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 2277 to 2326 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
285	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Measured	Divided	23326.5	19296.4	1.20885	
285	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Squared	Subtracted	32117	40054	7937	
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Ranked	Divided	224.647	203.242	1.10532	
285	transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	Rooted	Subtracted	108.653	100.352	8.301	
286	60s ribosomal protein l30. [source:swissprot;acc:p04645]	Ranked	Subtracted	242.593	265.365	22.772	
286	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Ranked	Divided	224.633	203.251	1.1052	
286	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Measured	Divided	23316	19288.8	1.20878	
286	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Squared	Subtracted	32056.4	39965.8	7909.4	
286	rna-binding protein. [source:refseq;acc:nm_019027]	Measured	Subtracted	4069.83	5252.17	1182.34	
286	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	Rooted	Divided	51.8717	46.3287	1.11965	
286	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Squared	Divided	6693.64	8564.94	1.27956	
286	transforming protein n-ras. [source:swissprot;acc:p01111]	Rooted	Subtracted	108.65	100.35	8.3	
287	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Ranked	Divided	240.758	266.079	1.10517	
287	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Measured	Subtracted	4069.83	5252.17	1182.34	
287	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Squared	Divided	6693.64	8564.94	1.27956	
287	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Rooted	Divided	51.8714	46.3281	1.11965	
287	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Measured	Divided	23303.1	19279.5	1.2087	
287	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Ranked	Subtracted	225.217	202.459	22.758	
287	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Rooted	Subtracted	97.1967	105.302	8.1053	
287	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Squared	Subtracted	28878.8	36783.5	7904.7	
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Ranked	Divided	240.758	266.078	1.10517	
288	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Measured	Divided	23422.4	19380.3	1.20857	
288	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Squared	Divided	6693.64	8564.94	1.27956	
288	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	Rooted	Divided	51.8789	46.3416	1.11949	
288	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Measured	Subtracted	4069.83	5252.17	1182.34	
288	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Squared	Subtracted	28896.2	36767	7870.8	
288	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Rooted	Subtracted	55.8956	63.9636	8.068	
288	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Ranked	Subtracted	234.691	257.442	22.751	
289	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Measured	Subtracted	4069.83	5252.17	1182.34	
289	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Ranked	Divided	272.781	246.892	1.10486	
289	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Squared	Divided	6693.64	8564.94	1.27956	
289	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	Rooted	Divided	57.4274	64.2609	1.11899	
289	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Rooted	Subtracted	55.8956	63.9636	8.068	
289	syntaxin 6. [source:swissprot;acc:o43752]	Ranked	Subtracted	234.673	257.414	22.741	
289	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Squared	Subtracted	28896.2	36767	7870.8	
289	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Measured	Divided	4682.88	5646.19	1.20571	
290	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Squared	Divided	15734.4	20126.8	1.27916	
290	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Rooted	Divided	75.6323	67.6572	1.11788	
290	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Measured	Subtracted	4071.1	5251.75	1180.65	
290	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Squared	Subtracted	28896.2	36767	7870.8	
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Ranked	Divided	231.969	210.064	1.10428	
290	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Ranked	Subtracted	242.109	264.79	22.681	
290	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Measured	Divided	4991.48	6014.08	1.20487	
290	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Rooted	Subtracted	66.1122	74.1438	8.0316	
291	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	Ranked	Subtracted	241.509	264.163	22.654	
291	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]	Ranked	Divided	251.679	228.037	1.10368	
291	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Measured	Subtracted	5894.75	7073.65	1178.9	
291	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Rooted	Subtracted	66.1064	74.1074	8.001	
291	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Measured	Divided	44490.5	36927.5	1.20481	
291	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	Squared	Divided	59016.1	75486.9	1.27909	

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/