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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 1330 to 1379 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	green	red	network_comparison
665	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	Subtracted	202.166	214.254	12.088
666	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]		238.38	250.465	12.085
	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]	Divided	216.576	229.072	1.0577
667	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Subtracted	238.38	250.465	12.085
668	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	Divided	216.576	229.072	1.0577
	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	Subtracted	232.419	244.495	12.076
669	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]		244.534	232.601	11.933
	synapsin i (brain protein 4.1). [swissprot;acc:p17600]	Divided	216.576	229.072	1.0577
670	autoantigen ngp-1. [swissprot;acc:q13823]		236.817	250.302	1.05694
	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]	Subtracted	244.534	232.601	11.933
671	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Divided	199.398	210.739	1.05688
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Subtracted	244.534	232.601	11.933
672	dok-like protein. [refseq;acc:nm_024872]		204.622	216.504	11.882
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Divided	199.398	210.739	1.05688
673	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Subtracted	204.622	216.504	11.882
	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	Divided	214.355	226.497	1.05664
674	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Subtracted	204.622	216.504	11.882
	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Divided	214.355	226.497	1.05664
675	single-minded homolog 1. [swissprot;acc:p81133]
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Subtracted	204.622	216.504	11.882
676	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	Divided	245.613	232.469	1.05654
	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	Subtracted	257.636	245.84	11.796
677	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]		233.483	245.246	11.763
	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	Divided	216.745	228.944	1.05628
678	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	Subtracted	214.405	226.135	11.73
	sorting nexin 5. [swissprot;acc:q9y5x3]	Divided	220.175	208.482	1.05609
679	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		125.389	132.413	1.05602
	sorting nexin 5. [swissprot;acc:q9y5x3]	Subtracted	220.175	208.482	11.693
680	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Divided	125.389	132.413	1.05602
	sr rich protein. [refseq;acc:nm_032870]	Subtracted	213.64	225.293	11.653
681	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Divided	125.389	132.413	1.05602
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Subtracted	208.987	220.593	11.606
682	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	125.389	132.413	1.05602
	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	Subtracted	234.458	246.055	11.597
683	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Divided	125.389	132.413	1.05602
	osteoclast stimulating factor 1. [swissprot;acc:q92882]	Subtracted	243.289	231.809	11.48
684	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Divided	125.389	132.413	1.05602
	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	Subtracted	235.027	223.58	11.447
685	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Divided	125.389	132.413	1.05602
686	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
	multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234]	Subtracted	235.027	223.58	11.447
687	dendritic cell protein. [refseq;acc:nm_006360]		211.685	223.121	11.436
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Divided	125.389	132.413	1.05602
688	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]		250.823	237.554	1.05586
	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	Subtracted	211.685	223.121	11.436
689	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Divided	128.225	135.379	1.05579
690	cpz gene product. [refseq;acc:nm_003652]	Subtracted	211.685	223.121	11.436

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.