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

Results: HTML CSV LaTeX

Showing element 773 to 822 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
49	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Measured	Subtracted	1	24806.9	20369.9	4437
	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Squared			201896	131906	69990
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Ranked			350	290	60
	dead-box protein. [refseq;acc:nm_018665]			0	10628.3	14486	3857.7
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Squared	Divided		8.10857	43.7473	5.39519
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Measured	Subtracted		153	662	509
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Rooted	Divided	1	27.7254	44.0299	1.58807
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]		Subtracted		137.446	120.823	16.623
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Measured	Divided		779.167	1390.33	1.78438
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Rooted	Subtracted	0	21.8651	29.828	7.9629
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]		Divided		14.1508	8.89106	1.59158
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Measured			72	151	2.09722
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Ranked		1	133	105	1.26667
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]			0	9249.73	13091.4	1.41533
			Subtracted				3841.67
	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Measured		1	24473.9	20127.8	4346.1
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Ranked			350	290	60
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared			173408	242989	69581
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Rooted	Divided	0	11.0328	6.96286	1.58452
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]			1	27.7254	44.0299	1.58807
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		Subtracted		137.446	120.823	16.623
	mstp028 protein. [refseq;acc:nm_031954]	Squared		0	105962	110835	4873
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Measured	Divided	1	779.167	1390.33	1.78438
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Squared		0	10.974	2.38124	4.60852
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]			1	28994.2	17134.8	1.69212
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Rooted	Subtracted	0	7.74597	0	7.74597
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Measured	Divided		44	21	2.09524
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]		Subtracted		4962.34	5469.68	507.34
51	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	Squared	Divided		0.872309	3.99932	4.58475
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]			1	28994.2	17134.8	1.69212
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Ranked	Subtracted		350	290	60
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Squared		0	21584.2	16770.2	4814
	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	Measured		1	23640.2	19479.8	4160.4
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Ranked		0	12143.8	8356.02	3787.78
		Rooted			14.8299	22.5463	7.7164
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]			1	137.446	120.823	16.623
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Squared			173408	242989	69581
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Ranked	Divided	0	7168	5102	1.40494
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Rooted		1	27.7254	44.0299	1.58807
	nanos (fragment). [sptrembl;acc:q8wy41]			0	19.4165	12.2882	1.58009
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Measured		1	779.167	1390.33	1.78438
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]			0	184.422	88.5622	2.0824
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]		Subtracted		4962.34	5469.68	507.34
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Ranked	Divided	1	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]			0	3284	4554.5	1.38688
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Measured		1	779.167	1390.33	1.78438
	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]		Subtracted		23422.4	19380.3	4042.1
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Divided	0	999.28	481.725	2.07438
	fos-related antigen 2. [swissprot;acc:p15408]	Squared	Subtracted		6691.06	2188.28	4502.78

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.