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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

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Showing element 712 to 761 of 66312 in total

Filtered  : 1

Rank	description	Hugo	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
45	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	no value	Subtracted	Squared	Low confidence	82347.8	61881.5	20466.3
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	MFAP4	Divided	Ranked		242.742	217.217	1.11751
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	no value	Subtracted	Squared	High confidence	110342	184298	73956
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	FOSB	Divided	Ranked		204.641	161.051	1.27066
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	PPP1R7	Subtracted	Measured		27642.5	22440.4	5202.1
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	FOS	Divided	Rooted	Low confidence	66.5831	75.4064	1.13252
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	RGS12	Subtracted			54.8296	63.2347	8.4051
	transcription factor jun-b. [swissprot;acc:p17275]	JUNB	Divided	Measured		6613.42	7678.76	1.16109
	transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9]	BACH2	Subtracted			8313.02	9645.34	1332.32
46	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	ATG3	Divided	Squared	High confidence	129597	73157.5	1.77148
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	no value	Subtracted	Rooted	Low confidence	75.6323	67.6572	7.9751
	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	CPSF4		Measured	High confidence	24896.4	20431.7	4464.7
	deltex 2. [refseq;acc:nm_020892]	DTX2	Divided	Rooted		27.634	43.9629	1.5909
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	FOSL1		Ranked		204.642	161.068	1.27053
	jun dimerization protein. [refseq;acc:nm_130469]	no value		Rooted	Low confidence	66.5831	75.4064	1.13252
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	MAGED4	Subtracted		High confidence	137.446	120.823	16.623
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	MAGEA9		Squared	Low confidence	82347.8	61881.5	20466.3
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	MAGEB4	Divided					1.33073
	neuralized-like. [refseq;acc:nm_004210]	NEURL	Subtracted	Ranked	High confidence	332.326	266.948	65.378
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	NEUROD2	Divided	Measured		779.167	1390.33	1.78438
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	PAPOLA	Subtracted	Squared		210445	136779	73666
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	no value		Ranked	Low confidence	242.742	217.217	25.525
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	PPP1R14D	Divided					1.11751
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	SEPT7	Subtracted	Measured		11616	12942.3	1326.3
	transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867]	BACH1	Divided			8313.02	9645.34	1.16027
47	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	CHD3			High confidence	779.167	1390.33	1.78438
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	DTX1		Rooted		27.7078	44.017	1.58861
	exocyst complex component sec5. [swissprot;acc:q96kp1]	EXOC2	Subtracted	Squared		210335	136716	73619
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	FCN2	Divided	Ranked	Low confidence	242.742	217.217	1.11751
	fos-related antigen 2. [swissprot;acc:p15408]	FOSL2		Rooted		66.6469	75.3812	1.13105
	gbp protein isoform a. [refseq;acc:nm_017870]	TMEM132A		Ranked	High confidence	325.586	256.492	1.26938
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	MAGEE2	Subtracted	Rooted		137.446	120.823	16.623
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	MAGEA8		Squared	Low confidence	82347.8	61881.5	20466.3
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	MAGED2	Divided					1.33073
	nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236]	NFE2L2		Measured		8313.02	9645.34	1.16027
	rab11-family interacting protein 4. [refseq;acc:nm_032932]	RAB11FIP4	Subtracted			7407.56	8696.7	1289.14
				Rooted		73.6221	81.4944	7.8723
	testis-specific protein tex28. [swissprot;acc:o15482]	TEX28P2		Ranked		259.517	235.017	24.5
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	TOB2			High confidence	350	290	60
	trs85 homolog. [swissprot;acc:q9y2l5]	KIAA1012		Measured		24896.4	20431.7	4464.7
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	no value	Divided	Squared		98517.9	56927.2	1.73059
48	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	GOSR2	Subtracted	Ranked	Low confidence	259.517	235.017	24.5
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	CDK2AP2	Divided	Measured	High confidence	779.167	1390.33	1.78438
	eferin. [swissprot;acc:o75154]	RAB11FIP3	Subtracted		Low confidence	7407.56	8696.7	1289.14
				Rooted		73.6221	81.4944	7.8723
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	GABARAP	Divided	Ranked	High confidence	65.4586	83.0461	1.26868
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	LASS2		Squared		6300.2	10703.5	1.69891
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	no value	Subtracted	Rooted		137.446	120.823	16.623
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	MAGEC1		Squared	Low confidence	82347.8	61881.5	20466.3
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	PAPOLG			High confidence	210199	136638	73561

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.