Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.8.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7622	0.085
27DAP/17DAP	0.99297	1
39DAP/27DAP	0.82143	0.392
41DAP/39DAP	0.96446	0.83
42DAP/41DAP	1.1449	0.691
43DAP/42DAP	1.26093	0.491
47DAP/43DAP	1.0763	0.873
52DAP/47DAP	0.92818	0.772
57DAP/52DAP	0.76881	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95143	0.442
17DAP/reference	1.09973	0.22
27DAP/reference	0.95595	0.457
39DAP/reference	1.0063	0.975
41DAP/reference	0.98792	0.814
42DAP/reference	0.96802	0.305
43DAP/reference	1.15374	0.069
47DAP/reference	0.91931	0.077
52DAP/reference	0.83239	0.158
57DAP/reference	0.9282	0.199

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9213	0.415
27DAP/17DAP	1.23039	0.482
39DAP/27DAP	1.0426	0.587
41DAP/39DAP	1.02656	0.896
42DAP/41DAP	0.98695	0.85
43DAP/42DAP	1.27954	0.066
47DAP/43DAP	0.97344	0.87
52DAP/47DAP	0.9464	0.702
57DAP/52DAP	1.07941	0.67
57DAP/7DAP	0.84592	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38949	0.058
17DAP/reference	1.32413	0.016
27DAP/reference	1.41345	0.011
39DAP/reference	1.87831	0.005
41DAP/reference	1.34735	0.027
42DAP/reference	1.52537	0.008
43DAP/reference	1.57273	0.006
47DAP/reference	1.38587	0.44
52DAP/reference	1.63698	0.007
57DAP/reference	2.17429	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94254	0.532
17DAP/reference	0.94806	0.487
27DAP/reference	0.96255	0.501
39DAP/reference	0.90978	0.265
41DAP/reference	0.87272	0.048
42DAP/reference	1.22995	0.744
43DAP/reference	0.98872	0.646
47DAP/reference	1.08914	0.467
52DAP/reference	0.86445	0.078
57DAP/reference	1.1073	0.363

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87615	0.135
17DAP/reference	0.88278	0.364
27DAP/reference	1.22998	0.034
39DAP/reference	1.32379	0.1
41DAP/reference	1.13005	0.257
42DAP/reference	1.56322	0.06
43DAP/reference	1.45259	0.077
47DAP/reference	1.12668	0.355
52DAP/reference	2.62516	0.028
57DAP/reference	2.13126	0.673

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96739	1
26DAP/20DAP	0.97134	1
34DAP/26DAP	0.91887	0.741
51DAP/34DAP	1.25974	0.126
52DAP/51DAP	0.96669	1
53DAP/52DAP	1.14572	0.723
55DAP/53DAP	1.01732	1
57DAP/55DAP	0.98743	0.909
62DAP/57DAP	0.96371	0.994
68DAP/62DAP	0.84984	0.722
68DAP/14DAP	0.96933	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.76616	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.89895	0.446
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	0.96644	0.961
1-1-2/M82	0.97224	1
12-2/M82	N/A	N/A
12-4/M82	1.32074	1
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	1.05574	0.695
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.02365	1
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.88003	0.642
6-2/M82	N/A	N/A
6-3/M82	1.08056	1
7-1/M82	0.72804
7-2/M82	0.85916	0.881
9-3-2/M82	1.24306

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85388	0.243
IL2-6/WTpooled	1.74462
IL7-5/WTpooled	0.94038	1
IL7-3/WTpooled	1.19595	1
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.92724	0.699
WT/WTpooled	1.34555	0.911

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	0.95489	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04044	0.921
DC3000/delta hrp 6h	0.79325	0.95
DC3000/delta hrp 12h	1.14127	1
DC3000/delta hrp 24h	1.14783	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.4301	0.121
DC3000 delta B/DC3000 delta AB	1.14172	0.298

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06597	1
Exp 36h	1.75311	0.693
Exp 60h	1.26409	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00389	1
Var 0h	1.00966	0.98
Var 12h I row2-row1	0.93164	0.77
Var 12h NI row2-row1	1.13702	0.649
Var 36h I row2-row1	1.39913	0.742
Var 36h NI row2-row1	0.89861	0.706
Var 60h I row2-row1	0.77432	0.439
Var 60h NI row2-row1	0.8296	0.572
Time course 0hI-0hNI	1.11243	0.63
Time course 12hI-12hNI	1.04813	0.773
Time course 36hI-36hNI	1.25123	0.025
Time course 60hI-60hNI	1.30079	0.012

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)	1.09463	0.326
transgenic ySAMdc/azygous control (breaker)	0.91094	0.251
transgenic ySAMdc/azygous control (red)	0.96589	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00444	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26741	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23839	0.14
Manapal/WT (break)	0.92228	1
Manapal/WT (red)	0.8977	0.315