Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85285	0.265
27DAP/17DAP	1.14599	0.849
39DAP/27DAP	1.22776	0.87
41DAP/39DAP	1.17599	0.728
42DAP/41DAP	1.24315	1
43DAP/42DAP	1.24324	1
47DAP/43DAP	1.30361	0.965
52DAP/47DAP	0.91488	0.685
57DAP/52DAP	0.80007	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79114	0.08
17DAP/reference	0.98649	0.737
27DAP/reference	1.07655	0.88
39DAP/reference	0.89989	0.174
41DAP/reference	0.88405	0.085
42DAP/reference	0.94847	0.287
43DAP/reference	0.90108	0.155
47DAP/reference	1.02325	1
52DAP/reference	1.00647	0.636
57DAP/reference	1.05428	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.98104	0.135
27DAP/17DAP	1.55101	0.233
39DAP/27DAP	0.85193	0.529
41DAP/39DAP	0.95494	0.91
42DAP/41DAP	0.80398	0.213
43DAP/42DAP	0.8911	0.383
47DAP/43DAP	1.11171	0.822
52DAP/47DAP	1.1544	0.851
57DAP/52DAP	1.44804	0.234
57DAP/7DAP	0.75722

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98187	0.495
17DAP/reference	0.88463	0.144
27DAP/reference	0.89659	0.109
39DAP/reference	0.65432	0.011
41DAP/reference	0.67286	0.022
42DAP/reference	0.72001	0.013
43DAP/reference	0.79708	0.086
47DAP/reference	0.95819	0.671
52DAP/reference	1.0451	1
57DAP/reference	0.78055	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9126	0.426
17DAP/reference	0.99132	0.693
27DAP/reference	0.79923	0.067
39DAP/reference	0.92441	0.33
41DAP/reference	0.92468	0.34
42DAP/reference	0.95936	0.482
43DAP/reference	0.9649	0.494
47DAP/reference	0.84646	0.092
52DAP/reference	0.94459	0.28
57DAP/reference	0.7055	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93021	0.489
17DAP/reference	1.02887	0.728
27DAP/reference	0.83881	0.073
39DAP/reference	0.88993	0.028
41DAP/reference	0.87541	0.209
42DAP/reference	0.88356	0.22
43DAP/reference	0.64355	0.064
47DAP/reference	0.83315	0.093
52DAP/reference	1.24114	0.917
57DAP/reference	0.92006	0.141

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86662	0.89
26DAP/20DAP	1.40176	0.806
34DAP/26DAP	1.15653	1
51DAP/34DAP	1.06881	0.844
52DAP/51DAP	1.71007	0.202
53DAP/52DAP	1.12202	1
55DAP/53DAP	1.11992	0.764
57DAP/55DAP	1.19263	0.61
62DAP/57DAP	1.09124	1
68DAP/62DAP	1.04336	1
68DAP/14DAP	1.40302	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73532	0.087

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	1.3392
Ripe Pepper/Ripe Tomato	0.44162
Mature Eggplant/Ripe Tomato	0.87749

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.29343
1-1-2/M82	0.87792
12-2/M82	N/A	N/A
12-4/M82	0.70167	0.358
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	0.75043
5-3/M82	0.95175	1
6-2/M82	N/A	N/A
6-3/M82	1.02017
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	1.33241	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.93187	1
IL12-4/WTpooled	1.04082	0.891
IL1-4/WTpooled	0.88853
WT/WTpooled	1.09156	0.874

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	0.95198	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03907	1
DC3000/delta hrp 6h	0.75746	0.95
DC3000/delta hrp 12h	1.12433	1
DC3000/delta hrp 24h	1.59717	0.283

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	0.89505	0.638

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7621	0.328
Exp 36h	1.4591	0.326
Exp 60h	0.92098	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04478	1
Var 0h	1.14981	0.782
Var 12h I row2-row1	1.16656	0.654
Var 12h NI row2-row1	0.90959	0.906
Var 36h I row2-row1	2.09847
Var 36h NI row2-row1	0.68839	1
Var 60h I row2-row1	1.13754	1
Var 60h NI row2-row1	0.87311	1
Time course 0hI-0hNI	1.28995	0.719
Time course 12hI-12hNI	1.072	0.741
Time course 36hI-36hNI	1.07012	1
Time course 60hI-60hNI	1.10655	0.673

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)	1.00502	0.921
transgenic ySAMdc/azygous control (breaker)	0.99998	1
transgenic ySAMdc/azygous control (red)	1.03595	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07007	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88483	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71222	0.172
Manapal/WT (break)	0.99643	1
Manapal/WT (red)	N/A	N/A