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 2630 to 2679 of 3228 in total

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

Rank	description	red	green	network_comparison	
2630	polymerase (rna) iii (dna directed) (62kd). [source:refseq;acc:nm_006468]	3985.17	3928.38	1.01446	
2631	highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101]	4508.81	4446.41	1.01403	
2632	histone h4. [source:swissprot;acc:p02304]	6072.17	6155.08	1.01365	
2633	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [source:swissprot;acc:q9h1d9]	4000.73	3947.54	1.01347	
2634	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [source:refseq;acc:nm_016183]	3640.58	3688.96	1.01329	
2635	hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [source:refseq;acc:nm_006410]	7197.82	7291.66	1.01304	
2636	ba207c16.2 (fragment). [source:sptrembl;acc:q9nql7]	7017.82	7108.89	1.01298	
2637	protein kinase nyd-sp25. [source:refseq;acc:nm_033516]	6527.56	6608.61	1.01242	
2638	insulin gene enhancer protein isl-2 (islet-2). [source:swissprot;acc:q96a47]	7433.72	7525.14	1.0123	
2639	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [source:swissprot;acc:o43280]	6742.48	6814.18	1.01063	
2640	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513]	5339.06	5395.25	1.01052	
2641	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [source:swissprot;acc:p28715]	3377.01	3411.47	1.0102	
2642	vam6/vps39-like protein (hvam6p). [source:swissprot;acc:q96jc1]	5935.71	5876.22	1.01012	
2643	microtubule-associated protein 4 (map 4). [source:swissprot;acc:p27816]	5935.71	5876.22	1.01012	
2644	ubiquilin 1 isoform 1. [source:refseq;acc:nm_013438]	9125.08	9217	1.01007	
2645	ataxin-1 ubiquitin-like interacting protein. [source:refseq;acc:nm_020131]	9128.19	9218.44	1.00989	
2646	mct-1 protein. [source:refseq;acc:nm_014060]	4778.28	4732.13	1.00975	
2647	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	4778.28	4732.13	1.00975	
2648	tumor protein d54 (hd54) (d52-like 2). [source:swissprot;acc:o43399]	6365.03	6424.56	1.00935	
2649	jm4 protein. [source:refseq;acc:nm_007213]	7133.06	7067.09	1.00933	
2650	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [source:swissprot;acc:q14457]	9150.44	9234.09	1.00914	
2651	26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [source:swissprot;acc:p47210]	9150.44	9234.09	1.00914	
2652	tumor protein d52 (n8 protein). [source:swissprot;acc:p55327]	6349.55	6407.25	1.00909	
2653	tumor protein d53 (hd53) (d52-like 1). [source:swissprot;acc:q16890]	6349.23	6406.72	1.00905	
2654	cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [source:refseq;acc:nm_006407]	7118.22	7055.43	1.0089	
2655	nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [source:swissprot;acc:o00221]	8290.91	8220.11	1.00861	
2656	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [source:refseq;acc:nm_014596]	4191.15	4226.86	1.00852	
2657	sorting nexin 6 (traf4-associated factor 2). [source:swissprot;acc:q9unh7]	5327.58	5371.47	1.00824	
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	

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/