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 red green network_comparison
Results: HTML CSV LaTeX Showing element 1508 to 1557 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
377	ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	Squared	33044.9	40781.4	1.23412	
378	60s ribosomal protein l30. [source:swissprot;acc:p04645]	Ranked	242.593	265.365	1.09387	
378	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Squared	15034.5	18552.2	1.23398	
378	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Measured	12471.7	14561.7	1.16758	
378	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	Rooted	50.5816	45.8738	1.10263	
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	Ranked	241.509	264.163	1.0938	
379	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [source:refseq;acc:nm_005763]	Squared	33010.8	40732.2	1.23391	
379	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Rooted	59.5128	65.604	1.10235	
379	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Measured	6704.44	7811.45	1.16512	
380	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Measured	12998.5	15138.2	1.16461	
380	calcyphosine. [source:swissprot;acc:q13938]	Rooted	59.5128	65.604	1.10235	
380	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	Squared	32991.5	40704.5	1.23379	
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Ranked	242.109	264.79	1.09368	
381	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Rooted	59.5128	65.604	1.10235	
381	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Measured	5246.01	6109.31	1.16456	
381	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	Squared	32987.4	40698.5	1.23376	
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	Ranked	200.586	183.423	1.09357	
382	40s ribosomal protein s23. [source:swissprot;acc:p39028]	Rooted	49.8325	45.2077	1.1023	
382	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	Measured	4533.74	5279.4	1.16447	
382	rna-binding protein. [source:refseq;acc:nm_019027]	Squared	15043.7	18560.1	1.23375	
382	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	Ranked	200.791	183.66	1.09328	
383	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	Rooted	49.8325	45.2077	1.1023	
383	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Squared	15043.7	18560.1	1.23375	
383	hepatoma-derived growth factor-related protein 2. [source:refseq;acc:nm_032631]	Measured	4533.74	5279.4	1.16447	
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	Ranked	237.862	217.739	1.09242	
384	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	Rooted	50.7723	46.0607	1.10229	
384	cgi-142; hepatoma-derived growth factor 2. [source:refseq;acc:nm_016073]	Measured	4533.74	5279.4	1.16447	
384	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Squared	15043.7	18560.1	1.23375	
384	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]	Ranked	266.421	244.236	1.09083	
385	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]	Rooted	50.7723	46.0607	1.10229	
385	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Squared	15043.7	18560.1	1.23375	
385	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	Measured	4533.74	5279.4	1.16447	
385	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Ranked	266.421	244.236	1.09083	
386	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	Ranked	242.238	264.11	1.09029	
386	60s ribosomal protein l8. [source:swissprot;acc:p25120]	Measured	4533.74	5279.4	1.16447	
386	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Rooted	50.0513	45.4124	1.10215	
386	scratch; scratch 1. [source:refseq;acc:nm_031309]	Squared	40388.9	49827.5	1.23369	
387	40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	Ranked	242.238	264.11	1.09029	
387	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	Rooted	50.3345	45.6718	1.10209	
387	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Squared	15053	18568	1.23351	
387	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	Measured	4533.74	5279.4	1.16447	
388	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [source:sptrembl;acc:q9nq03]	Squared	40315.7	49716.4	1.23318	
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	Measured	4533.74	5279.4	1.16447	
388	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	Rooted	50.3345	45.6718	1.10209	
388	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Ranked	227.575	208.756	1.09015	
389	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Rooted	50.3345	45.6718	1.10209	
389	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	Squared	31819.7	39222.2	1.23264	
389	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	Measured	4533.74	5279.4	1.16447	
389	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Ranked	227.575	208.756	1.09015	
390	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	Ranked	241.828	263.62	1.09011	

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/