Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83591	0.331
27DAP/17DAP	1.75717	0.411
39DAP/27DAP	1.0045	0.719
41DAP/39DAP	0.68025	0.22
42DAP/41DAP	1.32039	0.752
43DAP/42DAP	0.90021	0.829
47DAP/43DAP	0.90348	0.591
52DAP/47DAP	1.63234	0.784
57DAP/52DAP	1.08756	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92703	0.224
17DAP/reference	0.7854	0.031
27DAP/reference	0.98056	0.61
39DAP/reference	0.87122	0.188
41DAP/reference	0.65818	0.011
42DAP/reference	0.8919	0.033
43DAP/reference	0.88286	0.129
47DAP/reference	0.89854	0.077
52DAP/reference	1.03924	0.548
57DAP/reference	1.09952	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80634	0.35
27DAP/17DAP	0.77764	0.508
39DAP/27DAP	1.10794	0.646
41DAP/39DAP	1.58195	0.034
42DAP/41DAP	0.6973	0.013
43DAP/42DAP	0.92007	0.538
47DAP/43DAP	1.13271	0.779
52DAP/47DAP	0.95383	0.893
57DAP/52DAP	1.30373	0.303
57DAP/7DAP	1.22766	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22581	0.157
17DAP/reference	1.50758	0.009
27DAP/reference	1.20602	0.017
39DAP/reference	1.49145	0.009
41DAP/reference	1.47657	0.021
42DAP/reference	1.40091	0.03
43DAP/reference	1.65244	0.021
47DAP/reference	1.1204	0.235
52DAP/reference	1.15514	0.197
57DAP/reference	1.3729	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85219	0.09
17DAP/reference	0.75779	0.017
27DAP/reference	0.8739	0.115
39DAP/reference	0.95215	0.404
41DAP/reference	1.19195	0.248
42DAP/reference	1.01002	0.723
43DAP/reference	0.62122	0.002
47DAP/reference	1.05578	0.675
52DAP/reference	0.88717	0.043
57DAP/reference	0.97817	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20463	0.196
17DAP/reference	1.21497	0.436
27DAP/reference	1.54587	0.023
39DAP/reference	1.41254	0.017
41DAP/reference	1.22913	0.168
42DAP/reference	1.25243	0.052
43DAP/reference	0.98342	0.639
47DAP/reference	0.94849	0.383
52DAP/reference	1.15181	0.724
57DAP/reference	1.0303	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17123	0.966
26DAP/20DAP	0.8631	1
34DAP/26DAP	0.92917	0.917
51DAP/34DAP	0.7379	0.193
52DAP/51DAP	1.35545	0.045
53DAP/52DAP	2.73237	0.37
55DAP/53DAP	0.89991	0.663
57DAP/55DAP	0.73847	0.318
62DAP/57DAP	1.07985	0.902
68DAP/62DAP	2.27066	0.041
68DAP/14DAP	1.29324	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.17273	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	5.1809	0.015
Immature Eggplant/Mature Eggplant	1.69005	0.053
Ripe Pepper/Ripe Tomato	0.36179
Mature Eggplant/Ripe Tomato	2.53375

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.83732
12-2/M82	N/A	N/A
12-4/M82	0.92921
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	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	1.48175
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.39194	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.90724	0.277
IL2-6/WTpooled	1.62436	0.395
IL7-5/WTpooled	7.58767	0.75
IL7-3/WTpooled	1.0888	1
IL12-4/WTpooled	1.84891	0.525
IL1-4/WTpooled	0.91773	1
WT/WTpooled	1.0078	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	1.14281	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15929	0.921
DC3000/delta hrp 6h	0.98555	0.95
DC3000/delta hrp 12h	1.13548	1
DC3000/delta hrp 24h	1.39923	0.031

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	3.00188

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00618	1
Exp 36h	1.59463	0.489
Exp 60h	1.5692	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03403	1
Var 0h	1.0581	0.98
Var 12h I row2-row1	1.34488	0.222
Var 12h NI row2-row1	1.56757	0.649
Var 36h I row2-row1	1.08038	0.601
Var 36h NI row2-row1	1.00835	1
Var 60h I row2-row1	0.80189	0.285
Var 60h NI row2-row1	0.93056	0.932
Time course 0hI-0hNI	1.21367	0.182
Time course 12hI-12hNI	2.20607	0.004
Time course 36hI-36hNI	2.78203	0.004
Time course 60hI-60hNI	9.78424	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)	1.19801	0.339
transgenic ySAMdc/azygous control (breaker)	0.52216	0.15
transgenic ySAMdc/azygous control (red)	0.8402	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93495	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74318	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.60519	0.14
Manapal/WT (break)	1.25128	1
Manapal/WT (red)	1.10811	1