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

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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1851 to 1900 of 16578 in total 
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
463	PRRX1	paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [source:swissprot;acc:p54821]	Divided	Low confidence	194.41	201.036	1.03408	
463	SF3A2	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Subtracted	High confidence	223.648	207.62	16.028	
464		huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Subtracted	Low confidence	201.418	194.664	6.754	
464	ELL2	rna polymerase ii elongation factor ell2. [source:swissprot;acc:o00472]	Divided	Low confidence	198.618	205.369	1.03399	
464	FNBP1	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6]	Divided	High confidence	210.578	226.764	1.07686	
464	KLF5	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887]	Subtracted	High confidence	223.648	207.62	16.028	
465	CHRNA7	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Divided	High confidence	248.152	267.226	1.07686	
465	ELL2	rna polymerase ii elongation factor ell2. [source:swissprot;acc:o00472]	Subtracted	Low confidence	198.618	205.369	6.751	
465	HS3ST6	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Divided	Low confidence	207.812	200.994	1.03392	
465	ING2	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	Subtracted	High confidence	224.662	240.673	16.011	
466	ADCY6	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Divided	High confidence	248.152	267.226	1.07686	
466	CXorf9	chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [source:refseq;acc:nm_018990]	Subtracted	Low confidence	204.331	211.075	6.744	
466	HS3ST3A1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Divided	Low confidence	207.812	200.994	1.03392	
466	PRPF31	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	Subtracted	High confidence	225.661	209.651	16.01	
467	ADCY5	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Divided	High confidence	248.152	267.226	1.07686	
467	DDX31	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	Subtracted	High confidence	248.56	232.579	15.981	
467	HS3ST3B1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Divided	Low confidence	207.812	200.994	1.03392	
467	PRPF19	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Subtracted	Low confidence	202.01	195.266	6.744	
468	HS3ST2	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Divided	Low confidence	207.812	200.994	1.03392	
468	LRRC15	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	Divided	High confidence	248.152	267.226	1.07686	
468	POLR2L	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	Subtracted	High confidence	237.627	253.604	15.977	
468	TMOD4	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [source:swissprot;acc:q9nzq9]	Subtracted	Low confidence	209.136	202.478	6.658	
469	DCPS	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Divided	Low confidence	207.812	200.994	1.03392	
469	FEM1B	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Divided	High confidence	248.152	267.226	1.07686	
469	KCNA2	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [source:swissprot;acc:p16389]	Subtracted	High confidence	226.789	210.818	15.971	
469	TMOD3	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [source:swissprot;acc:q9nyl9]	Subtracted	Low confidence	209.136	202.478	6.658	
470		splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Divided	Low confidence	198.464	191.96	1.03388	
470	ING1	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	Subtracted	High confidence	224.535	240.476	15.941	
470	LRRC3	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Divided	High confidence	248.152	267.226	1.07686	
470	TMOD1	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [source:swissprot;acc:p28289]	Subtracted	Low confidence	209.136	202.478	6.658	
471	LAMC1	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Divided	High confidence	248.152	267.226	1.07686	
471	RBM39	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	Divided	Low confidence	208.29	201.499	1.0337	
471	SNX9	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [source:swissprot;acc:q9y5x1]	Subtracted	Low confidence	209.136	202.478	6.658	
471	ZNF622	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	Subtracted	High confidence	250.942	235.004	15.938	
472	PLRG1	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Divided	Low confidence	201.847	195.283	1.03361	
472	SLC45A2	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	Subtracted	High confidence	250.942	235.004	15.938	
472	SLC46A2	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Divided	High confidence	248.152	267.226	1.07686	
472	TMOD2	neuronal tropomodulin (n-tmod) (tropomodulin 2). [source:swissprot;acc:q9nzr1]	Subtracted	Low confidence	209.136	202.478	6.658	
473		guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Subtracted	High confidence	250.942	235.004	15.938	
473	EXOC1	exocyst complex component sec3 (bm-012). [source:swissprot;acc:q9nv70]	Divided	Low confidence	209.111	202.34	1.03346	
473	PRPF31	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	Divided	High confidence	225.661	209.651	1.07637	
473	TNK2	activated p21cdc42hs kinase. [source:refseq;acc:nm_005781]	Subtracted	Low confidence	209.136	202.478	6.658	
474	KCNA1	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [source:swissprot;acc:q09470]	Subtracted	High confidence	226.727	210.816	15.911	
474	KCNA2	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [source:swissprot;acc:p16389]	Divided	High confidence	226.789	210.818	1.07576	
474	PRPF40B	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Subtracted	Low confidence	201.429	194.776	6.653	
474	RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Divided	Low confidence	171.213	165.68	1.0334	
475	FUCA2	fucosidase, alpha-l- 2, plasma. [source:refseq;acc:nm_032020]	Divided	Low confidence	202.311	195.778	1.03337	
475	KCNA1	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [source:swissprot;acc:q09470]	Divided	High confidence	226.727	210.816	1.07547	
475	MEMO1P	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	Subtracted	High confidence	236.964	252.86	15.896	
475	SLC7A5	large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [source:swissprot;acc:q01650]	Subtracted	Low confidence	201.466	194.819	6.647	

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/