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

Results: HTML CSV LaTeX

Showing element 7264 to 7313 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison
908	Rooted	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	Divided	62.6851	66.4615	1.06024
909	Measured	kinesin family member c3. [refseq;acc:nm_005550]		5995.49	6595.35	1.10005
		probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	Subtracted	3758.67	4322.87	564.2
	Ranked	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Divided	142.077	136.846	1.03823
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Subtracted	129.219	121.261	7.958
	Squared	atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]	Divided	28767.1	33317.5	1.15818
		metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Subtracted	23598.8	27286.9	3688.1
	Rooted	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]		62.3496	66.0388	3.6892
		propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166]	Divided	62.6851	66.4615	1.06024
910	Measured	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Subtracted	3766.03	4329.37	563.34
		sipl protein. [refseq;acc:nm_018269]	Divided	6522.94	7175.18	1.09999
	Ranked	bet3 homolog. [swissprot;acc:o43617]	Subtracted	129.219	121.261	7.958
		uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	Divided	217.168	209.207	1.03805
	Squared	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]		19732.4	22852.4	1.15812
		serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269]	Subtracted	25660.4	29342.7	3682.3
	Rooted	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]		67.7551	71.4422	3.6871
		programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	Divided	55.9078	59.2557	1.05988
911	Measured	ad24 protein. [refseq;acc:nm_022451]	Subtracted	3753.71	4315.95	562.24
		prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	Divided	4982.81	5480.91	1.09996
	Ranked	ero1-like. [refseq;acc:nm_014584]		217.168	209.207	1.03805
		mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	Subtracted	225.955	218.015	7.94
	Squared	bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814]		22573.3	26254.5	3681.2
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Divided	13688.1	15849.2	1.15788
	Rooted	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Subtracted	58.5869	62.2732	3.6863
		retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	Divided	64.1165	67.9451	1.05971
912	Measured	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]		4982.81	5480.91	1.09996
		transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Subtracted	3847.31	4409.22	561.91
	Ranked	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]		225.939	218.013	7.926
		wd-repeat protein 3. [swissprot;acc:q9unx4]	Divided	243.896	234.96	1.03803
	Squared	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]		30826.4	35693.3	1.15788
		serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6]	Subtracted	26914.1	30594.2	3680.1
	Rooted	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]		58.5944	62.2766	3.6822
		retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	Divided	64.1184	67.9467	1.05971
913	Measured	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Subtracted	3847.31	4409.22	561.91
		ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	Divided	5768.5	6342.05	1.09943
	Ranked	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	Subtracted	243.297	235.373	7.924
		prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	Divided	210.863	218.878	1.03801
	Squared	ran-gtp binding protein (fragment). [sptrembl;acc:o60518]		30802.6	35663.9	1.15782
		serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956]	Subtracted	26914.1	30594.2	3680.1
	Rooted	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	Divided	82.0749	86.9643	1.05957
		mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	Subtracted	58.6002	62.2793	3.6791
914	Measured	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	Divided	6513.45	7161	1.09942
		hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]	Subtracted	4997	5557.17	560.17
	Ranked	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]		237.558	229.677	7.881
		pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399]	Divided	210.863	218.878	1.03801
	Squared	15 kda selenoprotein precursor. [swissprot;acc:o60613]		29772.1	34456.5	1.15734
		glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]	Subtracted	26914.1	30594.2	3680.1
	Rooted	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995]	Divided	61.4687	65.1194	1.05939
		vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050]	Subtracted	62.4102	66.0829	3.6727
915	Measured	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	Divided	6289.72	6911.96	1.09893

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.