Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.13.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21609	0.575
27DAP/17DAP	1.11309	0.845
39DAP/27DAP	1.82359	0.173
41DAP/39DAP	1.0684	0.914
42DAP/41DAP	0.73482	0.774
43DAP/42DAP	1.14318	1
47DAP/43DAP	0.74345	0.263
52DAP/47DAP	1.65063	0.278
57DAP/52DAP	1.06982	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90776	0.254
17DAP/reference	0.88679	0.298
27DAP/reference	0.9689	0.567
39DAP/reference	0.9878	0.855
41DAP/reference	0.95565	0.434
42DAP/reference	1.13943	0.016
43DAP/reference	1.11225	0.019
47DAP/reference	0.94555	0.116
52DAP/reference	0.99239	0.668
57DAP/reference	0.9806	0.526

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84517	0.185
27DAP/17DAP	0.97993	0.887
39DAP/27DAP	1.14191	0.308
41DAP/39DAP	0.97612	0.98
42DAP/41DAP	1.27661	0.065
43DAP/42DAP	1.0352	0.192
47DAP/43DAP	1.08991	0.681
52DAP/47DAP	0.82669	0.161
57DAP/52DAP	1.09361	0.434
57DAP/7DAP	1.16517	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29079	0.041
17DAP/reference	1.049	0.102
27DAP/reference	1.26673	0.008
39DAP/reference	1.08249	0.024
41DAP/reference	1.2262	0.022
42DAP/reference	1.64767	0.008
43DAP/reference	2.05605	0.007
47DAP/reference	1.74476	0.017
52DAP/reference	1.7166	0.009
57DAP/reference	1.07301	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0208	0.894
17DAP/reference	0.883	0.08
27DAP/reference	1.16735	0.068
39DAP/reference	0.92137	0.069
41DAP/reference	0.99892	0.666
42DAP/reference	0.98753	0.655
43DAP/reference	0.833	0.016
47DAP/reference	0.87154	0.062
52DAP/reference	0.68422	0.004
57DAP/reference	0.66327	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09291	0.366
17DAP/reference	0.85627	0.028
27DAP/reference	1.11482	0.227
39DAP/reference	1.38977	0.019
41DAP/reference	1.15391	0.022
42DAP/reference	1.6627	0.009
43DAP/reference	1.54455	0.01
47DAP/reference	0.86274	0.011
52DAP/reference	1.21727	0.398
57DAP/reference	1.0174	0.954

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97729	1
26DAP/20DAP	1.09094	0.727
34DAP/26DAP	0.94532	0.606
51DAP/34DAP	1.27677	0.051
52DAP/51DAP	0.93903	0.151
53DAP/52DAP	1.06612	0.768
55DAP/53DAP	0.9101	0.098
57DAP/55DAP	1.14376	0.764
62DAP/57DAP	0.90104	0.28
68DAP/62DAP	1.16959	0.353
68DAP/14DAP	1.52203	0.084

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.61074	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.72564	0.201
Mature Green Tomato/Ripe Tomato	0.75312	0.119
Immature Eggplant/Mature Eggplant	1.91787	0.05
Ripe Pepper/Ripe Tomato	0.54942	0.224
Mature Eggplant/Ripe Tomato	0.28977	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9931	1
1-1-2/M82	1.23543	0.972
12-2/M82	0.94421	0.955
12-4/M82	1.07405	1
1-3/M82	1.11155	0.479
2-1-1/M82	0.82365	0.565
2-1/M82	0.96492	1
2-6/M82	0.96317	1
3-2/M82	0.99955	1
4-1-1/M82	1.06639	1
4-1/M82	1.00408	1
4-3-2/M82	1.03786	1
4-3/M82	0.95066	0.72
5-3/M82	0.83613	1
6-2/M82	1.02423	1
6-3/M82	0.98397	0.916
7-1/M82	0.93162	0.803
7-2/M82	0.94473	0.881
9-3-2/M82	1.23669	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89832
IL2-6/WTpooled	1.18745	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88327	1
IL12-4/WTpooled	0.92848	1
IL1-4/WTpooled	1.1192	1
WT/WTpooled	1.04605	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	1.44896	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99106	1
DC3000/delta hrp 6h	0.89373	0.95
DC3000/delta hrp 12h	1.02957	1
DC3000/delta hrp 24h	1.02569	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07915	0.134
DC3000 delta B/DC3000 delta AB	1.07583	0.449

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14779	1
Exp 36h	1.33401	1
Exp 60h	1.19375	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98065	1
Var 0h	1.12059	0.594
Var 12h I row2-row1	1.06409	0.379
Var 12h NI row2-row1	1.02938	1
Var 36h I row2-row1	1.15094	1
Var 36h NI row2-row1	0.92589	0.61
Var 60h I row2-row1	1.17727	1
Var 60h NI row2-row1	1.08609	0.904
Time course 0hI-0hNI	1.1234	0.486
Time course 12hI-12hNI	1.0314	0.77
Time course 36hI-36hNI	0.98134	0.601
Time course 60hI-60hNI	1.97004	0.008

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)	1.22264	0.482
transgenic ySAMdc/azygous control (breaker)	0.93383	0.49
transgenic ySAMdc/azygous control (red)	1.06206	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.18874	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9787	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02789	1
Manapal/WT (break)	1.07419	0.183
Manapal/WT (red)	0.92142	0.315