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 Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1568 to 1617 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
784	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]	Divided	5874.77	6533.36	1.1121	
785	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [source:swissprot;acc:q9y5r4]	Divided	4997	5557.17	1.1121	
785	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [source:swissprot;acc:p00387]	Subtracted	6289.72	6911.96	622.24	
786	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [source:swissprot;acc:q15815]	Subtracted	6499.89	7121.77	621.88	
786	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	Divided	9304.83	10347.3	1.11204	
787	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Subtracted	9720.64	9099.1	621.54	
787	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	Divided	5890.49	6547.9	1.11161	
788	transformer-2 protein homolog (tra-2 alpha). [source:swissprot;acc:q13595]	Subtracted	6472.38	7092.65	620.27	
788	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]	Divided	5890.41	6547.81	1.11161	
789	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]	Divided	5890.59	6547.99	1.1116	
789	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [source:swissprot;acc:o00410]	Subtracted	6167.33	6785.98	618.65	
790	ran-gtp binding protein (fragment). [source:sptrembl;acc:o60518]	Subtracted	6165.1	6783.01	617.91	
790	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]	Divided	5890.88	6548.28	1.1116	
791	monoglyceride lipase; lysophospholipase-like. [source:refseq;acc:nm_007283]	Subtracted	6544.26	7159.43	615.17	
791	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	Divided	4025.3	4474.3	1.11154	
792	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [source:swissprot;acc:o14645]	Divided	6772.75	7526.2	1.11125	
792	target of myb protein 1. [source:swissprot;acc:o60784]	Subtracted	5640.79	6255.85	615.06	
793	huntingtin-associated protein-interacting protein (duo protein). [source:swissprot;acc:o60229]	Subtracted	5641.11	6255.99	614.88	
793	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	Divided	5036.92	5596.36	1.11107	
794	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [source:swissprot;acc:p11388]	Divided	6441.17	7154.55	1.11075	
794	triple functional domain protein (ptprf interacting protein). [source:swissprot;acc:o75962]	Subtracted	5641.12	6255.99	614.87	
795	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	Divided	6441.14	7154.13	1.11069	
795	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [source:refseq;acc:nm_144678]	Subtracted	5641.53	6256.17	614.64	
796	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [source:swissprot;acc:q9y287]	Subtracted	6362.64	6976.1	613.46	
796	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Divided	6834.54	7590.49	1.11061	
797	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [source:swissprot;acc:q14974]	Divided	6834.54	7590.49	1.11061	
797	integral membrane protein 2c (transmembrane protein bri3) (npd018). [source:swissprot;acc:q9nqx7]	Subtracted	6362.64	6976.1	613.46	
798	integral membrane protein 2a (e25 protein). [source:swissprot;acc:o43736]	Subtracted	6362.64	6976.1	613.46	
798	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	Divided	6834.54	7590.49	1.11061	
799	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Subtracted	5222.71	5834.57	611.86	
799	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Divided	6834.54	7590.49	1.11061	
800	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	Subtracted	3583.56	4194.95	611.39	
800	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	Divided	6075.55	6746.92	1.1105	
801	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	Divided	6456.35	7169.75	1.1105	
801	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Subtracted	779.167	1390.33	611.163	
802	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Subtracted	779.167	1390.33	611.163	
802	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Divided	6455.66	7168.82	1.11047	
803	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Subtracted	779.167	1390.33	611.163	
803	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Divided	6455.02	7167.96	1.11045	
804	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	6770.78	7517.97	1.11036	
804	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Subtracted	779.167	1390.33	611.163	
805	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Divided	4708.61	5226.71	1.11003	
805	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Subtracted	779.167	1390.33	611.163	
806	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	Divided	4708.61	5226.71	1.11003	
806	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Subtracted	779.167	1390.33	611.163	
807	40s ribosomal protein s19. [source:swissprot;acc:p39019]	Divided	4708.61	5226.71	1.11003	
807	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Subtracted	779.167	1390.33	611.163	
808	60s ribosomal protein l31. [source:swissprot;acc:p12947]	Divided	4708.61	5226.71	1.11003	
808	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Subtracted	779.167	1390.33	611.163	
809	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [source:swissprot;acc:p49760]	Subtracted	6435.94	7045.75	609.81	

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/