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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green Gene Network Comparison Type Value Type Rank red description Interaction Map Filtered network_comparison

Results: HTML CSV LaTeX

Showing element 6408 to 6457 of 77072 in total

green	Network Comparison Type	Value Type	Rank	red	description	Interaction Map	Filtered	network_comparison
27.182	Subtracted	Rooted	644	27.912	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Low confidence	0	0.73
27.1942	Divided		836	27.188	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]			1.00023
27.1942	Subtracted		836	27.188				0.0062
27.2079	Divided		415	29.3397	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]			1.07835
27.2079	Subtracted		352	29.3397				2.1318
27.2466	Divided		748	26.8813	60s ribosomal protein l12. [swissprot;acc:p30050]			1.01359
27.2466	Subtracted		742	26.8813	60s ribosomal protein l12. [swissprot;acc:p30050]			0.3653
27.2528	Divided		746	26.8851	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]			1.01368
27.2528	Subtracted		741	26.8851				0.3677
27.2559	Divided		744	26.8871	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]			1.01372
27.2559	Subtracted		740	26.8871				0.3688
27.2805	Divided	Squared	5	314.926	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	High confidence	1	11.544
			6		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]
			7		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]
			8		db83 protein. [swissprot;acc:p57088]
	Subtracted		2702		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]			287.645
			2703		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]
			2704		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]
			2705		db83 protein. [swissprot;acc:p57088]
27.2883	Divided	Rooted	609	28.2011	dna-crosslink repair gene snm1. [refseq;acc:nm_014881]	Low confidence	0	1.03345
	Divided		610		t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283]			1.03345
	Subtracted		602		dna-crosslink repair gene snm1. [refseq;acc:nm_014881]			0.9128
	Subtracted		603		t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283]			0.9128
27.3392	Divided		828	27.3043	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]			1.00128
27.3392	Subtracted		829	27.3043				0.0349
27.3399	Divided		599	26.4018	ubiquitin and ribosomal protein s27a precursor; ubiquitin carboxyl extension protein 80; 40s ribosomal protein s27a; ubiquitin; ubiquitin-cep80. [refseq;acc:nm_002954]			1.03553
27.3399	Subtracted		596	26.4018				0.9381
27.399	Divided		416	25.4103	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]			1.07826
27.399	Subtracted		372	25.4103				1.9887
27.4107	Divided		713	26.9172	rna binding protein. [refseq;acc:nm_032509]			1.01833
27.4107	Subtracted		707	26.9172	rna binding protein. [refseq;acc:nm_032509]			0.4935
27.4116	Divided		256	24.8155	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	High confidence		1.10462
27.4116	Subtracted		215	24.8155		High confidence		2.5961
27.4612	Divided		587	28.4926	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Low confidence		1.03756
27.4612	Subtracted		572	28.4926				1.0314
27.5154	Divided		127	33.4653	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]			1.21624
27.5154	Subtracted		45	33.4653				5.9499
27.6157	Divided		524	26.2898	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]			1.05043
27.6157	Subtracted		498	26.2898				1.3259
27.6396	Divided		467	25.9809	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]			1.06384
27.6396	Subtracted		435	25.9809				1.6587
27.662	Divided		635	28.4675	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]			1.02912
27.662	Subtracted		625	28.4675				0.8055
27.6672	Divided		516	26.3179	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]			1.05127
27.6672	Subtracted		494	26.3179				1.3493
27.6684	Divided		766	27.3739	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]			1.01076
27.6684	Subtracted		760	27.3739				0.2945
27.6917	Divided		449	25.9427	protein phosphatase methylesterase-1. [refseq;acc:nm_016147]			1.06742
27.6917	Subtracted		405	25.9427				1.749
27.7265	Divided		248	30.7397	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	High confidence		1.10868

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/