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

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Showing element 563 to 612 of 3228 in total

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

Rank	green	description	red	network_comparison
563	207.121	calcyphosine. [swissprot;acc:q13938]	220.744	1.06577
564		crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
565	121.261	sedlin. [swissprot;acc:o14582]	129.219	1.06563
566		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
567		bet3 homolog. [swissprot;acc:o43617]
568	212.38	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	226.3	1.06554
569		t54 protein. [swissprot;acc:q92917]
570	215.631	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	229.709	1.06529
571	254.099	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	238.529	1.06528
572	213.945	cbf1 interacting corepressor. [refseq;acc:nm_004882]	227.86	1.06504
573		evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]
574	208.264	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	221.807	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]
576	250.419	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	235.18	1.0648
577	210.944	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	224.606	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]
579	231.796	zinc finger protein t86. [swissprot;acc:o00488]	246.805	1.06475
580	252.038	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
581	252.492	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	237.28	1.06411
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	230.362	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	216.557	1.06375
589	214.546	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
590	204.279	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	217.215	1.06333
591	230.439	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	216.72	1.0633
592	97.4011	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	91.63	1.06298
593	218.406	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	232.118	1.06278
594	210.136	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	223.282	1.06256
595	199.849	vav proto-oncogene. [swissprot;acc:p15498]	212.2	1.0618
596	199.908	vav-3 protein. [swissprot;acc:q9ukw4]	212.253	1.06175
597	200.212	vav-2 protein. [swissprot;acc:p52735]	212.526	1.0615
598	234.095	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
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]
601	218.792	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	206.274	1.06069
602		microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
603	212.945	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	225.829	1.0605
604	230.978	60s ribosomal protein l15. [swissprot;acc:p39030]	217.862	1.0602
605	233.441	histone h2b.c (h2b/c). [swissprot;acc:q99880]	247.47	1.0601
606		histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
607		histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
608		histone h2b. [refseq;acc:nm_175055]
609		histone h2b.s (h2b/s). [swissprot;acc:p57053]
610		histone h2b.d (h2b/d). [swissprot;acc:q99877]
611		histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]
612		testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]

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.