Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.13.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15607	0.932
27DAP/17DAP	1.20235	0.832
39DAP/27DAP	0.82817	0.447
41DAP/39DAP	1.11639	0.691
42DAP/41DAP	0.76888	0.774
43DAP/42DAP	1.0433	1
47DAP/43DAP	1.2293	0.746
52DAP/47DAP	0.8776	0.643
57DAP/52DAP	1.13638	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96811	0.442
17DAP/reference	1.17012	0.017
27DAP/reference	1.01448	0.925
39DAP/reference	1.21392	0.025
41DAP/reference	1.20342	0.102
42DAP/reference	1.03309	1
43DAP/reference	1.05948	0.787
47DAP/reference	0.99561	0.636
52DAP/reference	0.88726	0.067
57DAP/reference	0.89941	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89722	0.484
27DAP/17DAP	0.98519	0.919
39DAP/27DAP	1.01691	0.977
41DAP/39DAP	1.08743	0.909
42DAP/41DAP	0.75214	0.037
43DAP/42DAP	1.26181	0.297
47DAP/43DAP	1.16398	0.61
52DAP/47DAP	1.01793	0.945
57DAP/52DAP	0.94404	0.605
57DAP/7DAP	0.96435	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17134	0.368
17DAP/reference	1.81328	0.006
27DAP/reference	1.58778	0.006
39DAP/reference	1.91755	0.007
41DAP/reference	1.91845	0.013
42DAP/reference	2.01476	0.006
43DAP/reference	2.20259	0.007
47DAP/reference	1.49381	0.165
52DAP/reference	1.55587	0.033
57DAP/reference	1.58239	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02414	0.952
17DAP/reference	1.09049	0.311
27DAP/reference	1.28902	0.149
39DAP/reference	0.98578	0.539
41DAP/reference	0.94571	0.307
42DAP/reference	1.0177	1
43DAP/reference	0.94142	0.486
47DAP/reference	1.05759	0.24
52DAP/reference	0.94837	0.259
57DAP/reference	1.08517	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40695	0.023
17DAP/reference	1.19175	0.436
27DAP/reference	2.18696	0.015
39DAP/reference	1.79083	0.015
41DAP/reference	1.7399	0.014
42DAP/reference	1.20973	0.364
43DAP/reference	1.39074	0.28
47DAP/reference	0.87978	0.076
52DAP/reference	1.90479	0.061
57DAP/reference	1.17199	0.814

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99547	1
26DAP/20DAP	0.98264	1
34DAP/26DAP	1.07441	1
51DAP/34DAP	1.438	0.377
52DAP/51DAP	1.0292	0.792
53DAP/52DAP	0.98303	0.96
55DAP/53DAP	0.89803	0.478
57DAP/55DAP	1.14174	0.805
62DAP/57DAP	1.23301	0.217
68DAP/62DAP	1.02488	0.834
68DAP/14DAP	0.93992	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69677	0.046

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

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	1.0637
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	0.80704
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	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	0.92464	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.38971	0.362
IL12-4/WTpooled	1.13039	0.891
IL1-4/WTpooled	1.28535	1
WT/WTpooled	0.9084	0.764

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	3.19022

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	2.28543	0.921
DC3000/delta hrp 6h	1.21524
DC3000/delta hrp 12h	1.02883	1
DC3000/delta hrp 24h	0.69894

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04621	1
Exp 36h	N/A	N/A
Exp 60h	1.04871	1

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	1.16805	0.782
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	2.45671
Var 36h I row2-row1	0.78423
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.95321	1
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	1.05708	0.95
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)	1.1138	0.318
transgenic ySAMdc/azygous control (breaker)	0.67034	0.137
transgenic ySAMdc/azygous control (red)	0.99874	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01749	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6812	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.77108	0.216