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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 6408 to 6457 of 77072 in total

green	Network Comparison Type	Value Type	Rank	description	Interaction Map	red	network_comparison	Filtered
27.182	Subtracted	Rooted	644	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Low confidence	27.912	0.73	0
27.1942	Divided		836	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]		27.188	1.00023
27.1942	Subtracted		836			27.188	0.0062
27.2079	Divided		415	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]		29.3397	1.07835
27.2079	Subtracted		352			29.3397	2.1318
27.2466	Divided		748	60s ribosomal protein l12. [swissprot;acc:p30050]		26.8813	1.01359
27.2466	Subtracted		742	60s ribosomal protein l12. [swissprot;acc:p30050]		26.8813	0.3653
27.2528	Divided		746	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]		26.8851	1.01368
27.2528	Subtracted		741			26.8851	0.3677
27.2559	Divided		744	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]		26.8871	1.01372
27.2559	Subtracted		740			26.8871	0.3688
27.2805	Divided	Squared	5	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	High confidence	314.926	11.544	1
			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	dna-crosslink repair gene snm1. [refseq;acc:nm_014881]	Low confidence	28.2011	1.03345	0
	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	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]		27.3043	1.00128
27.3392	Subtracted		829			27.3043	0.0349
27.3399	Divided		599	ubiquitin and ribosomal protein s27a precursor; ubiquitin carboxyl extension protein 80; 40s ribosomal protein s27a; ubiquitin; ubiquitin-cep80. [refseq;acc:nm_002954]		26.4018	1.03553
27.3399	Subtracted		596			26.4018	0.9381
27.399	Divided		416	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]		25.4103	1.07826
27.399	Subtracted		372			25.4103	1.9887
27.4107	Divided		713	rna binding protein. [refseq;acc:nm_032509]		26.9172	1.01833
27.4107	Subtracted		707	rna binding protein. [refseq;acc:nm_032509]		26.9172	0.4935
27.4116	Divided		256	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	High confidence	24.8155	1.10462
27.4116	Subtracted		215		High confidence	24.8155	2.5961
27.4612	Divided		587	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Low confidence	28.4926	1.03756
27.4612	Subtracted		572			28.4926	1.0314
27.5154	Divided		127	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]		33.4653	1.21624
27.5154	Subtracted		45			33.4653	5.9499
27.6157	Divided		524	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]		26.2898	1.05043
27.6157	Subtracted		498			26.2898	1.3259
27.6396	Divided		467	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]		25.9809	1.06384
27.6396	Subtracted		435			25.9809	1.6587
27.662	Divided		635	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]		28.4675	1.02912
27.662	Subtracted		625			28.4675	0.8055
27.6672	Divided		516	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]		26.3179	1.05127
27.6672	Subtracted		494			26.3179	1.3493
27.6684	Divided		766	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]		27.3739	1.01076
27.6684	Subtracted		760			27.3739	0.2945
27.6917	Divided		449	protein phosphatase methylesterase-1. [refseq;acc:nm_016147]		25.9427	1.06742
27.6917	Subtracted		405			25.9427	1.749
27.7265	Divided		248	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	High confidence	30.7397	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/