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 368 to 417 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
368	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [source:swissprot;acc:o60508]	5082.66	5959.99	1.17261	
369	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	3583.56	4194.95	1.17061	
370	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	4108.15	4808.93	1.17058	
371	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	5067.02	5926.46	1.16961	
372	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	5067	5926.17	1.16956	
373	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	5066.99	5926.1	1.16955	
374	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	5066.93	5925.38	1.16942	
375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	4700.42	5492.63	1.16854	
376	44050 protein. [source:refseq;acc:nm_178832]	17385.9	14889.2	1.16769	
377	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	17385.9	14889.2	1.16769	
378	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	12471.7	14561.7	1.16758	
379	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	6704.44	7811.45	1.16512	
380	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	12998.5	15138.2	1.16461	
381	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	5246.01	6109.31	1.16456	
382	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	4533.74	5279.4	1.16447	
383	hepatoma-derived growth factor-related protein 2. [source:refseq;acc:nm_032631]	4533.74	5279.4	1.16447	
384	cgi-142; hepatoma-derived growth factor 2. [source:refseq;acc:nm_016073]	4533.74	5279.4	1.16447	
385	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	4533.74	5279.4	1.16447	
386	60s ribosomal protein l8. [source:swissprot;acc:p25120]	4533.74	5279.4	1.16447	
387	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	4533.74	5279.4	1.16447	
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	4533.74	5279.4	1.16447	
389	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	4533.74	5279.4	1.16447	
390	rw1 protein (fragment). [source:swissprot;acc:q92545]	4533.74	5279.4	1.16447	
391	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	3658.76	3144.39	1.16358	
392	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	3641.89	4236.95	1.16339	
393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	4490.28	5222.25	1.16301	
394	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	4490.28	5222.25	1.16301	
395	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	4532.73	5269.33	1.16251	
396	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	6563.65	7627.29	1.16205	
397	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	5367.04	6233.12	1.16137	
398	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	5084.26	5904.1	1.16125	
399	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	5201.41	4479.76	1.16109	
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	5201.41	4479.76	1.16109	
401	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	5201.41	4479.76	1.16109	
402	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	5201.41	4479.76	1.16109	
403	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	5201.41	4479.76	1.16109	
404	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	5201.41	4479.76	1.16109	
405	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	5201.41	4479.76	1.16109	
406	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	5201.41	4479.76	1.16109	
407	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	6603.41	7664.65	1.16071	
408	dok-like protein. [source:refseq;acc:nm_024872]	6102.59	7081.46	1.1604	
409	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	6102.59	7081.46	1.1604	
410	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	6102.59	7081.46	1.1604	
411	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	6102.59	7081.46	1.1604	
412	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	3594.31	4169.95	1.16015	
413	vav proto-oncogene. [source:swissprot;acc:p15498]	6644.99	7707.8	1.15994	
414	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	6744.05	5815.13	1.15974	
415	vav-3 protein. [source:swissprot;acc:q9ukw4]	6647.43	7706.18	1.15927	
416	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [source:swissprot;acc:p41227]	4509.54	5223.95	1.15842	
417	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	4522.71	5233.14	1.15708	

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/