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

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Showing element 51 to 100 of 3228 in total

Hugo  : no value
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence

Rank	description	red	green	network_comparison
454	40s ribosomal protein s26. [swissprot;acc:p02383]	210.224	226.578	1.07779
534	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]	250.942	235.004	1.06782
549	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	207.26	194.346	1.06645
558	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	135.087	144.041	1.06628
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	129.219	121.261	1.06563
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	226.3	212.38	1.06554
572	cbf1 interacting corepressor. [refseq;acc:nm_004882]	227.86	213.945	1.06504
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	235.18	250.419	1.0648
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
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]	247.47	233.441	1.0601
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]
613	histone h2b.e (h2b/e). [swissprot;acc:q99879]
624	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	214.256	202.139	1.05994
634	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	226.523	213.786	1.05958
640	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	217.67	230.596	1.05938
642	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
650	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	228.986	216.276	1.05877
652	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	248.994	235.255	1.0584
653	dok-like protein. [refseq;acc:nm_024872]	216.504	204.622	1.05807
658	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	229.072	216.576	1.0577
679	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	132.413	125.389	1.05602
682	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
686	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
700	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	220.438	209.118	1.05413
704	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
708	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
723	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	244.842	232.577	1.05274
724	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
729	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	208.874	219.708	1.05187
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	232.601	244.534	1.0513
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
747	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	250.465	238.38	1.0507
751	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	223.463	212.875	1.04974
767	rho interacting protein 3. [refseq;acc:nm_015134]	213.803	224.224	1.04874
775	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	226.003	215.541	1.04854
776	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	225.996	215.535
782	translin. [swissprot;acc:q15631]	224.385	235.131	1.04789
789	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	224.244	234.511	1.04578
792	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
795	serpin b11. [swissprot;acc:q96p15]
797	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
831	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	231.734	222.222	1.0428
832	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
846	methyltransferase like 2. [refseq;acc:nm_018396]	147.211	153.371	1.04184
859	60s ribosomal protein l39. [swissprot;acc:p02404]	234.025	224.958	1.04031
860	60s ribosomal protein l18a. [swissprot;acc:q02543]
867	40s ribosomal protein s3a. [swissprot;acc:p49241]	225.689	234.674	1.03981
870	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	211.908	203.832	1.03962

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.