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 1233 to 1282 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
617	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Divided	5162.52	5822.47	1.12783	
617	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Subtracted	4532.73	5269.33	736.6	
618	dna mismatch repair protein mlh3 (mutl protein homolog 3). [source:swissprot;acc:q9uhc1]	Subtracted	6327.86	7064.13	736.27	
618	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Divided	7878.27	8879.08	1.12703	
619	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	Divided	3879.99	4371.24	1.12661	
619	ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	Subtracted	6811.2	7547.35	736.15	
620	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [source:refseq;acc:nm_005763]	Subtracted	6807.78	7543.28	735.5	
620	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	Divided	6227.87	7012.9	1.12605	
621	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Divided	4115.39	4633.96	1.12601	
621	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	Subtracted	6805.86	7540.99	735.13	
622	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	Divided	6228.42	7013.21	1.126	
622	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	Subtracted	6805.45	7540.5	735.05	
623	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	Divided	6228.39	7013.19	1.126	
623	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	Subtracted	4490.28	5222.25	731.97	
624	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	Subtracted	4490.28	5222.25	731.97	
624	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	Divided	6228.39	7013.19	1.126	
625	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	Divided	6228.39	7013.19	1.126	
625	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Subtracted	5291.92	6020.19	728.27	
626	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	Divided	6228.39	7013.19	1.126	
626	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	Subtracted	8618.32	9340.98	722.66	
627	limkain b1. [source:refseq;acc:nm_019081]	Divided	6228.39	7013.19	1.126	
627	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [source:swissprot;acc:o60315]	Subtracted	8618.32	9340.98	722.66	
628	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	Divided	6228.39	7013.19	1.126	
628	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [source:swissprot;acc:p37275]	Subtracted	8618.32	9340.98	722.66	
629	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	Divided	6228.39	7013.19	1.126	
629	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Subtracted	5201.41	4479.76	721.65	
630	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Subtracted	5201.41	4479.76	721.65	
630	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	Divided	6228.39	7013.19	1.126	
631	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Subtracted	5201.41	4479.76	721.65	
631	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	Divided	6228.39	7013.19	1.126	
632	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Divided	6228.39	7013.19	1.126	
632	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	Subtracted	5201.41	4479.76	721.65	
633	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Subtracted	5201.41	4479.76	721.65	
633	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	Divided	6228.39	7013.19	1.126	
634	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	Divided	6228.39	7013.19	1.126	
634	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Subtracted	5201.41	4479.76	721.65	
635	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	Divided	6228.97	7013.53	1.12595	
635	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Subtracted	5201.41	4479.76	721.65	
636	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [source:swissprot;acc:p28066]	Divided	5713.41	6432.92	1.12593	
636	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Subtracted	5201.41	4479.76	721.65	
637	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	Subtracted	4889.21	5610.52	721.31	
637	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Divided	7756.51	8731.76	1.12573	
638	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	Subtracted	4889.71	5610.69	720.98	
638	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	Divided	7755.69	8730.74	1.12572	
639	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	Subtracted	4890.51	5610.95	720.44	
639	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Divided	7753.59	8728.13	1.12569	
640	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [source:swissprot;acc:q06545]	Subtracted	4890.51	5610.95	720.44	
640	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Divided	4811.02	5414.64	1.12547	
641	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [source:swissprot;acc:o00217]	Subtracted	4890.51	5610.95	720.44	
641	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	Divided	4810.85	5414.21	1.12542	

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/