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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 530 to 579 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
530	LSM6	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	227.483	212.994	1.06803	
531	PRPF19	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	223.356	209.149	1.06793	
532	ZNF622	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	250.942	235.004	1.06782	
533	SLC45A2	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	250.942	235.004	1.06782	
534		guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	250.942	235.004	1.06782	
535	POLR2H	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434]	236.662	252.708	1.0678	
536	SSB	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	242.531	227.136	1.06778	
537	DHX15	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	229.803	215.301	1.06736	
538	POLR2L	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	237.627	253.604	1.06724	
539	MEMO1P	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	236.964	252.86	1.06708	
540	SEPHS2	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	222.156	208.201	1.06703	
541	MICAL2	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	222.156	208.201	1.06703	
542	INPP4B	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	222.156	208.201	1.06703	
543	SEPHS1	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	222.156	208.201	1.06703	
544	INPP4A	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	222.156	208.201	1.06703	
545	EIF6	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	248.866	233.287	1.06678	
546	WAS	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	207.222	194.262	1.06671	
547	CRK	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	207.26	194.346	1.06645	
548	ABL2	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	207.26	194.346	1.06645	
549		proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	207.26	194.346	1.06645	
550	HCK	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	207.26	194.346	1.06645	
551	GRAP2	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	207.261	194.347	1.06645	
552	CRKL	crk-like protein. [source:swissprot;acc:p46109]	207.26	194.346	1.06645	
553	ABL1	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	207.26	194.346	1.06645	
554	FYN	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	207.26	194.346	1.06645	
555	FGR	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	207.26	194.346	1.06645	
556	CUTL1	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	207.27	194.368	1.06638	
557	CUTL2	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	207.272	194.371	1.06637	
558		ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	135.087	144.041	1.06628	
559	WASL	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	207.309	194.452	1.06612	
560	SOS1	son of sevenless protein homolog 1 (sos-1). [source:swissprot;acc:q07889]	205.74	193.021	1.06589	
561	SOS2	son of sevenless protein homolog 2 (sos-2). [source:swissprot;acc:q07890]	205.89	193.183	1.06578	
562	GULP1	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	220.744	207.121	1.06577	
563	CAPS	calcyphosine. [source:swissprot;acc:q13938]	220.744	207.121	1.06577	
564	CRNKL1	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	220.744	207.121	1.06577	
565	ZNF547	sedlin. [source:swissprot;acc:o14582]	129.219	121.261	1.06563	
566		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	129.219	121.261	1.06563	
567	TRAPPC3	bet3 homolog. [source:swissprot;acc:o43617]	129.219	121.261	1.06563	
568		putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	226.3	212.38	1.06554	
569	GPKOW	t54 protein. [source:swissprot;acc:q92917]	226.3	212.38	1.06554	
570	SFRS11	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	229.709	215.631	1.06529	
571	MDH2	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	238.529	254.099	1.06528	
572		cbf1 interacting corepressor. [source:refseq;acc:nm_004882]	227.86	213.945	1.06504	
573	GPATCH1	evolutionarily conserved g-patch domain containing. [source:refseq;acc:nm_018025]	227.86	213.945	1.06504	
574	MOBKL3	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source:refseq;acc:nm_015387]	221.807	208.264	1.06503	
575	DNAJB11	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [source:swissprot;acc:q9ubs4]	221.807	208.264	1.06503	
576		dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	235.18	250.419	1.0648	
577	PRSS7	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	224.606	210.944	1.06477	
578	SF3B2	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	224.606	210.944	1.06477	
579	ZNF593	zinc finger protein t86. [source:swissprot;acc:o00488]	246.805	231.796	1.06475	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/