Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1332 to 1381 of 8289 in total

Network Comparison Type	Divided
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Interaction Map	red	green	network_comparison	
666	SOS2	son of sevenless protein homolog 2 (sos-2). [source:swissprot;acc:q07890]	Low confidence	200.639	195.092	1.02843	
667	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	High confidence	229.072	216.576	1.0577	
667	RNF144B	ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [source:sptrembl;acc:q9bx39]	Low confidence	208.62	202.855	1.02842	
668	ABLIM1	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	High confidence	229.072	216.576	1.0577	
668	MIOX	inositol oxygenase (ec 1.13.99.1) (myo-inositol oxygenase) (aldehyde reductase-like 6) (renal-specific oxidoreductase) (kidney-specific protein 32). [source:swissprot;acc:q9ugb7]	Low confidence	212.062	206.202	1.02842	
669	CYP3A43	cytochrome p450 3a43 (ec 1.14.14.1). [source:swissprot;acc:q9hb55]	Low confidence	203.712	198.082	1.02842	
669	SYN1	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	High confidence	229.072	216.576	1.0577	
670		tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	Low confidence	204.551	198.901	1.02841	
670	GNL2	autoantigen ngp-1. [source:swissprot;acc:q13823]	High confidence	250.302	236.817	1.05694	
671	ITGB1	integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [source:swissprot;acc:p05556]	Low confidence	206.277	200.582	1.02839	
671	NUBP1	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	High confidence	210.739	199.398	1.05688	
672	CYP3A7	cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [source:swissprot;acc:p24462]	Low confidence	203.727	198.116	1.02832	
672	NUBP2	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	High confidence	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). [source:swissprot;acc:o14936]	High confidence	226.497	214.355	1.05664	
673	DDX31	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	Low confidence	203.604	197.996	1.02832	
674	HIF3A	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	High confidence	226.497	214.355	1.05664	
674	PRSS7	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Low confidence	204.81	199.174	1.0283	
675	CYP3A5	cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [source:swissprot;acc:p20815]	Low confidence	203.702	198.095	1.0283	
675	SIM1	single-minded homolog 1. [source:swissprot;acc:p81133]	High confidence	226.497	214.355	1.05664	
676	DUT	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	Low confidence	202.698	197.124	1.02828	
676	POLR2G	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	High confidence	232.469	245.613	1.05654	
677	CCDC53	protein ad-016 (protein cgi-116) (x0009). [source:swissprot;acc:q9y3c0]	Low confidence	207.03	201.339	1.02827	
677	LSM4	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	High confidence	228.944	216.745	1.05628	
678	CYP3A4	cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [source:swissprot;acc:p08684]	Low confidence	203.747	198.152	1.02824	
678	SNX5	sorting nexin 5. [source:swissprot;acc:q9y5x3]	High confidence	208.482	220.175	1.05609	
679		homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	High confidence	132.413	125.389	1.05602	
679	YEATS4	glioma-amplified sequence-41; numa binding protein 1. [source:refseq;acc:nm_006530]	Low confidence	198.424	192.974	1.02824	
680	EDEM2	putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [source:swissprot;acc:q9bv94]	Low confidence	196.228	190.844	1.02821	
680	HOXB4	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	High confidence	132.413	125.389	1.05602	
681		sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	Low confidence	206.115	200.462	1.0282	
681	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	High confidence	132.413	125.389	1.05602	
682		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	High confidence	132.413	125.389	1.05602	
682	DDX54	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Low confidence	204.263	198.663	1.02819	
683	CDK2AP2	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Low confidence	216.618	210.69	1.02814	
683	HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	High confidence	132.413	125.389	1.05602	
684		repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	Low confidence	199.669	194.204	1.02814	
684	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	High confidence	132.413	125.389	1.05602	
685	HOXA5	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	High confidence	132.413	125.389	1.05602	
685	TDO2	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [source:swissprot;acc:p48775]	Low confidence	201.719	196.209	1.02808	
686		homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	High confidence	132.413	125.389	1.05602	
686	NEUROG2	neurogenin 2 (fragment). [source:swissprot;acc:q9h2a3]	Low confidence	216.554	210.642	1.02807	
687	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	High confidence	132.413	125.389	1.05602	
687	NEUROD2	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Low confidence	216.554	210.642	1.02807	
688	NEUROD6	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Low confidence	216.552	210.641	1.02806	
688	POLR2D	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	High confidence	237.554	250.823	1.05586	
689	NEUROD1	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Low confidence	216.552	210.641	1.02806	
689	TCP1	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	High confidence	135.379	128.225	1.05579	
690	NEUROD4	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Low confidence	216.552	210.641	1.02806	
690	SNW1	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	High confidence	220.593	208.987	1.05553	
691	BCAS2	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [source:refseq;acc:nm_005872]	High confidence	217.602	206.195	1.05532	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/