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

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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	red	network_comparison	green
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]	207.261	1.06645	194.347
552	crk-like protein. [swissprot;acc:p46109]	207.26		194.346
553	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]
554	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]
555	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
556	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	207.27	1.06638	194.368
557	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	207.272	1.06637	194.371
558	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	135.087	1.06628	144.041
559	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	207.309	1.06612	194.452
560	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	205.74	1.06589	193.021
561	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	205.89	1.06578	193.183
562	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	220.744	1.06577	207.121
563	calcyphosine. [swissprot;acc:q13938]
564	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
565	sedlin. [swissprot;acc:o14582]	129.219	1.06563	121.261
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
567	bet3 homolog. [swissprot;acc:o43617]
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	226.3	1.06554	212.38
569	t54 protein. [swissprot;acc:q92917]
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	229.709	1.06529	215.631
571	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	238.529	1.06528	254.099
572	cbf1 interacting corepressor. [refseq;acc:nm_004882]	227.86	1.06504	213.945
573	evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]
574	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	221.807	1.06503	208.264
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]
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	235.18	1.0648	250.419
577	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	224.606	1.06477	210.944
578	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]
579	zinc finger protein t86. [swissprot;acc:o00488]	246.805	1.06475	231.796
580	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	236.751	1.06457	252.038
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	237.28	1.06411	252.492
582	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
583	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]
584	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]
585	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
586	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
587	homeobox protein barh-like 2. [swissprot;acc:q9umq3]
588	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	216.557	1.06375	230.362
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]	228.215	1.06371	214.546
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	217.215	1.06333	204.279
591	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	216.72	1.0633	230.439
592	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	91.63	1.06298	97.4011
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	232.118	1.06278	218.406
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	223.282	1.06256	210.136
595	vav proto-oncogene. [swissprot;acc:p15498]	212.2	1.0618	199.849
596	vav-3 protein. [swissprot;acc:q9ukw4]	212.253	1.06175	199.908
597	vav-2 protein. [swissprot;acc:p52735]	212.526	1.0615	200.212
598	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	248.463	1.06138	234.095
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]
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]

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
- 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.