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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 544 to 593 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	green	red	network_comparison	
272	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	0	7759.61	7163.55	1.08321	
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	1	267.352	241.373	1.10763	
273	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	0	11770.9	12748.1	1.08302	
274	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	0	11298.4	10432.4	1.08301	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	1	267.352	241.373	1.10763	
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	1	267.352	241.373	1.10763	
275	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	0	11674.1	10783	1.08264	
276	60s ribosomal protein l32. [source:swissprot;acc:p02433]	1	266.969	241.13	1.10716	
276	60s ribosomal protein l9. [source:swissprot;acc:p32969]	0	9922.33	10741.6	1.08257	
277	40s ribosomal protein s29. [source:swissprot;acc:p30054]	1	267.642	241.849	1.10665	
277	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	0	10251.6	11096.8	1.08245	
278	40s ribosomal protein s11. [source:swissprot;acc:p04643]	1	267.088	241.399	1.10642	
278	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	0	10763.4	11644	1.08181	
279	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5]	0	9812.39	10614.2	1.08171	
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	1	228.42	252.644	1.10605	
280	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	0	11471.2	10620.1	1.08014	
280	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	1	228.356	252.512	1.10578	
281	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	1	267.335	241.808	1.10557	
281	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [source:swissprot;acc:q9nry6]	0	13514.5	12522.7	1.0792	
282	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). [source:swissprot;acc:q09028]	1	228.297	252.39	1.10553	
282	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	0	8732.68	8095.69	1.07868	
283	60s ribosomal protein l11. [source:swissprot;acc:p39026]	1	267.346	241.828	1.10552	
283	lifeguard; kiaa0950 protein. [source:refseq;acc:nm_012306]	0	11959.2	11107.1	1.07672	
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	1	203.235	224.657	1.10541	
284	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	0	16041.6	14898.9	1.0767	
285	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	0	9925.58	10686	1.07661	
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	1	203.242	224.647	1.10532	
286	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	0	11367.3	12228.2	1.07573	
286	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	1	203.251	224.633	1.1052	
287	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	1	266.079	240.758	1.10517	
287	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	0	16590.3	17842.7	1.07549	
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	1	266.078	240.758	1.10517	
288	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	0	16053	14930.6	1.07517	
289	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	0	14091.9	15147.2	1.07489	
289	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	1	246.892	272.781	1.10486	
290	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	0	14091.9	15147.2	1.07489	
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	1	210.064	231.969	1.10428	
291	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [source:refseq;acc:nm_003902]	0	11731.8	10922.9	1.07406	
291	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	1	228.037	251.679	1.10368	
292	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	1	266.414	241.411	1.10357	
292	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	0	9574.98	10280.5	1.07368	
293	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	1	265.717	240.782	1.10356	
293	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	0	9583.27	10287.1	1.07344	
294	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [source:refseq;acc:nm_016567]	1	265.717	240.782	1.10356	
294	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [source:swissprot;acc:q16514]	0	13025.1	13981.5	1.07343	
295	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	1	202.423	223.273	1.103	
295	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [source:swissprot;acc:q9y690]	0	12751.8	13687.7	1.07339	
296	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [source:swissprot;acc:p36776]	0	10941.8	10194.1	1.07335	
296	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	1	266.12	241.282	1.10294	
297	60s ribosomal protein l7. [source:swissprot;acc:p18124]	1	259.984	235.727	1.1029	

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/