Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04496	0.851
27DAP/17DAP	1.08711	0.859
39DAP/27DAP	0.9365	0.549
41DAP/39DAP	1.13386	0.696
42DAP/41DAP	1.00974	1
43DAP/42DAP	1.03152	1
47DAP/43DAP	0.9411	0.76
52DAP/47DAP	0.92182	0.757
57DAP/52DAP	1.0052	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86662	0.455
17DAP/reference	N/A	N/A
27DAP/reference	0.92839
39DAP/reference	0.90946
41DAP/reference	1.08013	0.714
42DAP/reference	1.82037	0.108
43DAP/reference	0.45305
47DAP/reference	1.26592
52DAP/reference	0.94306	0.167
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07164	0.372
27DAP/17DAP	0.80905
39DAP/27DAP	1.08154	0.532
41DAP/39DAP	0.95762	0.997
42DAP/41DAP	0.90521	0.545
43DAP/42DAP	1.10586	0.014
47DAP/43DAP	N/A	N/A
52DAP/47DAP	N/A	N/A
57DAP/52DAP	0.96788	0.697
57DAP/7DAP	0.91464

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91129	0.138
17DAP/reference	1.0162	0.477
27DAP/reference	0.96644	0.185
39DAP/reference	0.95086	0.043
41DAP/reference	0.92464	0.022
42DAP/reference	0.94044	0.038
43DAP/reference	0.95521	0.105
47DAP/reference	0.90189	0.128
52DAP/reference	0.88539	0.027
57DAP/reference	0.94065	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00008	0.993
17DAP/reference	0.98581	0.626
27DAP/reference	0.94123	0.452
39DAP/reference	0.94943	0.33
41DAP/reference	0.98247	0.545
42DAP/reference	1.14823	0.621
43DAP/reference	1.02175	0.827
47DAP/reference	2.12116	0.098
52DAP/reference	0.98462	0.433
57DAP/reference	1.04825	0.166

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97871	0.23
17DAP/reference	0.96142	0.477
27DAP/reference	0.99747	0.843
39DAP/reference	0.95375	0.122
41DAP/reference	0.93723	0.264
42DAP/reference	0.94013	0.172
43DAP/reference	0.93205	0.237
47DAP/reference	0.93996	0.286
52DAP/reference	0.87174	0.089
57DAP/reference	0.91291	0.124

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99091	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.98754	1
51DAP/34DAP	1.06964	0.719
52DAP/51DAP	1.07189
53DAP/52DAP	1.12228
55DAP/53DAP	1.25514
57DAP/55DAP	1.43492	0.559
62DAP/57DAP	0.98392	0.994
68DAP/62DAP	0.83405	0.29
68DAP/14DAP	1.0288	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01108	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04427	1
Mature Green Tomato/Ripe Tomato	0.38078	0.017
Immature Eggplant/Mature Eggplant	1.18123	0.198
Ripe Pepper/Ripe Tomato	0.86801
Mature Eggplant/Ripe Tomato	1.4495	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00296	1
1-1-2/M82	1.17144	1
12-2/M82	0.98391	0.955
12-4/M82	0.95875	0.282
1-3/M82	0.95118	0.501
2-1-1/M82	1.01072	1
2-1/M82	1.20522	1
2-6/M82	0.94983	1
3-2/M82	0.99344	1
4-1-1/M82	1.11917	1
4-1/M82	0.85571	0.737
4-3-2/M82	1.10447	0.508
4-3/M82	0.97216	1
5-3/M82	1.01309	1
6-2/M82	1.06493	1
6-3/M82	0.98277	1
7-1/M82	0.98659	1
7-2/M82	0.95747	1
9-3-2/M82	1.1362	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95281	1
IL2-6/WTpooled	1.16201	0.659
IL7-5/WTpooled	0.73349	1
IL7-3/WTpooled	0.96328	0.31
IL12-4/WTpooled	1.06705	0.516
IL1-4/WTpooled	0.91474	0.435
WT/WTpooled	1.02318	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	0.86319

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04345	0.921
DC3000/delta hrp 6h	1.24278	1
DC3000/delta hrp 12h	0.97701	1
DC3000/delta hrp 24h	1.02541	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0871	0.408
DC3000 delta B/DC3000 delta AB	1.04762	0.558

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.94348	0.406
Exp 60h	0.96481	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96535	1
Var 0h	1.08632	1
Var 12h I row2-row1	1.04749	0.736
Var 12h NI row2-row1	0.96779	0.906
Var 36h I row2-row1	1.64228	0.908
Var 36h NI row2-row1	1.06477	1
Var 60h I row2-row1	1.86653	1
Var 60h NI row2-row1	1.30563	0.904
Time course 0hI-0hNI	1.10381	0.799
Time course 12hI-12hNI	0.96971	0.836
Time course 36hI-36hNI	0.8475	0.084
Time course 60hI-60hNI	0.74319	0.015

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)	0.90883	0.428
transgenic ySAMdc/azygous control (breaker)	0.78178	0.142
transgenic ySAMdc/azygous control (red)	1.16616	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95635	0.181

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96123	1
Manapal/WT (break)	0.97178	1
Manapal/WT (red)	1.0853	0.413