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

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Showing element 6408 to 6457 of 29840 in total

Interaction Map  : High confidence

red	Network Comparison Type	Value Type	Rank	description	green	Filtered	network_comparison
57.7168	Subtracted	Rooted	2568	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312]	58.2731	1	0.5563
			2569	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
			2570	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]
57.8009	Divided		1247	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]	55.3045		1.04514
	Subtracted		1406				2.4964
57.805	Divided		734	loh1cr12. [refseq;acc:nm_058169]	61.7803		1.06877
			735	unr protein. [swissprot;acc:o75534]
	Subtracted		833	loh1cr12. [refseq;acc:nm_058169]			3.9753
			834	unr protein. [swissprot;acc:o75534]
57.808	Divided		2094	gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793]	59.2765		1.0254
	Subtracted		2165				1.4685
57.8256	Divided		2623	40s ribosomal protein s3a. [swissprot;acc:p49241]	57.434		1.00682
	Subtracted		2635				0.3916
57.8417	Divided	Squared	59	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	218.049	0	3.76975
	Subtracted		246				160.207
57.8563	Divided	Rooted	1265	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	55.3779	1	1.04475
	Subtracted		1414				2.4784
57.8738	Divided		2650	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	58.2094		1.0058
	Subtracted		2659				0.3356
57.8919	Divided		1136	caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844]	60.7081		1.04865
	Subtracted		1242				2.8162
57.9068	Divided		280	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	64.8562		1.12001
			281	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
	Subtracted		344	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]			6.9494
			345	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
57.9415	Divided		2573	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	57.4389		1.00875
	Subtracted		2597				0.5026
57.9449	Divided		794	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	61.719		1.06513
	Subtracted		887				3.7741
57.9819	Divided		282	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	64.9302		1.11984
			283	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]
	Subtracted		346	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]			6.9483
			347	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]
57.9924	Divided		1266	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	60.5835		1.04468
	Subtracted		1347				2.5911
58	Divided	Ranked	23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	44		1.31818
			24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
			25	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
			26	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
			27	mitochondrial solute carrier protein. [refseq;acc:nm_145305]
	Subtracted		533	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]			14
			534	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
			538	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
			540	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
			545	mitochondrial solute carrier protein. [refseq;acc:nm_145305]
58.0178	Divided	Rooted	1220	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	60.6658		1.04564
	Subtracted		1320				2.648
58.0289	Divided		1013	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849]	61.136		1.05354
			1014	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]
			1015	n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569]

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.