Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.14.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07326	0.77
27DAP/17DAP	1.00118	1
39DAP/27DAP	0.86847	0.435
41DAP/39DAP	1.4264	0.225
42DAP/41DAP	1.12254	0.899
43DAP/42DAP	0.87165	0.776
47DAP/43DAP	0.9685	0.851
52DAP/47DAP	1.19818	0.578
57DAP/52DAP	0.99654	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34381	0.024
17DAP/reference	1.34122	0.117
27DAP/reference	1.17124	0.067
39DAP/reference	1.12155	0.249
41DAP/reference	1.48377	0.019
42DAP/reference	1.34194	0.001
43DAP/reference	1.04009	0.758
47DAP/reference	1.21157	0.011
52DAP/reference	1.274	0.092
57DAP/reference	1.06665	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00081	1
27DAP/17DAP	0.9803	0.821
39DAP/27DAP	0.95521	0.66
41DAP/39DAP	1.08724	0.565
42DAP/41DAP	0.98604	0.819
43DAP/42DAP	1.01523	0.664
47DAP/43DAP	1.00058	1
52DAP/47DAP	1.04936	0.81
57DAP/52DAP	0.9912	0.833
57DAP/7DAP	1.01794	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90177	0.129
17DAP/reference	0.82654	0.031
27DAP/reference	0.92295	0.058
39DAP/reference	0.823	0.013
41DAP/reference	0.83397	0.023
42DAP/reference	0.78427	0.01
43DAP/reference	0.77458	0.015
47DAP/reference	0.90552	0.383
52DAP/reference	0.73414	0.035
57DAP/reference	0.76532	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54506	0.046
17DAP/reference	1.58079	0.034
27DAP/reference	1.3131	0.05
39DAP/reference	1.34653	0.03
41DAP/reference	1.47586	0.01
42DAP/reference	1.41602	0.009
43DAP/reference	1.48932	0.016
47DAP/reference	1.42452	0.01
52DAP/reference	1.32167	0.011
57DAP/reference	1.4112	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93637	0.268
17DAP/reference	1.11435	0.343
27DAP/reference	5.55316	0.531
39DAP/reference	0.82327	0.028
41DAP/reference	0.94384	0.185
42DAP/reference	0.86099	0.108
43DAP/reference	1.05015	0.858
47DAP/reference	1.11196	0.562
52DAP/reference	0.86308	0.268
57DAP/reference	0.76496	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20968	0.966
26DAP/20DAP	1.03914	0.905
34DAP/26DAP	1.07296	0.542
51DAP/34DAP	0.98718	0.873
52DAP/51DAP	1.03138	0.708
53DAP/52DAP	1.03874	0.83
55DAP/53DAP	0.98694	0.864
57DAP/55DAP	1.21492	0.249
62DAP/57DAP	1.12821	0.767
68DAP/62DAP	0.95122	0.7
68DAP/14DAP	0.50591	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91979	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.04311	0.898
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.1153
Mature Eggplant/Ripe Tomato	0.86431	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00507	1
1-1-2/M82	0.91547	1
12-2/M82	1.06707	1
12-4/M82	0.97734	1
1-3/M82	0.90072	0.378
2-1-1/M82	0.93511	0.784
2-1/M82	N/A	N/A
2-6/M82	0.95209	1
3-2/M82	0.99091	1
4-1-1/M82	0.99729	1
4-1/M82	1.11703	0.344
4-3-2/M82	0.95408	1
4-3/M82	0.95987	1
5-3/M82	1.07346	1
6-2/M82	1.01679	1
6-3/M82	1.03352	1
7-1/M82	0.97302	1
7-2/M82	1.03272	1
9-3-2/M82	0.87003	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.65944	0.243
IL2-6/WTpooled	1.30313
IL7-5/WTpooled	1.40668	1
IL7-3/WTpooled	0.82339	1
IL12-4/WTpooled	0.98615	1
IL1-4/WTpooled	0.89569	0.562
WT/WTpooled	1.00676	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	1.00428	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96196	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.0801	1
DC3000/delta hrp 24h	1.03595	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02249	0.476
DC3000 delta B/DC3000 delta AB	1.03011	0.625

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15168	1
Exp 36h	1.22369	1
Exp 60h	1.2197	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98199	1
Var 0h	0.57653	1
Var 12h I row2-row1	0.99914	1
Var 12h NI row2-row1	1.00439	1
Var 36h I row2-row1	1.11116	1
Var 36h NI row2-row1	1.09547	1
Var 60h I row2-row1	1.12328	0.562
Var 60h NI row2-row1	1.01535	1
Time course 0hI-0hNI	1.01322	0.852
Time course 12hI-12hNI	0.98887	0.94
Time course 36hI-36hNI	0.87636	0.123
Time course 60hI-60hNI	0.72205	0.007

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)	1.27218	0.339
transgenic ySAMdc/azygous control (breaker)	0.88229	0.49
transgenic ySAMdc/azygous control (red)	1.02949	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.85591	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95279	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.17059	1
Manapal/WT (break)	1.0355	1
Manapal/WT (red)	1.23286	0.413