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	description	Gene	Hugo	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 551 to 600 of 3228 in total

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

Rank	description	Hugo	red	green	network_comparison
551	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]	GRAP2	207.261	194.347	1.06645
552	crk-like protein. [swissprot;acc:p46109]	CRKL	207.26	194.346
553	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	ABL1
554	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	FYN
555	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	FGR
556	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	CUTL1	207.27	194.368	1.06638
557	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	CUTL2	207.272	194.371	1.06637
558	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	no value	135.087	144.041	1.06628
559	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	WASL	207.309	194.452	1.06612
560	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	SOS1	205.74	193.021	1.06589
561	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	SOS2	205.89	193.183	1.06578
562	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	GULP1	220.744	207.121	1.06577
563	calcyphosine. [swissprot;acc:q13938]	CAPS
564	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	CRNKL1
565	sedlin. [swissprot;acc:o14582]	ZNF547	129.219	121.261	1.06563
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	no value
567	bet3 homolog. [swissprot;acc:o43617]	TRAPPC3
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	no value	226.3	212.38	1.06554
569	t54 protein. [swissprot;acc:q92917]	GPKOW
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	SFRS11	229.709	215.631	1.06529
571	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	MDH2	238.529	254.099	1.06528
572	cbf1 interacting corepressor. [refseq;acc:nm_004882]	no value	227.86	213.945	1.06504
573	evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]	GPATCH1
574	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	MOBKL3	221.807	208.264	1.06503
575	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]	DNAJB11
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	no value	235.18	250.419	1.0648
577	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	PRSS7	224.606	210.944	1.06477
578	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	SF3B2
579	zinc finger protein t86. [swissprot;acc:o00488]	ZNF593	246.805	231.796	1.06475
580	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	ZNRD1	236.751	252.038	1.06457
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	TLX3	237.28	252.492	1.06411
582	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]	BARX1
583	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]	OPN4
584	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]	TLX2
585	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]	TLX1
586	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]	HECTD1
587	homeobox protein barh-like 2. [swissprot;acc:q9umq3]	BARX2
588	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	SBDS	216.557	230.362	1.06375
589	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	no value	228.215	214.546	1.06371
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	RRM1	217.215	204.279	1.06333
591	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	RPP30	216.72	230.439	1.0633
592	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	PPP1R7	91.63	97.4011	1.06298
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	DR1	232.118	218.406	1.06278
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	CDC40	223.282	210.136	1.06256
595	vav proto-oncogene. [swissprot;acc:p15498]	VAV1	212.2	199.849	1.0618
596	vav-3 protein. [swissprot;acc:q9ukw4]	VAV3	212.253	199.908	1.06175
597	vav-2 protein. [swissprot;acc:p52735]	VAV2	212.526	200.212	1.0615
598	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	AKT1	248.463	234.095	1.06138
599	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]	AKT3
600	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	AKT2

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.