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 2658 to 2707 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2658	b-cell lymphoma 3-encoded protein (bcl-3 protein). [source:swissprot;acc:p20749]	8278.73	8211.05	1.00824	
2659	nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [source:swissprot;acc:p19838]	8277.7	8210.29	1.00821	
2660	nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [source:swissprot;acc:q15653]	8277.6	8210.21	1.00821	
2661	nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [source:swissprot;acc:q00653]	8277.66	8210.26	1.00821	
2662	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	4300.46	4334.66	1.00795	
2663	microtubule-actin crosslinking factor 1, isoform 4. [source:swissprot;acc:q96pk2]	4608.54	4576.35	1.00703	
2664	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [source:swissprot;acc:q03001]	4608.91	4576.78	1.00702	
2665	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5]	8936.97	8999.55	1.007	
2666	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	4591.08	4621.88	1.00671	
2667	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	4071.9	4099.01	1.00666	
2668	iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [source:swissprot;acc:p21399]	8222.61	8169.38	1.00652	
2669	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	4336.58	4310.3	1.0061	
2670	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	4336.62	4310.35	1.00609	
2671	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	4338.79	4313.52	1.00586	
2672	ubiquitin-specific protease otubain 2. [source:refseq;acc:nm_023112]	7350.69	7390.45	1.00541	
2673	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [source:swissprot;acc:p35268]	7780.98	7741.14	1.00515	
2674	sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [source:refseq;acc:nm_003864]	7780.98	7741.14	1.00515	
2675	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [source:swissprot;acc:p20172]	7780.98	7741.14	1.00515	
2676	atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [source:refseq;acc:nm_033450]	7780.98	7741.14	1.00515	
2677	lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [source:swissprot;acc:o00754]	7780.98	7741.14	1.00515	
2678	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	7780.98	7741.14	1.00515	
2679	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	5358.78	5384.44	1.00479	
2680	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [source:swissprot;acc:o75914]	5358.3	5383.94	1.00479	
2681	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [source:swissprot;acc:q13177]	5358.31	5383.94	1.00478	
2682	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [source:swissprot;acc:q9up83]	5358.3	5383.93	1.00478	
2683	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [source:swissprot;acc:q13153]	5358.3	5383.93	1.00478	
2684	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [source:swissprot;acc:q14155]	5357.73	5383.33	1.00478	
2685	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	3953.53	3972.32	1.00475	
2686	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	3953.53	3972.32	1.00475	
2687	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	3953.53	3972.32	1.00475	
2688	oligophrenin 1. [source:swissprot;acc:o60890]	3953.53	3972.32	1.00475	
2689	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	4113.79	4095.53	1.00446	
2690	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	4113.79	4095.53	1.00446	
2691	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	4113.79	4095.53	1.00446	
2692	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [source:swissprot;acc:q13950]	4113.79	4095.53	1.00446	
2693	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	4113.79	4095.53	1.00446	
2694	60s ribosomal protein l18. [source:swissprot;acc:q07020]	4113.79	4095.53	1.00446	
2695	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [source:swissprot;acc:q14249]	5176.92	5154.43	1.00436	
2696	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [source:swissprot;acc:o95831]	5176.92	5154.43	1.00436	
2697	t-box transcription factor tbx6 (t-box protein 6). [source:swissprot;acc:o95947]	5176.92	5154.43	1.00436	
2698	trub pseudouridine (psi) synthase homolog 1. [source:refseq;acc:nm_139169]	4163.36	4145.95	1.0042	
2699	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	5356.83	5378.19	1.00399	
2700	short coiled-coil protein; short coiled coil protein. [source:refseq;acc:nm_032547]	5239.33	5260	1.00395	
2701	dynein light chain 2. [source:refseq;acc:nm_080677]	5239.33	5260	1.00395	
2702	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [source:swissprot;acc:p17540]	8971.66	9006.92	1.00393	
2703	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	8972.87	9007.71	1.00388	
2704	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [source:swissprot;acc:p06732]	8980.12	9013.33	1.0037	
2705	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	4137.61	4152.72	1.00365	
2706	peptidyl prolyl isomerase h; cyclophilin h. [source:refseq;acc:nm_006347]	8979.61	9012.31	1.00364	
2707	prp18 pre-mrna processing factor 18 homolog. [source:refseq;acc:nm_003675]	8979.61	9012.31	1.00364	

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/