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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Filtered green Value Type description Rank Gene Interaction Map network_comparison red Network Comparison Type
Results: HTML CSV LaTeX Showing element 501 to 550 of 14920 in total 
Filtered	0
Interaction Map	High confidence
Network Comparison Type	Divided

green	Value Type	description	Rank	network_comparison	red	
29.1204	Rooted	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [source:swissprot;acc:q9np71]	345	1.05229	30.6431	
29.1579	Rooted	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	323	1.06018	27.5028	
29.1579	Rooted	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	324	1.06018	27.5028	
29.2291	Rooted	60s ribosomal protein l21. [source:swissprot;acc:p46778]	65	1.42072	20.5734	
29.2362	Rooted	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513]	304	1.07253	31.3568	
29.2445	Rooted	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	235	1.11792	26.1597	
29.2679	Rooted	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]	452	1.0174	29.7773	
29.4181	Rooted	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]	389	1.03521	30.454	
29.5305	Rooted	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [source:refseq;acc:nm_015409]	160	1.16158	34.3021	
29.5494	Rooted	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	281	1.08918	27.1299	
29.828	Rooted	importin 9. [source:refseq;acc:nm_018085]	72	1.36418	21.8651	
29.828	Rooted	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	73	1.36418	21.8651	
29.8694	Rooted	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	399	1.03317	30.8601	
29.9666	Rooted	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	85	1.33607	40.0375	
30.112	Rooted	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	298	1.07468	28.0195	
30.117	Rooted	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	275	1.0922	32.8937	
30.1206	Rooted	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	274	1.09221	32.8979	
30.1276	Rooted	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	297	1.07513	32.3911	
30.2263	Rooted	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	272	1.09252	33.0227	
30.4161	Rooted	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	279	1.09039	33.1655	
30.5361	Rooted	collagen alpha 5(iv) chain precursor. [source:swissprot;acc:p29400]	178	1.14872	35.0775	
30.5384	Rooted	similar to cg7020 gene product (fragment). [source:sptrembl;acc:q96ib4]	459	1.01471	30.9876	
30.7252	Rooted	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [source:swissprot;acc:o15143]	464	1.01265	30.3413	
30.8974	Rooted	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	289	1.0803	28.6008	
30.9731	Rooted	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	395	1.03421	32.0326	
30.9782	Rooted	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [source:refseq;acc:nm_015920]	396	1.03419	32.0372	
31.1453	Rooted	3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	376	1.03923	32.3671	
31.1803	Rooted	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [source:refseq;acc:nm_015247]	278	1.09092	34.0153	
31.1837	Rooted	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	339	1.05253	29.6274	
31.1839	Rooted	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	340	1.0525	29.6283	
31.1846	Rooted	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	341	1.05243	29.6311	
31.1848	Rooted	histone h2b. [source:refseq;acc:nm_175055]	342	1.05241	29.6319	
31.1848	Rooted	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	343	1.0524	29.632	
31.1851	Rooted	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	344	1.05238	29.633	
31.1879	Squared	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm_015650]	199	1.42582	21.8736	
31.257	Rooted	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	128	1.21489	37.9737	
31.257	Rooted	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	127	1.21489	37.9737	
31.4149	Rooted	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	255	1.10545	28.4183	
31.4916	Rooted	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	230	1.12255	35.3509	
31.5117	Rooted	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	374	1.04048	30.2858	
31.5389	Rooted	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	373	1.0407	30.3054	
31.6971	Rooted	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	365	1.04366	30.3712	
31.7228	Rooted	60s ribosomal protein l7. [source:swissprot;acc:p18124]	173	1.15305	27.512	
31.8678	Rooted	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	385	1.03612	30.7569	
32.0298	Rooted	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	370	1.04188	30.7424	
32.0874	Rooted	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [source:swissprot;acc:o75521]	287	1.08193	34.7164	
32.1981	Rooted	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	181	1.14566	28.1043	
32.2238	Rooted	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	363	1.04437	30.8547	
32.6803	Rooted	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [source:swissprot;acc:p52292]	90	1.32645	24.6374	
32.7487	Rooted	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	393	1.03458	33.8811	

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/