Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.8.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12294	0.697
27DAP/17DAP	1.2793	0.735
39DAP/27DAP	1.07106	0.882
41DAP/39DAP	1.04436	1
42DAP/41DAP	1.33755	0.196
43DAP/42DAP	1.21404	0.661
47DAP/43DAP	2.45387	0.196
52DAP/47DAP	0.72675	0.357
57DAP/52DAP	1.18812	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.51408	0.024
17DAP/reference	0.68893	0.011
27DAP/reference	0.81425	0.052
39DAP/reference	1.11059	0.857
41DAP/reference	0.94019	0.434
42DAP/reference	1.37308	0.001
43DAP/reference	2.70419	0.006
47DAP/reference	3.76153	0.001
52DAP/reference	2.94886	0.007
57DAP/reference	2.34388	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07225	0.662
27DAP/17DAP	1.08225	0.681
39DAP/27DAP	1.09287	0.548
41DAP/39DAP	0.97308	0.973
42DAP/41DAP	1.04041	0.999
43DAP/42DAP	1.54299	0.027
47DAP/43DAP	1.34474	0.017
52DAP/47DAP	1.04834	0.973
57DAP/52DAP	1.31428	0.12
57DAP/7DAP	1.80823	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.48834	0.058
17DAP/reference	0.54728	0.011
27DAP/reference	0.68616	0.01
39DAP/reference	0.791	0.017
41DAP/reference	0.80711	0.018
42DAP/reference	0.79373	0.023
43DAP/reference	0.86429	0.035
47DAP/reference	0.99294	0.671
52DAP/reference	0.78262	0.018
57DAP/reference	0.71999	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.45452	0.005
17DAP/reference	0.49492	0.003
27DAP/reference	0.9328	0.352
39DAP/reference	1.14844	0.657
41DAP/reference	0.93578	0.291
42DAP/reference	0.73677	0.019
43DAP/reference	0.76884	0.053
47DAP/reference	0.95502	0.359
52DAP/reference	0.70235	0.006
57DAP/reference	0.79403	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.49775	0.028
17DAP/reference	0.54855	0.045
27DAP/reference	0.51608	0.024
39DAP/reference	0.78673	0.02
41DAP/reference	0.7011	0.185
42DAP/reference	1.53135	0.017
43DAP/reference	2.22636	0.007
47DAP/reference	2.94183	0.004
52DAP/reference	3.49325	0.027
57DAP/reference	2.64724	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35858	0.966
26DAP/20DAP	1.04445	1
34DAP/26DAP	1.033	1
51DAP/34DAP	1.12538	0.597
52DAP/51DAP	0.82794	1
53DAP/52DAP	1.58638	0.049
55DAP/53DAP	1.09777	0.487
57DAP/55DAP	1.09109	0.915
62DAP/57DAP	0.53552	0.003
68DAP/62DAP	0.854	0.609
68DAP/14DAP	2.16695	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.55091	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.27907	0.068
Mature Green Tomato/Ripe Tomato	0.21764	0.017
Immature Eggplant/Mature Eggplant	0.88665	0.448
Ripe Pepper/Ripe Tomato	0.38504	0.293
Mature Eggplant/Ripe Tomato	0.13332	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.29456	0.877
1-1-2/M82	1.21882	1
12-2/M82	0.9714	1
12-4/M82	0.99868	1
1-3/M82	2.00375	0.248
2-1-1/M82	0.94991	0.784
2-1/M82	0.77308	0.74
2-6/M82	0.99344	1
3-2/M82	1.21116	0.549
4-1-1/M82	1.36543	1
4-1/M82	1.40196	1
4-3-2/M82	1.31292	0.284
4-3/M82	0.94611	1
5-3/M82	0.98174	1
6-2/M82	0.34126
6-3/M82	1.0693	1
7-1/M82	1.05946	1
7-2/M82	1.24609	1
9-3-2/M82	1.60199

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02124	1
IL7-5/WTpooled	1.32922
IL7-3/WTpooled	1.26742	1
IL12-4/WTpooled	0.79185	0.71
IL1-4/WTpooled	1.11388	0.426
WT/WTpooled	0.93954	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	1.00559	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02423	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.05128	1
DC3000/delta hrp 24h	1.02774	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96607	1
DC3000 delta B/DC3000 delta AB	1.07973	0.503

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.52328	1
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92895	1
Var 0h	0.44568	1
Var 12h I row2-row1	0.76476	0.418
Var 12h NI row2-row1	1.33612	0.649
Var 36h I row2-row1	1.01868	1
Var 36h NI row2-row1	0.84457	0.61
Var 60h I row2-row1	0.77177	0.374
Var 60h NI row2-row1	0.91673	0.318
Time course 0hI-0hNI	1.02663	0.867
Time course 12hI-12hNI	0.98406	0.95
Time course 36hI-36hNI	1.17128	0.063
Time course 60hI-60hNI	1.16554	0.426

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)	0.97902	0.722
transgenic ySAMdc/azygous control (breaker)	0.69217	0.173
transgenic ySAMdc/azygous control (red)	1.08727	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98131	0.27

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)	1.10267	1
Manapal/WT (break)	1.20503	1
Manapal/WT (red)	0.98662	0.863