Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.4.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21557	0.561
27DAP/17DAP	0.89	0.736
39DAP/27DAP	0.91245	0.594
41DAP/39DAP	1.3826	0.416
42DAP/41DAP	1.04908	0.974
43DAP/42DAP	0.89819	0.713
47DAP/43DAP	1.11638	0.733
52DAP/47DAP	1.16425	0.943
57DAP/52DAP	0.70514	0.688

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79806	0.047
17DAP/reference	0.94843	0.278
27DAP/reference	0.94199	0.249
39DAP/reference	0.96293	0.455
41DAP/reference	0.89224	0.114
42DAP/reference	0.86354	0.025
43DAP/reference	1.12815	0.126
47DAP/reference	0.98093	0.445
52DAP/reference	0.92681	0.25
57DAP/reference	0.9381	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70737	0.037
27DAP/17DAP	1.0523	0.9
39DAP/27DAP	1.09143	0.636
41DAP/39DAP	1.1316	0.773
42DAP/41DAP	1.05133	0.999
43DAP/42DAP	1.45326	0.042
47DAP/43DAP	1.04171	0.897
52DAP/47DAP	1.05702	0.819
57DAP/52DAP	1.04041	0.911
57DAP/7DAP	0.92563	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74894	0.091
17DAP/reference	0.91078	0.108
27DAP/reference	0.89349	0.171
39DAP/reference	1.06493	0.538
41DAP/reference	0.96315	0.412
42DAP/reference	0.91223	0.304
43DAP/reference	0.85558	0.013
47DAP/reference	0.95786	0.671
52DAP/reference	0.84456	0.035
57DAP/reference	0.90635	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17152	0.463
17DAP/reference	0.81468	0.027
27DAP/reference	0.83151	0.167
39DAP/reference	0.81732	0.014
41DAP/reference	0.93827	0.205
42DAP/reference	0.82349	0.01
43DAP/reference	1.0508	0.831
47DAP/reference	0.81512	0.015
52DAP/reference	0.89894	0.078
57DAP/reference	0.92049	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98478	0.607
17DAP/reference	0.93403	0.348
27DAP/reference	0.70481	0.038
39DAP/reference	0.85947	0.035
41DAP/reference	0.94538	0.417
42DAP/reference	0.85052	0.134
43DAP/reference	0.94291	0.158
47DAP/reference	1.28832	0.006
52DAP/reference	0.87233	0.368
57DAP/reference	1.00588	0.828

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.26675	0.966
26DAP/20DAP	1.78569	0.099
34DAP/26DAP	0.96404	0.945
51DAP/34DAP	1.34927	0.159
52DAP/51DAP	0.84657	1
53DAP/52DAP	1.40612	0.113
55DAP/53DAP	1.0053	0.852
57DAP/55DAP	0.88833	0.545
62DAP/57DAP	1.12695	0.622
68DAP/62DAP	1.36402	0.048
68DAP/14DAP	1.26804	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30159	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.31557	0.018
Immature Eggplant/Mature Eggplant	1.44252
Ripe Pepper/Ripe Tomato	0.39986	0.293
Mature Eggplant/Ripe Tomato	0.56684	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08939	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.04697	1
1-3/M82	0.80685
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	1.06398
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	0.96953	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.137
9-3-2/M82	0.86677

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96225	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95957	1
IL12-4/WTpooled	0.89893	0.71
IL1-4/WTpooled	1.12009
WT/WTpooled	1.05617	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	0.93645	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05175	0.921
DC3000/delta hrp 6h	1.15229	1
DC3000/delta hrp 12h	1.15793	1
DC3000/delta hrp 24h	1.23113	0.085

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11549	0.102
DC3000 delta B/DC3000 delta AB	1.18239	0.292

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02837	1
Exp 36h	1.60571	0.693
Exp 60h	1.42105	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.84206	0.933
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
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	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.9818	0.348
transgenic ySAMdc/azygous control (breaker)	0.88294	0.49
transgenic ySAMdc/azygous control (red)	0.92455	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95442	0.156

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76668	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93001	1
Manapal/WT (break)	1.1884	0.381
Manapal/WT (red)	1.19711	1