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

Results: HTML CSV LaTeX

Showing element 808 to 857 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison
101	SEPT6	septin 6. [swissprot;acc:q14141]	Squared	Subtracted	88953.6	124854	35900.4
102	CLP1	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]			121200	85473.4	35726.6
	CPEB4	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Rooted		19.9625	35.798	15.8355
	FIP1L1	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	Squared	Divided	214143	138337	1.54798
	FOSL1	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Ranked	Subtracted	204.642	161.068	43.574
	MAGED2	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]		Divided	88.2482	110.265	1.24949
	PSEN1	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Measured		2353.63	3225.65	1.3705
	RAP1GAP	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	Rooted		47.6504	36.9304	1.29028
	STAMBPL1	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Measured	Subtracted	11068	8508.5	2559.5
103	no value	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Squared	Divided	407289	263351	1.54656
	CHMP2A	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Measured	Subtracted	11068	8508.5	2559.5
	CPEB3	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Rooted		19.9625	35.798	15.8355
	CUL1	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Measured	Divided	2353.63	3225.65	1.3705
	FOS	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Rooted		60.8365	77.7233	1.27758
	JUNB	transcription factor jun-b. [swissprot;acc:p17275]	Ranked	Subtracted	201.144	158.868	42.276
	SYMPK	symplekin. [swissprot;acc:q92797]	Squared		124118	88668.8	35449.2
	TRO	trophinin. [swissprot;acc:q12816]	Ranked	Divided	88.2482	110.265	1.24949
104	no value	jun dimerization protein. [refseq;acc:nm_130469]	Rooted		60.8365	77.7233	1.27758
	CSTF2T	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	Squared	Subtracted	121579	87259.3	34319.7
	HOMER2	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Ranked	Divided	252.371	202.016	1.24926
	MSI2	musashi 2 isoform a. [refseq;acc:nm_138962]	Measured		4241.57	5810.79	1.36996
	PSCD1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Squared		407289	263351	1.54656
	RASAL2	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Rooted	Subtracted	19.9625	35.798	15.8355
	STAMBP	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Measured		11068	8508.5	2559.5
	TARDBP	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Ranked		256.228	298.438	42.21
105	no value	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	Rooted		63.7477	48.1588	15.5889
	FOSL2	fos-related antigen 2. [swissprot;acc:p15408]		Divided	60.8675	77.7168	1.27682
	GNB1	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Ranked		266.716	333.165	1.24914
	JUND	transcription factor jun-d. [swissprot;acc:p17535]		Subtracted	200.941	158.941	42
	MSI1	musashi 1. [refseq;acc:nm_002442]	Measured	Divided	4241.57	5810.79	1.36996
	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Squared		407289	263351	1.54656
	RALGDS	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]		Subtracted	90432.9	56304.2	34128.7
	VPS24	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Measured		11068	8508.5	2559.5
106	CHMP4A	protein hspc134 (protein cda04). [swissprot;acc:q9by43]
	COQ7	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Ranked	Divided	252.329	202.004	1.24913
	FOSB	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Rooted		60.8692	77.7165	1.27678
	NOSTRIN	nostrin. [refseq;acc:nm_052946]	Ranked	Subtracted	209.299	249.187	39.888
	PPP2R2D	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Rooted		63.7477	48.1589	15.5888
	PSCD4	cytohesin 4. [swissprot;acc:q9uia0]	Squared	Divided	407289	263351	1.54656
	SEPT4	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]		Subtracted	82624.3	115061	32436.7
	ZC3H14	nuclear protein ukp68. [refseq;acc:nm_024824]	Measured	Divided	4241.57	5810.79	1.36996
107	FOSL1	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Rooted		60.875	77.7152	1.27664
	HOMER1	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Ranked		252.309	201.998	1.24907
	NCBP2	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Measured		4266.04	5843.51	1.36977
	PPP2R2B	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	Rooted	Subtracted	63.7477	48.1594	15.5883
	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Squared	Divided	407289	263351	1.54656
	RGL1	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]		Subtracted	84857.8	53402.4	31455.4
	SEPT1	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Measured		14229.2	16780.7	2551.5
	SNF8	eap30 subunit of ell complex. [refseq;acc:nm_007241]	Ranked		209.299	249.187	39.888
108	no value	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Squared	Divided	19321	12542.6	1.54043

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.