Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.19.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94673	0.578
27DAP/17DAP	1.0536	0.92
39DAP/27DAP	1.11261	0.949
41DAP/39DAP	1.23213	0.915
42DAP/41DAP	0.9868	1
43DAP/42DAP	1.13669	0.974
47DAP/43DAP	1.05583	0.864
52DAP/47DAP	1.68401	0.608
57DAP/52DAP	1.31154	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22793	0.068
17DAP/reference	1.18865	0.021
27DAP/reference	1.17719	0.146
39DAP/reference	1.07455	0.144
41DAP/reference	1.03759	0.421
42DAP/reference	1.1381	0.005
43DAP/reference	1.11643	0.175
47DAP/reference	1.15642	0.026
52DAP/reference	1.38482	0.009
57DAP/reference	1.20429	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40555	0.379
27DAP/17DAP	1.07192	0.973
39DAP/27DAP	1.00252	1
41DAP/39DAP	1.04286	0.887
42DAP/41DAP	1.0328	0.984
43DAP/42DAP	1.01226	1
47DAP/43DAP	1.00466	0.989
52DAP/47DAP	1.42776	0.203
57DAP/52DAP	1.41805	0.096
57DAP/7DAP	0.85733	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99309	0.682
17DAP/reference	1.10556	0.822
27DAP/reference	0.89277	0.037
39DAP/reference	0.91932	0.264
41DAP/reference	1.05438	1
42DAP/reference	1.07432	0.889
43DAP/reference	0.98519	0.555
47DAP/reference	1.01103	1
52DAP/reference	0.85396	0.115
57DAP/reference	0.80117	0.059

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05374	0.687
17DAP/reference	0.97158	0.548
27DAP/reference	1.1318	0.235
39DAP/reference	1.35162	0.034
41DAP/reference	1.29825	0.027
42DAP/reference	1.17567	0.076
43DAP/reference	1.02281	0.787
47DAP/reference	1.02785	0.775
52DAP/reference	1.23241	0.012
57DAP/reference	1.15588	0.127

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33743	0.101
17DAP/reference	1.13436	0.641
27DAP/reference	1.07287	0.298
39DAP/reference	0.9165	0.122
41DAP/reference	0.95805	0.459
42DAP/reference	1.03237	0.816
43DAP/reference	1.0701	0.828
47DAP/reference	1.20733	0.14
52DAP/reference	0.89124	0.36
57DAP/reference	1.74707	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86225	1
26DAP/20DAP	1.12753	0.905
34DAP/26DAP	1.03206	1
51DAP/34DAP	N/A	N/A
52DAP/51DAP	2.25855	0.213
53DAP/52DAP	1.00666	1
55DAP/53DAP	1.38308	0.087
57DAP/55DAP	0.69365	0.094
62DAP/57DAP	1.10637	0.833
68DAP/62DAP	1.53881	0.285
68DAP/14DAP	1.22826	0.558

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81212	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86719	0.481
Mature Green Tomato/Ripe Tomato	0.6901	0.226
Immature Eggplant/Mature Eggplant	1.0719	0.554
Ripe Pepper/Ripe Tomato	0.91133	1
Mature Eggplant/Ripe Tomato	4.63099	0.373

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	0.67593	0.619
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	0.96561
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	1.3925	0.365
IL2-6/WTpooled	0.82946	0.473
IL7-5/WTpooled	1.02569	1
IL7-3/WTpooled	1.10585	1
IL12-4/WTpooled	1.03974	0.737
IL1-4/WTpooled	1.40162	1
WT/WTpooled	0.98141	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	1.29296	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16778	0.656
DC3000/delta hrp 6h	0.9858	0.95
DC3000/delta hrp 12h	1.15898	1
DC3000/delta hrp 24h	0.33667	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.92715
DC3000 delta B/DC3000 delta AB	1.1929	0.232

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97428	1
Exp 36h	0.86767	0.699
Exp 60h	0.92856	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96226	1
Var 0h	1.11195	0.98
Var 12h I row2-row1	0.81658	0.514
Var 12h NI row2-row1	1.28342	0.649
Var 36h I row2-row1	0.94581	1
Var 36h NI row2-row1	0.7373	0.584
Var 60h I row2-row1	0.9009	0.952
Var 60h NI row2-row1	0.82621	0.408
Time course 0hI-0hNI	1.06702	0.63
Time course 12hI-12hNI	1.11709	0.164
Time course 36hI-36hNI	1.94463	0.005
Time course 60hI-60hNI	2.79817	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)	0.96514	0.662
transgenic ySAMdc/azygous control (breaker)	0.93452	1
transgenic ySAMdc/azygous control (red)	0.98993	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92893	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.3886	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.66561	0.09
Manapal/WT (break)	1.15243	0.381
Manapal/WT (red)	2.82833	0.134