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

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Showing element 1380 to 1429 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	green	red	network_comparison
690	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Divided	208.987	220.593	1.05553
691	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]		206.195	217.602	1.05532
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Subtracted	211.685	223.121	11.436
692	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]	Divided	206.195	217.602	1.05532
	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	Subtracted	211.685	223.121	11.436
693	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]		206.195	217.602	11.407
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	Divided	234.847	222.554	1.05524
694	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]	Subtracted	206.195	217.602	11.407
	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	Divided	229.35	241.907	1.05475
695	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Subtracted	199.398	210.739	11.341
	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	Divided	214.405	226.135	1.05471
696	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Subtracted	199.398	210.739	11.341
	sr rich protein. [refseq;acc:nm_032870]	Divided	213.64	225.293	1.05455
697	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]		209.113	220.444	1.05419
		Subtracted			11.331
698	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]		209.118	220.438	11.32
	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	Divided		220.437	1.05413
699	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]			220.438
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Subtracted			11.32
700	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Divided			1.05413
701	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]
	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]	Subtracted			11.32
702	limkain b1. [refseq;acc:nm_019081]
	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]	Divided			1.05413
703	limkain b1. [refseq;acc:nm_019081]
	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]	Subtracted			11.32
704	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]	Divided			1.05413
705	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]	Subtracted			11.32
706		Divided			1.05413
	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]	Subtracted			11.32
707	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]	Divided			1.05413
708	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]	Subtracted			11.32
709	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]	Divided			1.05413
710	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	Subtracted		220.437	11.319
711	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]		209.123	220.431	11.308
	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	Divided	245.048	232.468	1.05411
712	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584]	Subtracted	243.933	232.762	11.171
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Divided	209.123	220.431	1.05407
713	dendritic cell protein. [refseq;acc:nm_006360]		211.685	223.121	1.05402
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Subtracted	235.583	224.434	11.149
714	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	Divided	211.685	223.121	1.05402
715	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]

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.