT (red)	0.93174	0.607