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 1077 to 1126 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
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	
1108	FOXK2	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	218.006	212.119	1.02775	
1109	TPT1	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	218.098	212.209	1.02775	
1110	GIT2	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	216.78	222.782	1.02769	
1111		apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	217.99	212.123	1.02766	
1112	HNF4G	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	251.863	258.829	1.02766	
1113	GADD45G	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	251.863	258.829	1.02766	
1114	GADD45A	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	251.863	258.829	1.02766	
1115	HNF4A	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [source:swissprot;acc:p41235]	251.863	258.829	1.02766	
1116	GADD45B	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [source:swissprot;acc:o75293]	251.863	258.829	1.02766	
1117	NXF5	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	168.989	164.46	1.02754	
1118	NXF3	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	168.995	164.467	1.02753	
1119	ATP6V0A2	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	218.528	212.676	1.02752	
1120	ATP6V0A4	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]	218.528	212.676	1.02752	
1121	ATP6V0A1	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]	218.529	212.676	1.02752	
1122	TCIRG1	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]	218.527	212.676	1.02751	
1123	NXF1	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	169.031	164.507	1.0275	
1124	PRDX5	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [source:swissprot;acc:p30044]	207.553	213.256	1.02748	
1125		dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [source:sptrembl;acc:q9ugb5]	204.404	210.022	1.02748	
1126	ATP6V0D2	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	218.487	212.656	1.02742	

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/