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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 958 to 1007 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
240	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Measured	7711.36	6265.79	1.23071	
240	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Rooted	137.446	120.823	1.13758	
240	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [source:swissprot;acc:q16539]	Squared	42411.6	55802.1	1.31573	
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	Ranked	227.357	254.15	1.11785	
241	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Rooted	137.446	120.823	1.13758	
241	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [source:swissprot;acc:p43681]	Squared	42411.6	55802.1	1.31573	
241	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]	Measured	7711.31	6265.76	1.23071	
242	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	Ranked	227.357	254.15	1.11785	
242	max protein. [source:swissprot;acc:p25912]	Measured	4640.26	5704.87	1.22943	
242	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Rooted	137.446	120.823	1.13758	
242	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [source:swissprot;acc:p32297]	Squared	42411.6	55802.1	1.31573	
243	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Measured	4246.95	5208.98	1.22652	
243	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	Ranked	227.357	254.15	1.11785	
243	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]	Squared	42411.6	55802.1	1.31573	
243	trophinin. [source:swissprot;acc:q12816]	Rooted	137.446	120.823	1.13758	
244	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	Ranked	227.357	254.15	1.11785	
244	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Squared	14728.8	19330.8	1.31245	
244	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Rooted	146.94	167.046	1.13683	
244	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Measured	4250.14	5211.25	1.22614	
245	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Squared	8875.01	6768.05	1.31131	
245	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Measured	4251.65	5212.33	1.22595	
245	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	Rooted	146.94	167.046	1.13683	
245	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Ranked	226.109	202.333	1.11751	
246	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Ranked	237.312	212.363	1.11748	
246	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Squared	8875.01	6768.05	1.31131	
246	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Measured	4252.66	5213.05	1.22583	
246	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Rooted	146.94	167.046	1.13683	
247	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Squared	8875.01	6768.05	1.31131	
247	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	Rooted	47.3621	53.8355	1.13668	
247	rna-binding protein. [source:refseq;acc:nm_019027]	Ranked	237.302	212.41	1.11719	
247	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Measured	6416.68	7865.15	1.22574	
248	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Ranked	237.302	212.41	1.11719	
248	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Squared	8875.01	6768.05	1.31131	
248	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Measured	6417.18	7859.6	1.22477	
248	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Rooted	56.0466	63.4808	1.13264	
249	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Squared	8875.01	6768.05	1.31131	
249	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Ranked	237.302	212.41	1.11719	
249	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Rooted	55.5965	62.9349	1.13199	
249	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Measured	6417.18	7859.59	1.22477	
250	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	Squared	69201.8	53013.4	1.30536	
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Ranked	237.302	212.41	1.11719	
250	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Rooted	55.5965	62.9349	1.13199	
250	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Measured	6417.18	7859.6	1.22477	
251	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	Squared	69165.6	52992.1	1.30521	
251	max protein. [source:swissprot;acc:p25912]	Rooted	56.3054	63.7148	1.13159	
251	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Ranked	186.172	166.661	1.11707	
251	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Measured	6417.18	7859.6	1.22477	
252	crk-like protein. [source:swissprot;acc:p46109]	Measured	6417.18	7859.6	1.22477	
252	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Ranked	237.292	212.457	1.11689	
252	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	Rooted	51.6736	58.4422	1.13099	

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