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

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Showing element 575 to 624 of 3228 in total

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

Rank	description	red	green	network_comparison
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]	221.807	208.264	1.06503
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	235.18	250.419	1.0648
577	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	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]
579	zinc finger protein t86. [swissprot;acc:o00488]	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]	236.751	252.038	1.06457
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	237.28	252.492	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	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	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]	228.215	214.546	1.06371
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	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]	216.72	230.439	1.0633
592	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	91.63	97.4011	1.06298
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	232.118	218.406	1.06278
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	223.282	210.136	1.06256
595	vav proto-oncogene. [swissprot;acc:p15498]	212.2	199.849	1.0618
596	vav-3 protein. [swissprot;acc:q9ukw4]	212.253	199.908	1.06175
597	vav-2 protein. [swissprot;acc:p52735]	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]	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]
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	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	206.274	218.792	1.06069
602	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
603	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	225.829	212.945	1.0605
604	60s ribosomal protein l15. [swissprot;acc:p39030]	217.862	230.978	1.0602
605	histone h2b.c (h2b/c). [swissprot;acc:q99880]	247.47	233.441	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]
613	histone h2b.e (h2b/e). [swissprot;acc:q99879]
614	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	214.257	202.125	1.06002
615	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]		202.132	1.05999
616	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
617	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]		202.135	1.05997
618	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	214.256	202.139	1.05994
619	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
620	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]		202.14
621	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
622	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
623	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]
624	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]		202.139

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.