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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2001 to 2050 of 16578 in total 
Value Type	Ranked
Filtered	1

Rank	Hugo	Network Comparison Type	description	Interaction Map	red	green	network_comparison	
501	CAPS	Divided	calcyphosine. [source:swissprot;acc:q13938]	Low confidence	204.363	197.899	1.03266	
501	CYC1	Divided	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	High confidence	238.704	255.68	1.07112	
501	SF4	Subtracted	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Low confidence	203.117	196.671	6.446	
501	TLX2	Subtracted	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [source:swissprot;acc:o43763]	High confidence	237.28	252.492	15.212	
502	ARHGAP26	Divided	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	High confidence	238.704	255.68	1.07112	
502	KIFAP3	Subtracted	kinesin-associated protein 3 (smg gds-associated protein). [source:swissprot;acc:q92845]	Low confidence	203.117	196.671	6.446	
502	SART1	Divided	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	Low confidence	200.271	193.957	1.03255	
502	TLX1	Subtracted	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [source:swissprot;acc:p31314]	High confidence	237.28	252.492	15.212	
503	FOXO4	Subtracted	putative fork head domain transcription factor afx1 (forkhead box protein o4). [source:swissprot;acc:p98177]	Low confidence	205.157	198.715	6.442	
503	HECTD1	Subtracted	hect domain containing protein 1 (fragment). [source:swissprot;acc:q9ult8]	High confidence	237.28	252.492	15.212	
503	RGN	Divided	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	High confidence	238.704	255.68	1.07112	
503	USP22	Divided	ubiquitin carboxyl-terminal hydrolase 22 (ec 3.1.2.15) (ubiquitin thiolesterase 22) (ubiquitin-specific processing protease 22) (deubiquitinating enzyme 22) (fragment). [source:swissprot;acc:q9upt9]	Low confidence	207.407	200.869	1.03255	
504		Subtracted	hemoglobin gamma-a and gamma-g chains. [source:swissprot;acc:p02096]	Low confidence	205.157	198.715	6.442	
504	BARX2	Subtracted	homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	High confidence	237.28	252.492	15.212	
504	OPHN1	Divided	oligophrenin 1. [source:swissprot;acc:o60890]	High confidence	238.704	255.68	1.07112	
504	RNF113A	Divided	zinc finger protein 183. [source:swissprot;acc:o15541]	Low confidence	205.192	198.726	1.03254	
505	APP	Subtracted	amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [source:swissprot;acc:p05067]	Low confidence	205.157	198.715	6.442	
505	NOC3L	Divided	ad24 protein. [source:refseq;acc:nm_022451]	High confidence	251.334	234.672	1.071	
505	PCNA	Divided	proliferating cell nuclear antigen (pcna) (cyclin). [source:swissprot;acc:p12004]	Low confidence	207.84	201.297	1.0325	
505	ZNF593	Subtracted	zinc finger protein t86. [source:swissprot;acc:o00488]	High confidence	246.805	231.796	15.009	
506	EXOSC4	Subtracted	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	High confidence	215.237	230.07	14.833	
506	FOXO4	Divided	putative fork head domain transcription factor afx1 (forkhead box protein o4). [source:swissprot;acc:p98177]	Low confidence	205.157	198.715	1.03242	
506	ING1	Divided	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	High confidence	224.535	240.476	1.071	
506	TTYH2	Subtracted	tweety homolog 2. [source:refseq;acc:nm_032646]	Low confidence	205.157	198.715	6.442	
507		Divided	hemoglobin gamma-a and gamma-g chains. [source:swissprot;acc:p02096]	Low confidence	205.157	198.715	1.03242	
507	EXOSC2	Subtracted	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	High confidence	215.237	230.07	14.833	
507	HBZ	Subtracted	hemoglobin zeta chain (hbaz). [source:swissprot;acc:p02008]	Low confidence	205.157	198.715	6.442	
507	WDR12	Divided	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	High confidence	251.299	234.729	1.07059	
508		Subtracted	alpha 2 globin. [source:refseq;acc:nm_000517]	Low confidence	205.157	198.715	6.442	
508	APP	Divided	amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [source:swissprot;acc:p05067]	Low confidence	205.157	198.715	1.03242	
508	CPA3	Divided	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	High confidence	177.698	190.24	1.07058	
508	LSM8	Subtracted	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	High confidence	228.255	213.422	14.833	
509	APLP1	Subtracted	amyloid-like protein 1 precursor (aplp) (aplp-1) [contains: c30]. [source:swissprot;acc:p51693]	Low confidence	205.157	198.715	6.442	
509	CPA6	Divided	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	High confidence	177.698	190.239	1.07057	
509	EXOSC3	Subtracted	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	High confidence	215.237	230.07	14.833	
509	TTYH2	Divided	tweety homolog 2. [source:refseq;acc:nm_032646]	Low confidence	205.157	198.715	1.03242	
510		Subtracted	myoglobin. [source:swissprot;acc:p02144]	Low confidence	205.157	198.715	6.442	
510	CPB2	Divided	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	High confidence	177.699	190.24	1.07057	
510	EXOSC5	Subtracted	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	High confidence	215.237	230.07	14.833	
510	HBZ	Divided	hemoglobin zeta chain (hbaz). [source:swissprot;acc:p02008]	Low confidence	205.157	198.715	1.03242	
511		Divided	alpha 2 globin. [source:refseq;acc:nm_000517]	Low confidence	205.157	198.715	1.03242	
511	HBQ1	Subtracted	hemoglobin theta-1 chain. [source:swissprot;acc:p09105]	Low confidence	205.157	198.715	6.442	
511	NOL1	Divided	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	High confidence	250.053	233.725	1.06986	
511	SLC35D2	Subtracted	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	High confidence	214.754	229.565	14.811	
512	APLP1	Divided	amyloid-like protein 1 precursor (aplp) (aplp-1) [contains: c30]. [source:swissprot;acc:p51693]	Low confidence	205.157	198.715	1.03242	
512	BOP1	Divided	block of proliferation 1. [source:swissprot;acc:q14137]	High confidence	250.794	234.433	1.06979	
512	DHX15	Subtracted	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	High confidence	229.803	215.301	14.502	
512	TTYH1	Subtracted	tweety homolog 1; tweety homolog. [source:refseq;acc:nm_020659]	Low confidence	205.156	198.715	6.441	
513		Divided	myoglobin. [source:swissprot;acc:p02144]	Low confidence	205.157	198.715	1.03242	
513	CYGB	Subtracted	cytoglobin (histoglobin) (hgb) (stellate cell activation-associated protein). [source:swissprot;acc:q8wwm9]	Low confidence	205.156	198.715	6.441	

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/