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 2180 to 2229 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1090	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	Divided	226.218	232.88	1.02945	
1091	block 23. [source:sptrembl;acc:q8nhw5]	Divided	226.205	232.858	1.02941	
1091	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [source:swissprot;acc:p32076]	Subtracted	225.103	230.928	5.825	
1092	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	Divided	226.203	232.855	1.02941	
1092	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [source:swissprot;acc:p37235]	Subtracted	225.094	230.913	5.819	
1093	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Divided	177.432	182.647	1.02939	
1093	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	Subtracted	218.484	212.675	5.809	
1094	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	Divided	219.655	213.385	1.02938	
1094	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	Subtracted	218.484	212.675	5.809	
1095	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	Divided	213.552	207.463	1.02935	
1095	sec13-related protein. [source:swissprot;acc:p55735]	Subtracted	218.484	212.675	5.809	
1096	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [source:swissprot;acc:q9y6m9]	Divided	212.345	206.339	1.02911	
1096	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [source:swissprot;acc:q96lb4]	Subtracted	218.484	212.675	5.809	
1097	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Divided	209.123	203.208	1.02911	
1097	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [source:swissprot;acc:p21281]	Subtracted	218.484	212.675	5.809	
1098	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [source:swissprot;acc:q9y2t2]	Divided	217.323	211.185	1.02906	
1098	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Subtracted	218.484	212.675	5.809	
1099	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]	Divided	217.315	211.183	1.02904	
1099	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [source:swissprot;acc:o75348]	Subtracted	218.484	212.675	5.809	
1100	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]	Divided	209.052	203.183	1.02889	
1100	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [source:swissprot;acc:p36543]	Subtracted	218.484	212.675	5.809	
1101	ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	Subtracted	218.484	212.675	5.809	
1101	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [source:swissprot;acc:q15046]	Divided	220.291	226.584	1.02857	
1102	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Divided	229.442	235.974	1.02847	
1102	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [source:refseq;acc:nm_005804]	Subtracted	218.484	212.675	5.809	
1103	ganglioside-induced differentiation-associated protein 1. [source:refseq;acc:nm_018972]	Subtracted	218.484	212.675	5.809	
1103	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [source:refseq;acc:nm_015920]	Divided	229.441	235.972	1.02846	
1104	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [source:swissprot;acc:q9ujm8]	Divided	231.922	238.486	1.0283	
1104	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [source:swissprot;acc:q9y5k8]	Subtracted	218.484	212.675	5.809	
1105	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Divided	191.139	185.882	1.02828	
1105	secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	Subtracted	218.484	212.675	5.809	
1106	pxr2b protein. [source:refseq;acc:nm_016559]	Divided	212.945	207.109	1.02818	
1106	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [source:swissprot;acc:q9ui12]	Subtracted	218.484	212.675	5.809	
1107	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]	Divided	204.603	210.324	1.02796	
1107	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [source:swissprot;acc:p15313]	Subtracted	218.483	212.676	5.807	
1108	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	Divided	218.006	212.119	1.02775	
1108	vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [source:swissprot;acc:q16864]	Subtracted	218.481	212.675	5.806	
1109	epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [source:refseq;acc:nm_139204]	Subtracted	221.939	216.143	5.796	
1109	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	Divided	218.098	212.209	1.02775	
1110	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	Divided	216.78	222.782	1.02769	
1110	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	Subtracted	159.13	164.917	5.787	
1111	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Divided	217.99	212.123	1.02766	
1111	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	Subtracted	159.165	164.951	5.786	
1112	epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	Subtracted	221.93	216.146	5.784	
1112	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	Divided	251.863	258.829	1.02766	
1113	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	Divided	251.863	258.829	1.02766	
1113	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Subtracted	91.63	97.4011	5.7711	
1114	diphthamide biosynthesis-like protein 2. [source:refseq;acc:nm_001384]	Subtracted	227.274	233.041	5.767	
1114	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	Divided	251.863	258.829	1.02766	
1115	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [source:swissprot;acc:o15120]	Subtracted	186.664	180.943	5.721	

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/