Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.20.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08026	0.786
27DAP/17DAP	1.04608	1
39DAP/27DAP	1.44989	0.318
41DAP/39DAP	0.61186	0.12
42DAP/41DAP	0.64135
43DAP/42DAP	1.11653	0.937
47DAP/43DAP	1.18347	0.633
52DAP/47DAP	1.14962	0.969
57DAP/52DAP	0.94282	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07757	0.611
17DAP/reference	1.04576	0.248
27DAP/reference	1.07432	0.322
39DAP/reference	1.11911	0.277
41DAP/reference	0.97512	0.814
42DAP/reference	1.11937	0.544
43DAP/reference	0.89521
47DAP/reference	0.98772	0.602
52DAP/reference	0.83708	0.128
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92289	0.542
27DAP/17DAP	0.96599	0.887
39DAP/27DAP	0.99838	0.984
41DAP/39DAP	0.96409	0.934
42DAP/41DAP	1.17559	0.719
43DAP/42DAP	1.21207	0.049
47DAP/43DAP	1.10531	0.52
52DAP/47DAP	1.09635	0.696
57DAP/52DAP	0.91227	0.391
57DAP/7DAP	1.02233	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98046	0.495
17DAP/reference	0.83067	0.011
27DAP/reference	0.71308	0.01
39DAP/reference	0.74338	0.013
41DAP/reference	0.7816	0.044
42DAP/reference	0.66685	0.01
43DAP/reference	0.78133	0.033
47DAP/reference	0.82418	0.079
52DAP/reference	0.78846	0.026
57DAP/reference	0.92768	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04285	0.41
17DAP/reference	1.03972	0.448
27DAP/reference	0.89296	0.071
39DAP/reference	0.94361	0.243
41DAP/reference	1.20454	0.372
42DAP/reference	0.99328	0.594
43DAP/reference	1.08683	0.503
47DAP/reference	1.01309	1
52DAP/reference	0.99759	0.713
57DAP/reference	1.15133	0.055

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86149	0.104
17DAP/reference	0.95936	0.56
27DAP/reference	0.83226	0.045
39DAP/reference	0.77971	0.014
41DAP/reference	0.77778	0.018
42DAP/reference	0.67432	0.016
43DAP/reference	0.7975	0.023
47DAP/reference	0.97623	0.494
52DAP/reference	0.77694	0.169
57DAP/reference	0.66774	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97801	1
26DAP/20DAP	1.14006	0.718
34DAP/26DAP	1.0126	1
51DAP/34DAP	0.80954	0.513
52DAP/51DAP	1.04381	0.888
53DAP/52DAP	1.18707	0.58
55DAP/53DAP	1.12807	0.622
57DAP/55DAP	1.08477	1
62DAP/57DAP	0.98636	1
68DAP/62DAP	1.01203	0.914
68DAP/14DAP	0.95522	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87669	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.43351	0.09
Mature Green Tomato/Ripe Tomato	0.71648	0.107
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.85816	0.233
Mature Eggplant/Ripe Tomato	0.88894	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92034	0.616
1-1-2/M82	0.87591	1
12-2/M82	1.11598	1
12-4/M82	1.00519	1
1-3/M82	0.86943	0.501
2-1-1/M82	1.03108
2-1/M82	1.61939
2-6/M82	1.03974	0.695
3-2/M82	N/A	N/A
4-1-1/M82	0.9626	1
4-1/M82	0.97086
4-3-2/M82	0.94147
4-3/M82	0.9617	1
5-3/M82	1.0456	0.572
6-2/M82	1.0602	1
6-3/M82	1.00831	1
7-1/M82	0.91828	1
7-2/M82	0.93801	0.796
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91129	0.321
IL2-6/WTpooled	0.99774	1
IL7-5/WTpooled	1.40698	0.792
IL7-3/WTpooled	1.02094	1
IL12-4/WTpooled	1.12585	0.737
IL1-4/WTpooled	1.33201	1
WT/WTpooled	0.97967	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	0.96484	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03912	0.921
DC3000/delta hrp 6h	1.20626	0.582
DC3000/delta hrp 12h	1.00647	1
DC3000/delta hrp 24h	1.03289

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31123
DC3000 delta B/DC3000 delta AB	1.26035	0.22

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1165	1
Exp 36h	0.86456	0.623
Exp 60h	0.75853	0.253

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	N/A	N/A
Var 12h I row2-row1	0.8211	0.39
Var 12h NI row2-row1	0.70484	0.627
Var 36h I row2-row1	0.64408
Var 36h NI row2-row1	0.89405	0.743
Var 60h I row2-row1	1.09465
Var 60h NI row2-row1	0.85684
Time course 0hI-0hNI	0.99301	1
Time course 12hI-12hNI	1.11069
Time course 36hI-36hNI	1.08797
Time course 60hI-60hNI	1.84858	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)	0.95389	0.348
transgenic ySAMdc/azygous control (breaker)	0.9279	0.49
transgenic ySAMdc/azygous control (red)	0.92391	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9623	0.12

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)	0.67184	0.172
Manapal/WT (break)	0.84446	1
Manapal/WT (red)	0.94977	0.424