MK5 Microarray Data

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

Results: HTML CSV LaTeX

Showing element 44 to 93 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	Hugo	description	Value Type	network_comparison	red	green
6	Divided	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Ranked	1.86667	15	28
	Subtracted	ATPBD1C	protein x 0004. [refseq;acc:nm_016301]		97	212	309
		PANK1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Rooted	23.245	145.551	168.796
		PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Squared	143938	407289	263351
		UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Measured	7563	44490.5	36927.5
7	Divided	HLX	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	1.49767	215	322
		SMPD2	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]	Measured	3.39764	1153.5	339.5
				Squared	11.544	314.926	27.2805
				Rooted	1.84327	33.9632	18.4255
	Subtracted	no value	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	132153	310840	442993
		MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured	7307	21185	28492
		PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Rooted	23.245	145.551	168.796
		UFC1	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked	76.2	288.754	212.554
8	Divided	HBS1L	hbs1-like. [refseq;acc:nm_006620]		1.49767	215	322
		TMEM33	db83 protein. [swissprot;acc:p57088]	Measured	3.39764	1153.5	339.5
				Squared	11.544	314.926	27.2805
				Rooted	1.84327	33.9632	18.4255
	Subtracted	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	104591	250303	354894
		JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Ranked	74	288	362
		PANK1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Measured	7307	21185	28492
		PANK3	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted	23.245	145.551	168.796
9	Divided	TOB2	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	3.21581	398.5	1281.5
				Squared	10.3414	37.5863	388.696
				Rooted	1.79326	19.9625	35.798
		XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked	1.45755	212	309
	Subtracted	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		74	288	362
		PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured	7307	21185	28492
		PPP1R7	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared	93652	256169	162517
		SLC25A43	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	23.245	145.551	168.796
10	Divided	ATPBD1C	protein x 0004. [refseq;acc:nm_016301]	Ranked	1.45755	212	309
		TOB1	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	3.21581	398.5	1281.5
				Squared	10.3414	37.5863	388.696
				Rooted	1.79326	19.9625	35.798
	Subtracted	MAGED4	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	89286	219048	129762
		PANK3	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Measured	7307	21185	28492
		SMPD2	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]	Ranked	74	288	362
		XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Rooted	22.169	51.6817	29.5127
11	Divided	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Measured	3.21581	398.5	1281.5
				Squared	10.3414	37.5863	388.696
				Rooted	1.79326	19.9625	35.798
		RINT1	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	1.45259	337	232
	Subtracted	ATPBD1C	protein x 0004. [refseq;acc:nm_016301]	Rooted	22.169	51.6817	29.5127
		MAGEE2	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared	89286	219048	129762
		SLC25A43	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Measured	7307	21185	28492
		TMEM33	db83 protein. [swissprot;acc:p57088]	Ranked	74	288	362
12	Divided	CPEB4	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Measured	3.21581	398.5	1281.5
				Squared	10.3414	37.5863	388.696
				Rooted	1.79326	19.9625	35.798
		RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	1.45259	337	232
	Subtracted	no value	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		69.377	266.856	336.233

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
- Hugo is the HGNC identifier if it exists
- 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.