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

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1513 to 1562 of 8289 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1

Rank	Hugo	description	Interaction Map	red	green	network_comparison
757	BPI	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]	High confidence	224.434	235.583	1.04968
	EGFR	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533]	Low confidence	211.344	205.788	1.027
758	ERBB2	receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626]		211.342	205.787	1.02699
	PLTP	phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]	High confidence	224.434	235.583	1.04968
759	ARD1A	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	Low confidence	200.18	194.922	1.02697
	OSTF1	osteoclast stimulating factor 1. [swissprot;acc:q92882]	High confidence	231.809	243.289	1.04952
760	NAT10	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]		246.055	234.458	1.04946
	TNPO3	transportin-sr; importin 12. [refseq;acc:nm_012470]	Low confidence	191.294	186.27	1.02697
761	CBLB	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	High confidence	213.325	203.303	1.0493
	NKX2-3	homeobox protein nkx-2.3 (homeobox protein nkx-2.3) (homeobox protein nk-2 homolog c). [swissprot;acc:q8tau0]	Low confidence	206.052	200.644	1.02695
762	CBL	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	High confidence	213.256	203.237	1.0493
	CHD3	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Low confidence	213.926	208.315	1.02694
763	CHD5	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]		213.929	208.318	1.02693
	N6AMT1	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5]	High confidence	228.78	218.091	1.04901
764	NKX2-5	homeobox protein nkx-2.5 (homeobox protein nk-2 homolog e) (cardiac- specific homeobox) (homeobox protein csx). [swissprot;acc:p52952]	Low confidence	206.038	200.638	1.02691
	PRPF3	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	High confidence	222.082	211.707	1.04901
765	HEMK1	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]		229.045	218.343
	PDIA3	protein disulfide isomerase a3 precursor (ec 5.3.4.1) (disulfide isomerase er-60) (erp60) (58 kda microsomal protein) (p58) (erp57) (58 kda glucose regulated protein). [swissprot;acc:p30101]	Low confidence	204.144	198.795	1.02691
766	CCNY	cyclin fold protein 1; cyclin-box carrying protein 1. [refseq;acc:nm_145012]		206.437	201.034	1.02688
	TRIOBP	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	High confidence	213.804	224.226	1.04875
767	no value	rho interacting protein 3. [refseq;acc:nm_015134]		213.803	224.224	1.04874
	SMARCB1	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824]	Low confidence	206.437	201.034	1.02688
768	CDC34	ubiquitin-conjugating enzyme e2-32 kda complementing (ec 6.3.2.19) (ubiquitin-protein ligase) (ubiquitin carrier protein) (e2-cdc34). [swissprot;acc:p49427]		199.792	194.573	1.02682
	DNAJB4	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4]	High confidence	210.946	221.225	1.04873
769	no value	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Low confidence	198.33	193.155	1.02679
	PERLD1	cab2. [refseq;acc:nm_033419]	High confidence	210.946	221.225	1.04873
770	DNAJB5	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]
	NR2C2	orphan nuclear receptor tr4 (orphan nuclear receptor tak1). [swissprot;acc:p49116]	Low confidence	206.636	212.168	1.02677
771	DNAJB1	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685]	High confidence	210.946	221.225	1.04873
	SNAP29	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	Low confidence	206.636	212.168	1.02677
772	ETF1	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]	High confidence	210.946	221.225	1.04873
	PPP1R3B	protein phosphatase 1, regulatory (inhibitor) subunit 3b. [refseq;acc:nm_024607]	Low confidence	203.48	198.181	1.02674
773	FBXL10	protein containing cxxc domain 2. [refseq;acc:nm_032590]		202.951	208.378
	VPS52	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	High confidence	210.946	221.225	1.04873
774	MCFD2	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]		225.996	215.535	1.04854
	UBAP2	ubiquitin associated protein 2 isoform 1; ad-012 protein. [refseq;acc:nm_018449]	Low confidence	205.905	200.545	1.02673
775	no value	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	High confidence	226.003	215.541	1.04854
	C16orf80	transcription factor iib. [refseq;acc:nm_013242]	Low confidence	205.668	200.313	1.02673
776	no value	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	High confidence	225.996	215.535	1.04854
	MAD1L1	mad1-like 1; mad1 (mitotic arrest deficient, yeast, homolog)-like 1; mitotic-arrest deficient 1, yeast, homolog-like 1; tumor protein p53 inducible protein 9. [refseq;acc:nm_003550]	Low confidence	208.017	202.601	1.02673
777	AP1S3	adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3]		204.807	199.484	1.02668
	HDAC1	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	High confidence	225.989	215.53	1.04853
778	SNX6	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]		209.191	219.332	1.04848
	WDR26	wd repeat domain 26. [refseq;acc:nm_025160]	Low confidence	188.145	183.258	1.02667
779	ABI2	abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759]		202.48	197.229	1.02662
	DCTD	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	High confidence	230.516	241.641	1.04826
780	no value	importin 9. [refseq;acc:nm_018085]	Low confidence	204.192	198.902	1.0266
	POLR2F	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584]	High confidence	232.762	243.933	1.04799
781	MRTO4	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]		245.84	257.636	1.04798
	PRMT7	protein arginine n-methyltransferase (ec 2.1.1.-). [swissprot;acc:q9nvm4]	Low confidence	203.591	198.319	1.02658

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.