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

Results: HTML CSV LaTeX

Showing element 1332 to 1381 of 6456 in total

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

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison
666	HES1	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]	Divided	229.072	216.576	1.0577
667	no value	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Subtracted	250.465	238.38	12.085
	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]	Divided	229.072	216.576	1.0577
668	ABLIM1	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
	FTSJ3	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	Subtracted	244.495	232.419	12.076
669	no value	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]		232.601	244.534	11.933
	SYN1	synapsin i (brain protein 4.1). [swissprot;acc:p17600]	Divided	229.072	216.576	1.0577
670	GNL2	autoantigen ngp-1. [swissprot;acc:q13823]		250.302	236.817	1.05694
	RANP1	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]	Subtracted	232.601	244.534	11.933
671	no value	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
	NUBP1	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Divided	210.739	199.398	1.05688
672	no value	dok-like protein. [refseq;acc:nm_024872]	Subtracted	216.504	204.622	11.882
	NUBP2	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Divided	210.739	199.398	1.05688
673	CASK	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]		226.497	214.355	1.05664
	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Subtracted	216.504	204.622	11.882
674	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
	HIF3A	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Divided	226.497	214.355	1.05664
675	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Subtracted	216.504	204.622	11.882
	SIM1	single-minded homolog 1. [swissprot;acc:p81133]	Divided	226.497	214.355	1.05664
676	MRTO4	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	Subtracted	245.84	257.636	11.796
	POLR2G	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	Divided	232.469	245.613	1.05654
677	FBL	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	Subtracted	245.246	233.483	11.763
	LSM4	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	Divided	228.944	216.745	1.05628
678	PPIL4	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	226.135	214.405	11.73
	SNX5	sorting nexin 5. [swissprot;acc:q9y5x3]	Divided	208.482	220.175	1.05609
679	no value	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		132.413	125.389	1.05602
	SNX5	sorting nexin 5. [swissprot;acc:q9y5x3]	Subtracted	208.482	220.175	11.693
680	HOXB4	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Divided	132.413	125.389	1.05602
	SFRS18	sr rich protein. [refseq;acc:nm_032870]	Subtracted	225.293	213.64	11.653
681	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Divided	132.413	125.389	1.05602
	SNW1	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Subtracted	220.593	208.987	11.606
682	no value	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	132.413	125.389	1.05602
	NAT10	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	Subtracted	246.055	234.458	11.597
683	HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Divided	132.413	125.389	1.05602
	OSTF1	osteoclast stimulating factor 1. [swissprot;acc:q92882]	Subtracted	231.809	243.289	11.48
684	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Divided	132.413	125.389	1.05602
	PFAS	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	Subtracted	223.58	235.027	11.447
685	ATIC	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]
	HOXA5	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Divided	132.413	125.389	1.05602
686	no value	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
	PAICS	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	223.58	235.027	11.447
687	EIF3M	dendritic cell protein. [refseq;acc:nm_006360]		223.121	211.685	11.436
	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Divided	132.413	125.389	1.05602
688	CPXM2	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	Subtracted	223.121	211.685	11.436
	POLR2D	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	Divided	237.554	250.823	1.05586
689	CPN1	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]	Subtracted	223.121	211.685	11.436
	TCP1	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Divided	135.379	128.225	1.05579
690	CPZ	cpz gene product. [refseq;acc:nm_003652]	Subtracted	223.121	211.685	11.436
	SNW1	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Divided	220.593	208.987	1.05553
691	BCAS2	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]		217.602	206.195	1.05532

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.