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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
description Rank Filtered Value Type Gene Interaction Map Network Comparison Type green red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

description	Rank	Filtered	Value Type	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	1	Squared	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	1	Measured	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	1	Ranked	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	1	Rooted	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	1	Squared	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	1	Measured	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	1	Ranked	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	1	Rooted	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	1	Squared	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	1	Measured	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	1	Rooted	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	1	Ranked	242.881	240.317	1.01067	
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	922	1	Squared	31257.4	27031.3	1.15634	
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	1339	1	Measured	6464.94	5988.06	1.07964	
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	2041	1	Rooted	65.2562	63.5421	1.02698	
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	2274	1	Ranked	214.801	213.642	1.00542	
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	899	1	Squared	34004.2	29345.7	1.15875	
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	1584	1	Ranked	220.432	216.891	1.01633	
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	1627	1	Measured	6463.9	6038.46	1.07046	
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	2366	1	Rooted	64.002	62.9164	1.01725	
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	2904	1	Measured	0.00001	0.00001	1	
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	2904	1	Ranked	0.00001	0.00001	1	
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	2904	1	Squared	0.00001	0.00001	1	
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	2904	1	Rooted	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	1	Squared	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	1	Measured	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	1	Rooted	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	1	Ranked	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	1	Rooted	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	1	Ranked	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	1	Measured	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	1	Squared	30796.3	31749.4	1.03095	
60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	1092	1	Ranked	232.855	226.203	1.02941	
60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	2254	1	Squared	24581.5	22719.3	1.08197	
60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	2258	1	Measured	5388.05	5150.31	1.04616	
60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	2720	1	Rooted	58.4068	58.3416	1.00112	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	233	0	Ranked	10560	9586.97	1.1015	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	313	0	Measured	6739.34	6131.07	1.09921	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	377	0	Rooted	47.6722	45.8794	1.03908	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	381	0	Squared	54614.9	49458.1	1.10427	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	898	1	Ranked	238.048	229.171	1.03874	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	2326	1	Squared	22261.9	20706.1	1.07514	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	2418	1	Measured	5039.78	4857.03	1.03763	
60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	2564	1	Rooted	56.3214	56.832	1.00907	
60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	720	1	Ranked	244.435	231.92	1.05396	
60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	1708	1	Rooted	54.3497	56.1247	1.03266	
60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	2743	1	Measured	4813.92	4824.49	1.0022	
60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	2745	1	Squared	21696.3	21770.6	1.00342	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	199	0	Ranked	10545.7	11781.8	1.11721	
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	261	0	Rooted	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/