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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1058 to 1107 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
1058	ATXN2L	ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	228.105	221.293	1.03078	
1059		ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	228.105	221.293	1.03078	
1060	NLK	nemo-like kinase; likely ortholog of mouse nemo like kinase. [source:refseq;acc:nm_016231]	218.162	211.648	1.03078	
1061	ERC1	elks protein. [source:refseq;acc:nm_015064]	218.162	211.648	1.03078	
1062	ZNF174	zinc finger protein 174 (aw-1). [source:swissprot;acc:q15697]	269.963	278.239	1.03066	
1063		zinc finger imprinted 2. [source:swissprot;acc:q9nzv7]	269.96	278.232	1.03064	
1064	ZNF24	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [source:swissprot;acc:p17028]	269.955	278.221	1.03062	
1065	ZSCAN12	zinc finger protein 305. [source:swissprot;acc:o43309]	269.954	278.219	1.03062	
1066	ZNF18	zinc finger protein 18 (zinc finger protein kox11) (fragment). [source:swissprot;acc:p17022]	269.956	278.223	1.03062	
1067	ZNF215	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	269.956	278.223	1.03062	
1068	ZNF274	zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [source:swissprot;acc:q96gc6]	269.953	278.215	1.03061	
1069	ZNF232	zinc finger protein 232. [source:swissprot;acc:q9uny5]	269.954	278.218	1.03061	
1070	ZNF394	zinc finger protein 99. [source:refseq;acc:nm_032164]	269.954	278.218	1.03061	
1071		dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]	231.277	238.356	1.03061	
1072	ZNF213	zinc finger protein 213 (putative transcription factor cr53). [source:swissprot;acc:o14771]	269.954	278.217	1.03061	
1073	WBP2	ww domain binding protein 2 (wbp-2). [source:swissprot;acc:q969t9]	216.901	210.485	1.03048	
1074	COPB2	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	174.387	179.697	1.03045	
1075	COPG	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	174.387	179.697	1.03045	
1076	COPZ1	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	174.387	179.697	1.03045	
1077	ARCN1	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	174.387	179.697	1.03045	
1078	PPIE	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	174.387	179.697	1.03045	
1079	COPZ2	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	174.387	179.697	1.03045	
1080	ZNF444	zinc finger protein 444; endothelial zinc finger protein 2. [source:refseq;acc:nm_018337]	269.896	278.093	1.03037	
1081	FAU	40s ribosomal protein s30. [source:swissprot;acc:q05472]	223.44	216.875	1.03027	
1082	PLEKHF2	phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	220.118	213.685	1.03011	
1083	SRD5A1	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [source:swissprot;acc:p18405]	220.118	213.685	1.03011	
1084	SRD5A2	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [source:swissprot;acc:p31213]	220.118	213.685	1.03011	
1085	DKC1	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	231.007	237.864	1.02968	
1086		similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	236.679	243.679	1.02958	
1087		zinc finger protein 277. [source:swissprot;acc:q9nrm2]	236.679	243.679	1.02958	
1088	ANXA11	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [source:swissprot;acc:p50995]	219.673	213.378	1.0295	
1089	CSTF3	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	121.428	125.004	1.02945	
1090		similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	226.218	232.88	1.02945	
1091		block 23. [source:sptrembl;acc:q8nhw5]	226.205	232.858	1.02941	
1092	RPLP0	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	226.203	232.855	1.02941	
1093	COPA	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	177.432	182.647	1.02939	
1094	ANXA7	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	219.655	213.385	1.02938	
1095	GTPBP3	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	213.552	207.463	1.02935	
1096	NDUFB9	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [source:swissprot;acc:q9y6m9]	212.345	206.339	1.02911	
1097	ATP2C2	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	209.123	203.208	1.02911	
1098	AP3M1	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [source:swissprot;acc:q9y2t2]	217.323	211.185	1.02906	
1099	AP3M2	adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [source:swissprot;acc:p53677]	217.315	211.183	1.02904	
1100	ATP2C1	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]	209.052	203.183	1.02889	
1101	KARS	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [source:swissprot;acc:q15046]	220.291	226.584	1.02857	
1102		40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	229.442	235.974	1.02847	
1103	RPS27L	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [source:refseq;acc:nm_015920]	229.441	235.972	1.02846	
1104	HAO1	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [source:swissprot;acc:q9ujm8]	231.922	238.486	1.0283	
1105	FDX1	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	191.139	185.882	1.02828	
1106	PEX5L	pxr2b protein. [source:refseq;acc:nm_016559]	212.945	207.109	1.02818	
1107	SPTLC2	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [source:swissprot;acc:o15270]	204.603	210.324	1.02796	

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