Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.1.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.60902	0.134
27DAP/17DAP	0.68161	0.184
39DAP/27DAP	0.65019	0.326
41DAP/39DAP	0.80079	0.291
42DAP/41DAP	0.79041	0.774
43DAP/42DAP	1.78047	0.527
47DAP/43DAP	0.65887	0.156
52DAP/47DAP	0.9059	0.712
57DAP/52DAP	1.20531	0.892

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79262	0.068
17DAP/reference	0.62417	0.014
27DAP/reference	1.0557	0.867
39DAP/reference	0.74884	0.058
41DAP/reference	0.55245	0.011
42DAP/reference	1.13167	0.609
43DAP/reference	1.11877	0.425
47DAP/reference	1.03727	0.535
52DAP/reference	1.63484	0.038
57DAP/reference	1.8258	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07471	0.515
27DAP/17DAP	1.03279	0.957
39DAP/27DAP	0.42415	0.029
41DAP/39DAP	1.40587	0.096
42DAP/41DAP	0.83408	0.108
43DAP/42DAP	0.63111	0.026
47DAP/43DAP	1.00124	0.971
52DAP/47DAP	1.0718	0.915
57DAP/52DAP	1.35994	0.154
57DAP/7DAP	0.75629	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.05643	0.031
17DAP/reference	3.50992	0.006
27DAP/reference	2.54089	0.006
39DAP/reference	3.29116	0.005
41DAP/reference	3.46753	0.019
42DAP/reference	3.50803	0.006
43DAP/reference	4.29569	0.006
47DAP/reference	1.72651	0.311
52DAP/reference	3.08494	0.008
57DAP/reference	2.30233	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.48064	0.008
17DAP/reference	0.51322	0.006
27DAP/reference	1.01876	0.711
39DAP/reference	1.06256	1
41DAP/reference	1.14157	0.099
42DAP/reference	1.08378	0.422
43DAP/reference	0.49021	0.013
47DAP/reference	0.80159	0.038
52DAP/reference	0.76624	0.004
57DAP/reference	0.3562	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.59618	0.037
17DAP/reference	1.87116	0.572
27DAP/reference	5.49546	0.021
39DAP/reference	3.4233	0.027
41DAP/reference	3.81402	0.008
42DAP/reference	3.3172	0.006
43DAP/reference	3.59403	0.008
47DAP/reference	1.04976	0.754
52DAP/reference	3.37823	0.15
57DAP/reference	3.47441	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25386	0.966
26DAP/20DAP	0.91153	1
34DAP/26DAP	1.1737	1
51DAP/34DAP	0.72769	0.06
52DAP/51DAP	1.49246	0.034
53DAP/52DAP	0.88636	0.544
55DAP/53DAP	0.81332	0.21
57DAP/55DAP	0.49699	0.032
62DAP/57DAP	2.09933	0.034
68DAP/62DAP	11.6149	0.107
68DAP/14DAP	17.0915	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.21482	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.93165	0.058
Mature Green Tomato/Ripe Tomato	23.6845	0.016
Immature Eggplant/Mature Eggplant	0.41349	0.062
Ripe Pepper/Ripe Tomato	1.14533	1
Mature Eggplant/Ripe Tomato	1.33035	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.92532
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	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.91795
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	0.8812	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.74974
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03739	1
IL2-6/WTpooled	1.05062	0.531
IL7-5/WTpooled	0.79164
IL7-3/WTpooled	1.0082	1
IL12-4/WTpooled	1.06974	0.891
IL1-4/WTpooled	1.04546	1
WT/WTpooled	0.95358	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	1.07696	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95093	1
DC3000/delta hrp 6h	1.15316	1
DC3000/delta hrp 12h	0.53496	1
DC3000/delta hrp 24h	0.49669	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56906	0.023
DC3000 delta B/DC3000 delta AB	0.58259	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95154	1
Exp 36h	0.89127	0.623
Exp 60h	0.77538	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94095
Var 0h	1.02978	0.98
Var 12h I row2-row1	0.67726	0.353
Var 12h NI row2-row1	1.14279	0.649
Var 36h I row2-row1	1.7681	0.908
Var 36h NI row2-row1	1.40834	1
Var 60h I row2-row1	1.0502
Var 60h NI row2-row1	1.0891	1
Time course 0hI-0hNI	0.97259	0.886
Time course 12hI-12hNI	0.90944	0.47
Time course 36hI-36hNI	0.86944	0.081
Time course 60hI-60hNI	0.10883	0.005

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)	1.31347	0.253
transgenic ySAMdc/azygous control (breaker)	1.80213	0.248
transgenic ySAMdc/azygous control (red)	1.323	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99337	0.673

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.05295	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.06278	0.088
Manapal/WT (break)	8.5982	0.13
Manapal/WT (red)	16.6941	0.142