MK5 Microarray Data

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	green	red	network_comparison

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Showing element 550 to 599 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	green	red	network_comparison
550	HCK	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	194.346	207.26	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). [swissprot;acc:o75791]	194.347	207.261
552	CRKL	crk-like protein. [swissprot;acc:p46109]	194.346	207.26
553	ABL1	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]
554	FYN	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]
555	FGR	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
556	CUTL1	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	194.368	207.27	1.06638
557	CUTL2	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	194.371	207.272	1.06637
558	no value	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	144.041	135.087	1.06628
559	WASL	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	194.452	207.309	1.06612
560	SOS1	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	193.021	205.74	1.06589
561	SOS2	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	193.183	205.89	1.06578
562	GULP1	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	207.121	220.744	1.06577
563	CAPS	calcyphosine. [swissprot;acc:q13938]
564	CRNKL1	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
565	ZNF547	sedlin. [swissprot;acc:o14582]	121.261	129.219	1.06563
566	no value	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
567	TRAPPC3	bet3 homolog. [swissprot;acc:o43617]
568	no value	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	212.38	226.3	1.06554
569	GPKOW	t54 protein. [swissprot;acc:q92917]
570	SFRS11	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	215.631	229.709	1.06529
571	MDH2	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	254.099	238.529	1.06528
572	no value	cbf1 interacting corepressor. [refseq;acc:nm_004882]	213.945	227.86	1.06504
573	GPATCH1	evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]
574	MOBKL3	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	208.264	221.807	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). [swissprot;acc:q9ubs4]
576	no value	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	250.419	235.18	1.0648
577	PRSS7	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	210.944	224.606	1.06477
578	SF3B2	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]
579	ZNF593	zinc finger protein t86. [swissprot;acc:o00488]	231.796	246.805	1.06475
580	ZNRD1	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	252.038	236.751	1.06457
581	TLX3	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	252.492	237.28	1.06411
582	BARX1	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
583	OPN4	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]
584	TLX2	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]
585	TLX1	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
586	HECTD1	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
587	BARX2	homeobox protein barh-like 2. [swissprot;acc:q9umq3]
588	SBDS	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	230.362	216.557	1.06375
589	no value	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	214.546	228.215	1.06371
590	RRM1	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	204.279	217.215	1.06333
591	RPP30	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	230.439	216.72	1.0633
592	PPP1R7	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	97.4011	91.63	1.06298
593	DR1	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	218.406	232.118	1.06278
594	CDC40	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	210.136	223.282	1.06256
595	VAV1	vav proto-oncogene. [swissprot;acc:p15498]	199.849	212.2	1.0618
596	VAV3	vav-3 protein. [swissprot;acc:q9ukw4]	199.908	212.253	1.06175
597	VAV2	vav-2 protein. [swissprot;acc:p52735]	200.212	212.526	1.0615
598	AKT1	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	234.095	248.463	1.06138
599	AKT3	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.