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

Results: HTML CSV LaTeX

Showing element 3682 to 3731 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
461	chromodomain y-like protein 2. [refseq;acc:nm_152342]	Squared	0	18606.3	18263.6	1.01876
	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Measured		1915.69	1892.44	1.01229
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Rooted		62.6706	61.8357	1.0135
	grb2-related adaptor protein. [swissprot;acc:q13588]	Measured	1	5986.65	6865.68	1.14683
	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
	scratch; scratch 1. [refseq;acc:nm_031309]		0	12164.9	12358.1	1.01588
	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	Squared	1	29544.1	35678.3	1.20763
462	40s ribosomal protein s3. [swissprot;acc:p23396]	Rooted		50.6274	46.236	1.09498
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Ranked	0	12189.6	12378.3	1.01548
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Squared		2400.71	2356.66	1.01869
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Measured		11170.7	11305	1.01202
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Ranked	1	254.434	236.224	1.07709
	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
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Rooted	0	18.5298	18.2858	1.01334
	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	1	29540.4	35672.6	1.20759
463	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
	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
	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	Measured	0	1262.65	1248.14	1.01163
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Ranked		5558.06	5473.99	1.01536
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Squared		2403.2	2359.13	1.01868
	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	Ranked	1	238.921	257.327	1.07704
	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
	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]		0	35.7784	35.3221	1.01292
464	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]			30.3413	30.7252	1.01265
	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	Ranked	1	210.578	226.764	1.07686
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		0	10076.4	9928.08	1.01494
	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Measured	1	4858.96	5568.85	1.1461
	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	Squared		54726.7	45358.5	1.20654
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Measured	0	2290.09	2264.37	1.01136
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Squared		18105.2	17795.2	1.01742
	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	1	50.2317	55.0025	1.09498
465	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Measured	0	6323	6254.09	1.01102
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Ranked	1	248.152	267.226	1.07686
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	Squared	0	79185.5	77891.7	1.01661
	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	Rooted		48.2804	48.8876	1.01258
	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]		1	50.2317	55.0025	1.09498
	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
	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	Ranked	0	9482.68	9620.66	1.01455
	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	Squared	1	25310.2	30537	1.20651
466	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
	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]		0	1543	1521	1.01446
		Rooted		78.4729	79.3914	1.0117
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Squared		363053	369010	1.01641
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Measured		1467.74	1483.62	1.01082
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Squared	1	25513.6	30779.5	1.2064
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Measured		3847.31	4409.22	1.14605
	vav-3 protein. [swissprot;acc:q9ukw4]	Rooted		66.089	72.3555	1.09482
467	40s ribosomal protein s5. [swissprot;acc:p46782]			50.4649	46.1093	1.09446
	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
	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Rooted	0	26.5153	26.8089	1.01107

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.