Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.10.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91425	0.496
27DAP/17DAP	0.88795	0.725
39DAP/27DAP	0.85561	0.425
41DAP/39DAP	0.69505	0.12
42DAP/41DAP	0.90703	1
43DAP/42DAP	1.2423	0.724
47DAP/43DAP	0.62825	0.115
52DAP/47DAP	0.7651	0.413
57DAP/52DAP	0.82404	0.778

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47488	0.024
17DAP/reference	1.25935	0.127
27DAP/reference	1.33427	0.012
39DAP/reference	1.31996	0.119
41DAP/reference	1.20751	0.203
42DAP/reference	1.03112	0.756
43DAP/reference	0.97348	0.691
47DAP/reference	0.81721	0.004
52DAP/reference	0.63397	0.013
57DAP/reference	0.77518	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0311	0.708
27DAP/17DAP	0.89318	0.227
39DAP/27DAP	0.75726	0.029
41DAP/39DAP	1.19812	0.799
42DAP/41DAP	0.92306	0.37
43DAP/42DAP	0.74128	0.024
47DAP/43DAP	0.83062	0.084
52DAP/47DAP	0.90536	0.624
57DAP/52DAP	0.91928	0.466
57DAP/7DAP	0.69934	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.81931	0.027
17DAP/reference	1.45111	0.011
27DAP/reference	1.02789	0.974
39DAP/reference	1.33719	0.017
41DAP/reference	1.02688	0.918
42DAP/reference	0.96329	0.355
43DAP/reference	1.04196	0.873
47DAP/reference	1.03377	1
52DAP/reference	1.04254	1
57DAP/reference	1.21055	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38405	0.063
17DAP/reference	1.36884	0.033
27DAP/reference	0.97407	0.519
39DAP/reference	0.92243	0.183
41DAP/reference	0.91015	0.199
42DAP/reference	0.88446	0.081
43DAP/reference	0.71559	0.024
47DAP/reference	0.95004	0.349
52DAP/reference	0.91861	0.078
57DAP/reference	0.74829	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.54351	0.015
17DAP/reference	1.80057	0.085
27DAP/reference	1.60426	0.013
39DAP/reference	1.69211	0.005
41DAP/reference	1.30853	0.15
42DAP/reference	1.26349	0.175
43DAP/reference	1.21587	0.071
47DAP/reference	1.02969	0.405
52DAP/reference	0.93567	0.415
57DAP/reference	1.11509	0.481

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01507	1
26DAP/20DAP	0.93332	1
34DAP/26DAP	1.19436	0.819
51DAP/34DAP	0.90403	0.555
52DAP/51DAP	0.86786	0.151
53DAP/52DAP	0.86882	0.445
55DAP/53DAP	1.11487	0.806
57DAP/55DAP	1.23087	0.805
62DAP/57DAP	1.20358	0.257
68DAP/62DAP	0.856	0.378
68DAP/14DAP	0.46603	0.08

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.86636	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.26019	0.058
Mature Green Tomato/Ripe Tomato	7.34062	0.015
Immature Eggplant/Mature Eggplant	0.58138	0.062
Ripe Pepper/Ripe Tomato	0.96638	1
Mature Eggplant/Ripe Tomato	3.64279	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88856	0.605
1-1-2/M82	1.41174
12-2/M82	0.92023
12-4/M82	0.72988	0.619
1-3/M82	1.68001
2-1-1/M82	N/A	N/A
2-1/M82	0.71759	0.322
2-6/M82	1.20567	0.385
3-2/M82	N/A	N/A
4-1-1/M82	1.07492
4-1/M82	0.56162	0.665
4-3-2/M82	1.38408	0.508
4-3/M82	0.79016	0.509
5-3/M82	0.88333	0.642
6-2/M82	0.9077	1
6-3/M82	1.1859
7-1/M82	0.89166
7-2/M82	1.68947
9-3-2/M82	1.72027	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.86964	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06287	0.921
DC3000/delta hrp 6h	1.04001	0.95
DC3000/delta hrp 12h	1.17448	1
DC3000/delta hrp 24h	0.46617	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.71311	0.023
DC3000 delta B/DC3000 delta AB	0.66891	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95261	1
Exp 36h	0.76675	0.623
Exp 60h	0.65654	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01961	1
Var 0h	0.81742	0.782
Var 12h I row2-row1	0.77667	0.357
Var 12h NI row2-row1	0.92258	0.713
Var 36h I row2-row1	1.08455	1
Var 36h NI row2-row1	1.06536	1
Var 60h I row2-row1	0.97939	1
Var 60h NI row2-row1	0.98006	1
Time course 0hI-0hNI	0.99564	1
Time course 12hI-12hNI	1.01326	0.849
Time course 36hI-36hNI	0.98695	0.632
Time course 60hI-60hNI	0.28655	0.006

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)	1.08243	0.455
transgenic ySAMdc/azygous control (breaker)	0.88695	0.49
transgenic ySAMdc/azygous control (red)	1.18671	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13771	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07539	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.54865	0.14
Manapal/WT (break)	2.05057	0.14
Manapal/WT (red)	1.52186	0.125