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

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

Results: HTML CSV LaTeX

Showing element 1458 to 1507 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence

green	description	Rank	network_comparison	red
211.622	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	1607	1.01588	214.982
211.648	elks protein. [refseq;acc:nm_015064]	1061	1.03078	218.162
	nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	1060
211.657	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818]	2280	1.00537	212.793
211.676	proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3]	2283	1.00536	212.81
211.685	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	717	1.05402	223.121
	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]	715
	cpz gene product. [refseq;acc:nm_003652]	716
	dendritic cell protein. [refseq;acc:nm_006360]	713
	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	718
	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	714
211.707	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	764	1.04901	222.082
211.757	tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399]	1301	1.02371	206.852
211.766	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	2448	1.00321	212.446
211.833	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526]	1553	1.01679	215.389
211.858	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750]	2273	1.00546	213.015
211.898	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	1667	1.01416	214.898
211.908	asc-1 complex subunit p100. [refseq;acc:nm_032204]	1374	1.02187	216.542
	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071]	1375
	glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]	1373
	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524]	1372
211.926	tumor protein d52 (n8 protein). [swissprot;acc:p55327]	1223	1.02493	206.771
211.936	tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890]	1222	1.02496	206.774
211.966	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	738	1.05123	222.825
211.99	proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062]	2530	1.00224	212.464
212.119	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167]	1108	1.02775	218.006
212.123	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	1111	1.02766	217.99
212.142	nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384]	1946	1.00986	214.234
212.209	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	1109	1.02775	218.098
212.25	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266]	2647	1.00116	212.496
212.254	p47 protein isoform a. [refseq;acc:nm_016143]	2201	1.00654	213.642
212.262	aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728]	2544	1.00192	212.67
212.275	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390]	1304	1.02357	207.387
212.281	f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907]	1824	1.0115	214.722
212.286	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	2434	1.00346	213.021
212.289	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	1325	1.02282	217.133
212.3	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787]	2431	1.00352	213.048
212.316	protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0]	1505	1.0181	216.158
212.321	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	479	1.07409	228.051
	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	478
212.328	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	1831	1.01139	214.746
212.363	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	246	1.11748	237.312
212.38	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	568	1.06554	226.3
	t54 protein. [swissprot;acc:q92917]	569
212.386	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049]	1687	1.01393	215.345
212.401	deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366]	2755	1.00001	212.403
	ran binding protein 11. [refseq;acc:nm_016338]	2597	1.00146	212.711
212.404	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]	800	1.04501	221.965
	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	799
212.41	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	248	1.11719	237.302

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.