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

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