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 red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2130 to 2179 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1065	zinc finger protein 305. [source:swissprot;acc:o43309]	Divided	269.954	278.219	1.03062	
1066	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Subtracted	124.434	118.318	6.116	
1066	zinc finger protein 18 (zinc finger protein kox11) (fragment). [source:swissprot;acc:p17022]	Divided	269.956	278.223	1.03062	
1067	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	Subtracted	213.552	207.463	6.089	
1067	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	Divided	269.956	278.223	1.03062	
1068	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [source:swissprot;acc:q9y6m9]	Subtracted	212.345	206.339	6.006	
1068	zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [source:swissprot;acc:q96gc6]	Divided	269.953	278.215	1.03061	
1069	candidate tumor suppressor in ovarian cancer 2. [source:refseq;acc:nm_080822]	Subtracted	229.243	235.246	6.003	
1069	zinc finger protein 232. [source:swissprot;acc:q9uny5]	Divided	269.954	278.218	1.03061	
1070	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	Subtracted	216.78	222.782	6.002	
1070	zinc finger protein 99. [source:refseq;acc:nm_032164]	Divided	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]	Divided	231.277	238.356	1.03061	
1071	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [source:swissprot;acc:o00566]	Subtracted	241.496	235.508	5.988	
1072	inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [source:swissprot;acc:q15181]	Subtracted	224.307	230.242	5.935	
1072	zinc finger protein 213 (putative transcription factor cr53). [source:swissprot;acc:o14771]	Divided	269.954	278.217	1.03061	
1073	inorganic pyrophosphatase 2 isoform 1. [source:refseq;acc:nm_176869]	Subtracted	224.307	230.242	5.935	
1073	ww domain binding protein 2 (wbp-2). [source:swissprot;acc:q969t9]	Divided	216.901	210.485	1.03048	
1074	aryl-hydrocarbon interacting protein-like 1. [source:swissprot;acc:q9nzn9]	Subtracted	224.307	230.242	5.935	
1074	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	Divided	174.387	179.697	1.03045	
1075	ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [source:swissprot;acc:o00170]	Subtracted	224.307	230.242	5.935	
1075	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	Divided	174.387	179.697	1.03045	
1076	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	Divided	174.387	179.697	1.03045	
1076	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Subtracted	209.123	203.208	5.915	
1077	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	Divided	174.387	179.697	1.03045	
1077	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	Subtracted	218.098	212.209	5.889	
1078	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	Subtracted	218.006	212.119	5.887	
1078	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	Divided	174.387	179.697	1.03045	
1079	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	Divided	174.387	179.697	1.03045	
1079	homeobox protein six1 (sine oculis homeobox homolog 1). [source:swissprot;acc:q15475]	Subtracted	221.286	215.399	5.887	
1080	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [source:swissprot;acc:q9uq80]	Subtracted	221.285	215.4	5.885	
1080	zinc finger protein 444; endothelial zinc finger protein 2. [source:refseq;acc:nm_018337]	Divided	269.896	278.093	1.03037	
1081	40s ribosomal protein s30. [source:swissprot;acc:q05472]	Divided	223.44	216.875	1.03027	
1081	homeobox protein six2 (sine oculis homeobox homolog 2). [source:swissprot;acc:q9npc8]	Subtracted	221.285	215.401	5.884	
1082	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]	Subtracted	209.052	203.183	5.869	
1082	phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	Divided	220.118	213.685	1.03011	
1083	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]	Divided	220.118	213.685	1.03011	
1083	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Subtracted	217.99	212.123	5.867	
1084	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]	Divided	220.118	213.685	1.03011	
1084	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [source:swissprot;acc:q93050]	Subtracted	218.529	212.676	5.853	
1085	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	Divided	231.007	237.864	1.02968	
1085	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	Subtracted	218.528	212.676	5.852	
1086	atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [source:refseq;acc:nm_020632]	Subtracted	218.528	212.676	5.852	
1086	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Divided	236.679	243.679	1.02958	
1087	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [source:swissprot;acc:q13488]	Subtracted	218.527	212.676	5.851	
1087	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Divided	236.679	243.679	1.02958	
1088	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [source:swissprot;acc:p50995]	Divided	219.673	213.378	1.0295	
1088	pxr2b protein. [source:refseq;acc:nm_016559]	Subtracted	212.945	207.109	5.836	
1089	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	Subtracted	218.487	212.656	5.831	
1089	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Divided	121.428	125.004	1.02945	
1090	neurocalcin delta. [source:swissprot;acc:p29554]	Subtracted	225.104	230.931	5.827	

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/