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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Rank Value Type Gene description Interaction Map Network Comparison Type red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 29840 in total 
Interaction Map	High confidence

Rank	Value Type	description	Network Comparison Type	red	Filtered	green	network_comparison	
4	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Divided	0.00001	0	89	8900000	
4	Measured	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Subtracted	18704	0	21730	3026	
4	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Divided	15	1	28	1.86667	
4	Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Divided	8906	0	21883	2.45711	
4	Ranked	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Subtracted	11525	0	21888	10363	
4	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	337	1	232	105	
4	Squared	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	407289	1	263351	143938	
4	Squared	hbs1-like. [source:refseq;acc:nm_006620]	Divided	1596.92	1	115.48	13.8285	
4	Squared	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Divided	0.00001	0	2.81207	281207	
4	Squared	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Subtracted	75446.7	0	105900	30453.3	
4	Rooted	hbs1-like. [source:refseq;acc:nm_006620]	Divided	50.9657	1	26.4292	1.92839	
4	Rooted	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	50.9657	1	26.4292	24.5365	
4	Rooted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Subtracted	29.3087	0	7.61577	21.6929	
4	Rooted	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Divided	0.00001	0	10.4403	1044030	
5	Measured	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	41482.5	1	33356.5	8126	
5	Measured	histone h4. [source:swissprot;acc:p02304]	Subtracted	21773.1	0	24446.3	2673.2	
5	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Divided	0.00001	0	89	8900000	
5	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	1153.5	1	339.5	3.39764	
5	Ranked	cytohesin 4. [source:swissprot;acc:q9uia0]	Divided	15	1	28	1.86667	
5	Ranked	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Subtracted	11525	0	21888	10363	
5	Ranked	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Divided	5510.5	0	11965.7	2.17144	
5	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Subtracted	212	1	309	97	
5	Squared	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	407289	1	263351	143938	
5	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Divided	0.00001	0	1.87479	187479	
5	Squared	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	314.926	1	27.2805	11.544	
5	Squared	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Subtracted	75446.7	0	105900	30453.3	
5	Rooted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	145.551	1	168.796	23.245	
5	Rooted	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Divided	0.00001	0	9.43398	943398	
5	Rooted	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	33.9632	1	18.4255	1.84327	
5	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Subtracted	19.0788	0	0	19.0788	
6	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Divided	0.00001	0	89	8900000	
6	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	1153.5	1	339.5	3.39764	
6	Measured	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	44490.5	1	36927.5	7563	
6	Measured	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Subtracted	13174.7	0	15605.1	2430.4	
6	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Divided	15	1	28	1.86667	
6	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Subtracted	5865	0	14977	9112	
6	Ranked	protein x 0004. [source:refseq;acc:nm_016301]	Subtracted	212	1	309	97	
6	Ranked	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	Divided	7523	0	15339.2	2.03897	
6	Squared	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Subtracted	73080.8	0	102814	29733.2	
6	Squared	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	407289	1	263351	143938	
6	Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Divided	0.00001	0	1.87479	187479	
6	Squared	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	314.926	1	27.2805	11.544	
6	Rooted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Divided	0.00001	0	9.43398	943398	
6	Rooted	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	33.9632	1	18.4255	1.84327	
6	Rooted	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Subtracted	145.551	1	168.796	23.245	
6	Rooted	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	Subtracted	12.1655	0	27.8029	15.6374	
7	Measured	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	21185	1	28492	7307	
7	Measured	sedlin. [source:swissprot;acc:o14582]	Divided	0.00001	0	43	4300000	
7	Measured	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Divided	1153.5	1	339.5	3.39764	
7	Measured	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Subtracted	13174.7	0	15605.1	2430.4	

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/