Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72905	0.128
27DAP/17DAP	1.24482	0.793
39DAP/27DAP	1.17733	0.702
41DAP/39DAP	1.12708	0.949
42DAP/41DAP	0.96351	1
43DAP/42DAP	1.24187	0.698
47DAP/43DAP	1.40198	0.52
52DAP/47DAP	1.21272	0.953
57DAP/52DAP	1.36952	0.568

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87993	0.159
17DAP/reference	0.8035	0.158
27DAP/reference	0.84289	0.018
39DAP/reference	0.86937	0.381
41DAP/reference	0.95492	0.667
42DAP/reference	0.79556	0.052
43DAP/reference	0.92885	0.464
47DAP/reference	0.86858	0.09
52DAP/reference	0.95579	0.438
57DAP/reference	0.69452	0.065

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80783	0.228
27DAP/17DAP	1.7167	0.028
39DAP/27DAP	0.76685	0.066
41DAP/39DAP	0.95737	0.885
42DAP/41DAP	1.0496	0.927
43DAP/42DAP	0.58153	0.028
47DAP/43DAP	1.18405	0.508
52DAP/47DAP	0.80723	0.096
57DAP/52DAP	1.29344	0.279
57DAP/7DAP	1.20005	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01291	1
17DAP/reference	1.05301	0.399
27DAP/reference	1.14736	0.131
39DAP/reference	1.09302	0.511
41DAP/reference	0.95829	0.431
42DAP/reference	1.03394	0.889
43DAP/reference	1.0506	0.603
47DAP/reference	0.96321	0.671
52DAP/reference	1.07457	0.636
57DAP/reference	1.05452	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95165	0.592
17DAP/reference	0.72324	0.007
27DAP/reference	0.95926	0.438
39DAP/reference	0.97223	0.442
41DAP/reference	1.06318	0.599
42DAP/reference	0.93469	0.189
43DAP/reference	0.7302	0.028
47DAP/reference	0.82318	0.021
52DAP/reference	1.02757	0.761
57DAP/reference	0.67358	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07696	0.408
17DAP/reference	0.92915	0.389
27DAP/reference	1.03893	0.903
39DAP/reference	1.00455	0.889
41DAP/reference	1.00425	0.826
42DAP/reference	1.1336	0.34
43DAP/reference	1.06312	0.949
47DAP/reference	0.84686	0.114
52DAP/reference	0.87747	0.228
57DAP/reference	1.76392	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99907	1
26DAP/20DAP	1.06487	1
34DAP/26DAP	1.0168	1
51DAP/34DAP	1.55348	0.137
52DAP/51DAP	1.1356	0.689
53DAP/52DAP	0.63449	0.122
55DAP/53DAP	0.91066	0.686
57DAP/55DAP	0.8107	0.527
62DAP/57DAP	1.81199	0.902
68DAP/62DAP	7.94147	0.053
68DAP/14DAP	5.30717	0.057

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72636	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	12.3169	1
Mature Green Tomato/Ripe Tomato	1.77349	0.044
Immature Eggplant/Mature Eggplant	43.1747	0.05
Ripe Pepper/Ripe Tomato	3.84855	1
Mature Eggplant/Ripe Tomato	1.09377	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.21709
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	1.01439
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11297	0.277
IL2-6/WTpooled	1.14112	0.531
IL7-5/WTpooled	1.09432	0.792
IL7-3/WTpooled	1.25408	1
IL12-4/WTpooled	0.95728	0.71
IL1-4/WTpooled	1.2535	0.426
WT/WTpooled	1.04355	0.999

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	0.95436	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07494	0.921
DC3000/delta hrp 6h	1.25768	1
DC3000/delta hrp 12h	1.03424	1
DC3000/delta hrp 24h	0.5117	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.40987
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93857	1
Exp 36h	0.5309	0.197
Exp 60h	0.48253	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98856	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.88993
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	0.99075	1
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	0.93171	0.692
Time course 12hI-12hNI	0.72459	0.033
Time course 36hI-36hNI	0.73756	0.044
Time course 60hI-60hNI	0.35416	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)	1.08964	0.297
transgenic ySAMdc/azygous control (breaker)	0.46287	0.129
transgenic ySAMdc/azygous control (red)	0.89573	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04755	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7462	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.62637	0.172
Manapal/WT (break)	0.90615	1
Manapal/WT (red)	1.01656	0.863