Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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description Rank Value Type Gene Filtered Network Comparison Type Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 14920 in total 
Network Comparison Type	Divided
Interaction Map	High confidence

description	Rank	Value Type	Filtered	green	red	network_comparison	
6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	642	Squared	1	19009.7	16123.9	1.17898	
6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	764	Measured	1	4729.12	4250.18	1.11269	
6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	1822	Ranked	1	243.085	240.32	1.01151	
6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	1905	Rooted	1	54.4076	52.8713	1.02906	
6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	643	Squared	1	19012.6	16126.5	1.17897	
6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	763	Measured	1	4729.67	4250.54	1.11272	
6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	1830	Ranked	1	243.069	240.32	1.01144	
6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	1894	Rooted	1	54.4127	52.8726	1.02913	
6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	644	Squared	1	19046	16156.3	1.17886	
6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	759	Measured	1	4736.03	4254.62	1.11315	
6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	1846	Rooted	1	54.4715	52.887	1.02996	
6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	1883	Ranked	1	242.881	240.317	1.01067	
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	922	Squared	1	31257.4	27031.3	1.15634	
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	1339	Measured	1	6464.94	5988.06	1.07964	
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	2041	Rooted	1	65.2562	63.5421	1.02698	
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	2274	Ranked	1	214.801	213.642	1.00542	
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	899	Squared	1	34004.2	29345.7	1.15875	
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	1584	Ranked	1	220.432	216.891	1.01633	
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	1627	Measured	1	6463.9	6038.46	1.07046	
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	2366	Rooted	1	64.002	62.9164	1.01725	
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	2904	Measured	1	0.00001	0.00001	1	
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	2904	Ranked	1	0.00001	0.00001	1	
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	2904	Squared	1	0.00001	0.00001	1	
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	2904	Rooted	1	0.00001	0.00001	1	
60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [source:swissprot;acc:p10809]	1238	Squared	1	26712.4	23538.3	1.13485	
60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [source:swissprot;acc:p10809]	1313	Measured	1	5899.85	5457.14	1.08112	
60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [source:swissprot;acc:p10809]	1830	Rooted	1	62.0316	60.2038	1.03036	
60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [source:swissprot;acc:p10809]	2588	Ranked	1	222.64	222.305	1.00151	
60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [source:swissprot;acc:q92993]	821	Rooted	1	65.2371	61.3164	1.06394	
60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [source:swissprot;acc:q92993]	826	Ranked	1	213.912	223.186	1.04335	
60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [source:swissprot;acc:q92993]	1751	Measured	1	6414.98	6011.57	1.06711	
60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [source:swissprot;acc:q92993]	2621	Squared	1	30796.3	31749.4	1.03095	
60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	1092	Ranked	1	232.855	226.203	1.02941	
60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	2254	Squared	1	24581.5	22719.3	1.08197	
60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	2258	Measured	1	5388.05	5150.31	1.04616	
60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	2720	Rooted	1	58.4068	58.3416	1.00112	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	233	Ranked	0	10560	9586.97	1.1015	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	313	Measured	0	6739.34	6131.07	1.09921	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	377	Rooted	0	47.6722	45.8794	1.03908	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	381	Squared	0	54614.9	49458.1	1.10427	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	898	Ranked	1	238.048	229.171	1.03874	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	2326	Squared	1	22261.9	20706.1	1.07514	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	2418	Measured	1	5039.78	4857.03	1.03763	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	2564	Rooted	1	56.3214	56.832	1.00907	
60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	720	Ranked	1	244.435	231.92	1.05396	
60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	1708	Rooted	1	54.3497	56.1247	1.03266	
60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	2743	Measured	1	4813.92	4824.49	1.0022	
60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	2745	Squared	1	21696.3	21770.6	1.00342	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	199	Ranked	0	10545.7	11781.8	1.11721	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	261	Rooted	0	24.6198	22.315	1.10328	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/