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 751 to 800 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
376	44050 protein. [source:refseq;acc:nm_178832]	Divided	17385.9	14889.2	1.16769	
376	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Subtracted	4251.65	5212.33	960.68	
377	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Subtracted	4252.66	5213.05	960.39	
377	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]	Divided	17385.9	14889.2	1.16769	
378	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Divided	12471.7	14561.7	1.16758	
378	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	Subtracted	6272.91	7226.06	953.15	
379	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Divided	6704.44	7811.45	1.16512	
379	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Subtracted	4244.95	5193.42	948.47	
380	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Divided	12998.5	15138.2	1.16461	
380	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Subtracted	4641.09	5588.75	947.66	
381	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Divided	5246.01	6109.31	1.16456	
381	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Subtracted	4641.09	5588.75	947.66	
382	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	Divided	4533.74	5279.4	1.16447	
382	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	Subtracted	2397.19	3343.62	946.43	
383	hepatoma-derived growth factor-related protein 2. [source:refseq;acc:nm_032631]	Divided	4533.74	5279.4	1.16447	
383	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Subtracted	4247.36	5192.61	945.25	
384	cgi-142; hepatoma-derived growth factor 2. [source:refseq;acc:nm_016073]	Divided	4533.74	5279.4	1.16447	
384	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	Subtracted	8061.05	9002.33	941.28	
385	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	Subtracted	8056.09	8996.46	940.37	
385	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	Divided	4533.74	5279.4	1.16447	
386	60s ribosomal protein l8. [source:swissprot;acc:p25120]	Divided	4533.74	5279.4	1.16447	
386	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Subtracted	1833.01	892.67	940.34	
387	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	Subtracted	1833.01	892.67	940.34	
387	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	Divided	4533.74	5279.4	1.16447	
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	Divided	4533.74	5279.4	1.16447	
388	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [source:swissprot;acc:o14497]	Subtracted	6252.58	7192.88	940.3	
389	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	Divided	4533.74	5279.4	1.16447	
389	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [source:swissprot;acc:o75340]	Subtracted	6252.58	7192.88	940.3	
390	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [source:refseq;acc:nm_020732]	Subtracted	6252.27	7192.51	940.24	
390	rw1 protein (fragment). [source:swissprot;acc:q92545]	Divided	4533.74	5279.4	1.16447	
391	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Subtracted	6251.99	7192.17	940.18	
391	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Divided	3658.76	3144.39	1.16358	
392	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Divided	3641.89	4236.95	1.16339	
392	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	Subtracted	6251.91	7192.08	940.17	
393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	Divided	4490.28	5222.25	1.16301	
393	grancalcin. [source:swissprot;acc:p28676]	Subtracted	6251.96	7192.13	940.17	
394	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	Divided	4490.28	5222.25	1.16301	
394	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	Subtracted	1834.33	895.134	939.196	
395	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	Subtracted	1834.36	895.194	939.166	
395	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Divided	4532.73	5269.33	1.16251	
396	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Subtracted	1834.52	895.507	939.013	
396	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Divided	6563.65	7627.29	1.16205	
397	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	Subtracted	1834.59	895.633	938.957	
397	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	Divided	5367.04	6233.12	1.16137	
398	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	Subtracted	1834.63	895.697	938.933	
398	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	Divided	5084.26	5904.1	1.16125	
399	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Divided	5201.41	4479.76	1.16109	
399	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Subtracted	4633.92	5572.85	938.93	
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Divided	5201.41	4479.76	1.16109	
400	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Subtracted	1834.73	895.893	938.837	

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/