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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2458 to 2507 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
2458	SLC13A2	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [source:swissprot;acc:q13183]	204.683	205.326	1.00314	
2459	CDS1	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	204.653	205.286	1.00309	
2460		pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	235.812	235.088	1.00308	
2461	SLC20A2	solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [source:refseq;acc:nm_006749]	235.812	235.088	1.00308	
2462	FDPS	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [source:swissprot;acc:p14324]	235.812	235.088	1.00308	
2463	PCDH15	protocadherin 15 precursor. [source:swissprot;acc:q96qu1]	235.812	235.088	1.00308	
2464	SLC20A1	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [source:refseq;acc:nm_005415]	235.812	235.088	1.00308	
2465	LMBR1L	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	235.812	235.088	1.00308	
2466	GLI1	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [source:swissprot;acc:p08151]	235.812	235.088	1.00308	
2467	SUFU	suppressor of fused. [source:refseq;acc:nm_016169]	235.812	235.088	1.00308	
2468	GLI3	zinc finger protein gli3. [source:swissprot;acc:p10071]	235.812	235.088	1.00308	
2469	LMBR1	limb region 1 protein; limb region 1. [source:refseq;acc:nm_022458]	235.812	235.088	1.00308	
2470	PGC	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [source:swissprot;acc:p20142]	235.812	235.088	1.00308	
2471	GLI2	zinc finger protein gli2 (tax helper protein). [source:swissprot;acc:p10070]	235.812	235.088	1.00308	
2472	TNS3	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [source:refseq;acc:nm_022748]	218.218	217.564	1.00301	
2473	MAPK8IP3	c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [source:swissprot;acc:q9upt6]	218.644	217.991	1.003	
2474	PSMC3	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [source:swissprot;acc:p17980]	216.64	217.285	1.00298	
2475	TENC1	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [source:refseq;acc:nm_015319]	218.219	217.571	1.00298	
2476	XYLB	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [source:refseq;acc:nm_005108]	211.205	210.577	1.00298	
2477	MRPL30	mitochondrial ribosomal protein l30 isoform a. [source:refseq;acc:nm_145212]	216.177	216.801	1.00289	
2478	PSMC6	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [source:swissprot;acc:q92524]	216.177	216.801	1.00289	
2479	PRR5	rho-gtpase-activating protein 8. [source:swissprot;acc:q9nsg0]	218.093	218.72	1.00287	
2480	ARHGAP1	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [source:swissprot;acc:q07960]	218.093	218.72	1.00287	
2481	KLC2	kinesin light chain 2 (klc 2). [source:swissprot;acc:q9h0b6]	218.093	218.72	1.00287	
2482	KIF5B	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [source:swissprot;acc:p33176]	218.093	218.72	1.00287	
2483	KIF5C	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [source:swissprot;acc:o60282]	218.093	218.72	1.00287	
2484	KIF5A	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [source:swissprot;acc:q12840]	218.093	218.72	1.00287	
2485	KLC1	kinesin light chain 1 (klc 1). [source:swissprot;acc:q07866]	218.093	218.72	1.00287	
2486	GTF3A	transcription factor iiia (factor a) (tfiiia). [source:swissprot;acc:q92664]	218.093	218.72	1.00287	
2487	EXOC1	exocyst complex component sec3 (bm-012). [source:swissprot;acc:q9nv70]	218.093	218.72	1.00287	
2488		hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [source:refseq;acc:nm_023934]	194.527	195.08	1.00284	
2489		dc11 protein. [source:refseq;acc:nm_020186]	194.527	195.08	1.00284	
2490	APPBP1	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [source:refseq;acc:nm_003905]	194.527	195.08	1.00284	
2491	ALAS2	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [source:swissprot;acc:p22557]	194.527	195.08	1.00284	
2492	UBE1C	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [source:refseq;acc:nm_003968]	194.527	195.08	1.00284	
2493	UBE1	ubiquitin-activating enzyme e1 (a1s9 protein). [source:swissprot;acc:p22314]	194.527	195.08	1.00284	
2494	SLC25A12	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [source:swissprot;acc:o75746]	194.527	195.08	1.00284	
2495	HHAT	melanoma antigen recognized by t cells 2. [source:refseq;acc:nm_018194]	194.527	195.08	1.00284	
2496	ALAS1	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	194.527	195.08	1.00284	
2497	SLC25A13	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [source:swissprot;acc:q9ujs0]	194.527	195.08	1.00284	
2498	NDUFAB1	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [source:swissprot;acc:o14561]	194.527	195.08	1.00284	
2499	NOB1	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [source:refseq;acc:nm_014062]	231.414	230.76	1.00283	
2500	BIRC5	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [source:swissprot;acc:o15392]	218.949	219.552	1.00275	
2501	ZMYND8	protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [source:swissprot;acc:q9ulu4]	217.398	216.809	1.00272	
2502	ZMYND11	adenovirus 5 e1a-binding protein (bs69 protein). [source:swissprot;acc:q15326]	217.417	216.844	1.00264	
2503	PSMC1	26s protease regulatory subunit 4 (p26s4). [source:swissprot;acc:q03527]	215.581	216.137	1.00258	
2504	TNS1	tensin. [source:refseq;acc:nm_022648]	218.238	217.682	1.00255	
2505	CBX5	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [source:swissprot;acc:p45973]	187.853	188.326	1.00252	
2506	C10orf83	44050 protein. [source:refseq;acc:nm_178832]	151.386	151.009	1.0025	
2507	PPP1R8	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	151.386	151.009	1.0025	

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/