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

Results: HTML CSV LaTeX

Showing element 1830 to 1879 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Value Type	red	green	network_comparison
458	MRPL36	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Rooted	50.2954	45.9216	1.09524
	NXF1	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	Squared	10950.4	13235.9	1.20871
	SRP9	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Ranked	235.922	218.925	1.07764
459	BAG3	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]		233.529	216.737	1.07748
	MYC	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	Measured	4892.16	5611.48	1.14704
	PEF1	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Squared	27096.7	32743.5	1.20839
	VAV1	vav proto-oncogene. [swissprot;acc:p15498]	Rooted	66.0892	72.3741	1.0951
460	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]		50.6156	46.2239	1.09501
	RRP1	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	Measured	3790.11	4346.98	1.14693
	SF3A2	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	Ranked	223.648	207.62	1.0772
	TMEM189	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349]	Squared	29547.4	35683.5	1.20767
461	no value	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Rooted	50.6156	46.2239	1.09501
	GRAP	grb2-related adaptor protein. [swissprot;acc:q13588]	Measured	5986.65	6865.68	1.14683
	KLF5	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]	Ranked	223.648	207.62	1.0772
	UGP2	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	Squared	29544.1	35678.3	1.20763
462	no value	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Measured	11383.2	9926.61	1.14674
	MKI67IP	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Ranked	254.434	236.224	1.07709
	RPS3	40s ribosomal protein s3. [swissprot;acc:p23396]	Rooted	50.6274	46.236	1.09498
	UBE2V2	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350]	Squared	29540.4	35672.6	1.20759
463	AKT1	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	Rooted	50.2317	55.0025	1.09498
	ATP2C1	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194]	Squared	25533.3	30810.8	1.20669
	DDX18	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	Measured	3720.18	4264.46	1.1463
	POLR3F	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	Ranked	238.921	257.327	1.07704
464	AKT3	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]	Rooted	50.2317	55.0025	1.09498
	FNBP1	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	Ranked	210.578	226.764	1.07686
	HHEX	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	Squared	54726.7	45358.5	1.20654
	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Measured	4858.96	5568.85	1.1461
465	AKT2	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	Rooted	50.2317	55.0025	1.09498
	CHRNA7	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Ranked	248.152	267.226	1.07686
	E2F1	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]	Measured	3847.31	4409.22	1.14605
	TRIT1	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	Squared	25310.2	30537	1.20651
466	ADCY6	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Ranked	248.152	267.226	1.07686
	ATP2C2	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Squared	25513.6	30779.5	1.2064
	E2F2	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Measured	3847.31	4409.22	1.14605
	VAV3	vav-3 protein. [swissprot;acc:q9ukw4]	Rooted	66.089	72.3555	1.09482
467	ADCY5	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Ranked	248.152	267.226	1.07686
	MTA1	metastasis-associated protein mta1. [swissprot;acc:q13330]	Measured	4864.25	5573.62	1.14583
	NUCB1	nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	Squared	23531.7	28371.6	1.20568
	RPS5	40s ribosomal protein s5. [swissprot;acc:p46782]	Rooted	50.4649	46.1093	1.09446
468	CCT3	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]		107.178	117.276	1.09422
	LRRC15	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Ranked	248.152	267.226	1.07686
	MLH1	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Squared	23531.7	28371.6	1.20568
	RBBP4	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	Measured	4869.15	5578.02	1.14558
469	no value	60s ribosomal protein l9. [swissprot;acc:p32969]	Rooted	51.1334	46.7335	1.09415
	FEM1B	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Ranked	248.152	267.226	1.07686
	NOL1	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Measured	3831.17	4388.74	1.14554
	NUCB2	nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]	Squared	23531.7	28371.6	1.20568
470	BOP1	block of proliferation 1. [swissprot;acc:q14137]	Measured	3796.24	4348.59	1.1455
	LRRC3	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Ranked	248.152	267.226	1.07686
	PPP2R1B	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Squared	10418.3	8641.84	1.20557

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.