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 Network Comparison Type Interaction Map green Filtered red network_comparison

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Showing element 51 to 100 of 29840 in total

Interaction Map

: High confidence

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

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/