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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 343 to 392 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	Divided	174.667	205.556	1.17685	
172	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Subtracted	201.515	228.752	27.237	
173	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Subtracted	201.515	228.752	27.237	
173	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Divided	227.032	193.056	1.17599	
174	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Divided	335	286	1.17133	
174	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Subtracted	228.1	200.968	27.132	
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Divided	199.949	234.187	1.17123	
175	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Subtracted	228.085	201.006	27.079	
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Divided	275.754	235.908	1.1689	
176	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Subtracted	271.016	244.167	26.849	
177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Divided	229.406	196.695	1.1663	
177	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Subtracted	241.07	267.88	26.81	
178	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Subtracted	241.07	267.88	26.81	
178	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Divided	226.887	194.72	1.1652	
179	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Divided	226.884	194.79	1.16476	
179	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	Subtracted	227.357	254.15	26.793	
180	pp3111 protein. [source:refseq;acc:nm_022156]	Subtracted	227.357	254.15	26.793	
180	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Divided	256.228	298.438	1.16474	
181	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Divided	229.818	267.265	1.16294	
181	syntaxin 18. [source:swissprot;acc:q9p2w9]	Subtracted	227.357	254.15	26.793	
182	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Divided	277.546	240.461	1.15422	
182	rd protein. [source:swissprot;acc:p18615]	Subtracted	227.357	254.15	26.793	
183	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Divided	228.306	198.011	1.153	
183	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	Subtracted	227.357	254.15	26.793	
184	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	Subtracted	227.357	254.15	26.793	
184	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Divided	274.027	237.79	1.15239	
185	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Divided	281.582	246.371	1.14292	
185	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	Subtracted	227.357	254.15	26.793	
186	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Divided	226.582	198.444	1.14179	
186	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	Subtracted	227.357	254.15	26.793	
187	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Divided	226.582	198.444	1.14179	
187	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	Subtracted	227.357	254.15	26.793	
188	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	Subtracted	227.357	254.15	26.793	
188	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Divided	226.582	198.444	1.14179	
189	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Subtracted	241.373	267.352	25.979	
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Divided	226.582	198.444	1.14179	
190	fad synthetase. [source:refseq;acc:nm_025207]	Subtracted	241.373	267.352	25.979	
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Divided	226.582	198.444	1.14179	
191	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Subtracted	241.373	267.352	25.979	
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Divided	226.582	198.444	1.14179	
192	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Subtracted	241.373	267.352	25.979	
192	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Divided	227.491	199.458	1.14055	
193	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	Subtracted	241.373	267.352	25.979	
193	musashi 1. [source:refseq;acc:nm_002442]	Divided	227.491	199.458	1.14055	
194	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Subtracted	241.373	267.352	25.979	
194	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Divided	227.491	199.458	1.14055	
195	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Subtracted	241.373	267.352	25.979	
195	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Divided	227.971	200.417	1.13748	
196	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Divided	263.215	231.407	1.13745	
196	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Subtracted	272.781	246.892	25.889	

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/