Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1812 to 1861 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
453	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Ranked	224.161	207.972	1.07784	
454	40s ribosomal protein s26. [source:swissprot;acc:p02383]	Ranked	210.224	226.578	1.07779	
454	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	Rooted	50.4595	46.0412	1.09596	
454	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Measured	3760.8	4315.06	1.14738	
454	sporulation-induced transcript 4-associated protein. [source:refseq;acc:nm_018312]	Squared	31620.5	38250.7	1.20968	
455	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:q13085]	Squared	31597.8	38216.9	1.20948	
455	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	Measured	4890.51	5610.95	1.14731	
455	mitochondrial import inner membrane translocase subunit tim22. [source:swissprot;acc:q9y584]	Ranked	210.225	226.578	1.07779	
455	zinc finger protein 291. [source:swissprot;acc:q9by12]	Rooted	50.4595	46.0413	1.09596	
456	atp synthase mitochondrial f1 complex assembly factor 2. [source:refseq;acc:nm_145691]	Ranked	210.225	226.578	1.07779	
456	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [source:swissprot;acc:q06545]	Measured	4890.51	5610.95	1.14731	
456	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	Squared	10933.6	13219.6	1.20908	
456	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	Rooted	50.4595	46.0413	1.09596	
457	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [source:swissprot;acc:o00217]	Measured	4890.51	5610.95	1.14731	
457	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	Squared	10936.1	13221.9	1.20901	
457	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	Rooted	50.4595	46.0413	1.09596	
457	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [source:swissprot;acc:p14927]	Ranked	210.225	226.578	1.07779	
458	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	Rooted	50.2954	45.9216	1.09524	
458	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	Measured	4890.55	5610.96	1.14731	
458	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	Squared	10950.4	13235.9	1.20871	
458	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Ranked	235.922	218.925	1.07764	
459	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	Ranked	233.529	216.737	1.07748	
459	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	Measured	4892.16	5611.48	1.14704	
459	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	Squared	27096.7	32743.5	1.20839	
459	vav proto-oncogene. [source:swissprot;acc:p15498]	Rooted	66.0892	72.3741	1.0951	
460	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	Measured	3790.11	4346.98	1.14693	
460	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Rooted	50.6156	46.2239	1.09501	
460	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Ranked	223.648	207.62	1.0772	
460	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [source:refseq;acc:nm_003349]	Squared	29547.4	35683.5	1.20767	
461	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Rooted	50.6156	46.2239	1.09501	
461	grb2-related adaptor protein. [source:swissprot;acc:q13588]	Measured	5986.65	6865.68	1.14683	
461	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). [source:swissprot;acc:q13887]	Ranked	223.648	207.62	1.0772	
461	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [source:swissprot;acc:q16851]	Squared	29544.1	35678.3	1.20763	
462	40s ribosomal protein s3. [source:swissprot;acc:p23396]	Rooted	50.6274	46.236	1.09498	
462	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	Ranked	254.434	236.224	1.07709	
462	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	Measured	11383.2	9926.61	1.14674	
462	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [source:refseq;acc:nm_003350]	Squared	29540.4	35672.6	1.20759	
463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	Measured	3720.18	4264.46	1.1463	
463	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [source:swissprot;acc:p98194]	Squared	25533.3	30810.8	1.20669	
463	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [source:swissprot;acc:q9h1d9]	Ranked	238.921	257.327	1.07704	
463	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [source:swissprot;acc:p31749]	Rooted	50.2317	55.0025	1.09498	
464	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6]	Ranked	210.578	226.764	1.07686	
464	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Measured	4858.96	5568.85	1.1461	
464	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [source:swissprot;acc:q03014]	Squared	54726.7	45358.5	1.20654	
464	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). [source:swissprot;acc:q9y243]	Rooted	50.2317	55.0025	1.09498	
465	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Ranked	248.152	267.226	1.07686	
465	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [source:swissprot;acc:p31751]	Rooted	50.2317	55.0025	1.09498	
465	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Measured	3847.31	4409.22	1.14605	
465	trna isopentenylpyrophosphate transferase. [source:refseq;acc:nm_017646]	Squared	25310.2	30537	1.20651	
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Ranked	248.152	267.226	1.07686	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/