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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2151 to 2200 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
1076	ATP2C2	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Subtracted	209.123	203.208	5.915	
1076	COPZ1	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	
1077	ARCN1	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	Divided	174.387	179.697	1.03045	
1077	TPT1	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	Subtracted	218.098	212.209	5.889	
1078	FOXK2	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	Subtracted	218.006	212.119	5.887	
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]	Divided	174.387	179.697	1.03045	
1079	COPZ2	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	Divided	174.387	179.697	1.03045	
1079	SIX1	homeobox protein six1 (sine oculis homeobox homolog 1). [source:swissprot;acc:q15475]	Subtracted	221.286	215.399	5.887	
1080	PA2G4	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [source:swissprot;acc:q9uq80]	Subtracted	221.285	215.4	5.885	
1080	ZNF444	zinc finger protein 444; endothelial zinc finger protein 2. [source:refseq;acc:nm_018337]	Divided	269.896	278.093	1.03037	
1081	FAU	40s ribosomal protein s30. [source:swissprot;acc:q05472]	Divided	223.44	216.875	1.03027	
1081	SIX2	homeobox protein six2 (sine oculis homeobox homolog 2). [source:swissprot;acc:q9npc8]	Subtracted	221.285	215.401	5.884	
1082	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]	Subtracted	209.052	203.183	5.869	
1082	PLEKHF2	phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	Divided	220.118	213.685	1.03011	
1083		apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Subtracted	217.99	212.123	5.867	
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]	Divided	220.118	213.685	1.03011	
1084	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]	Subtracted	218.529	212.676	5.853	
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]	Divided	220.118	213.685	1.03011	
1085	ATP6V0A2	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	
1085	DKC1	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	Divided	231.007	237.864	1.02968	
1086		similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Divided	236.679	243.679	1.02958	
1086	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]	Subtracted	218.528	212.676	5.852	
1087		zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Divided	236.679	243.679	1.02958	
1087	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]	Subtracted	218.527	212.676	5.851	
1088	ANXA11	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	PEX5L	pxr2b protein. [source:refseq;acc:nm_016559]	Subtracted	212.945	207.109	5.836	
1089	ATP6V0D2	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	Subtracted	218.487	212.656	5.831	
1089	CSTF3	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		similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	Divided	226.218	232.88	1.02945	
1090	NCALD	neurocalcin delta. [source:swissprot;acc:p29554]	Subtracted	225.104	230.931	5.827	
1091		block 23. [source:sptrembl;acc:q8nhw5]	Divided	226.205	232.858	1.02941	
1091	HPCA	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [source:swissprot;acc:p32076]	Subtracted	225.103	230.928	5.825	
1092	HPCAL1	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	
1092	RPLP0	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	Divided	226.203	232.855	1.02941	
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	
1093	COPA	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	
1094	ANXA7	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	Divided	219.655	213.385	1.02938	
1094	API5	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	GTPBP3	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	Divided	213.552	207.463	1.02935	
1095	SEC13	sec13-related protein. [source:swissprot;acc:p55735]	Subtracted	218.484	212.675	5.809	
1096	ATP6V1G3	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	
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]	Divided	212.345	206.339	1.02911	
1097	ATP2C2	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Divided	209.123	203.208	1.02911	
1097	ATP6V1B2	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	AP3M1	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	SEC31A	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Subtracted	218.484	212.675	5.809	
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]	Divided	217.315	211.183	1.02904	
1099	ATP6V1G1	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	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]	Divided	209.052	203.183	1.02889	
1100	ATP6V1E1	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	

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/