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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 375 to 424 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
188	GSTO2	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	Subtracted	227.357	254.15	26.793	
188	PRMT1	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	PCYT1A	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	PRMT8	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Divided	226.582	198.444	1.14179	
190	FLAD1	fad synthetase. [source:refseq;acc:nm_025207]	Subtracted	241.373	267.352	25.979	
190	SNRP70	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	LGTN	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Subtracted	241.373	267.352	25.979	
192	MSI2	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Divided	227.491	199.458	1.14055	
193	MSI1	musashi 1. [source:refseq;acc:nm_002442]	Divided	227.491	199.458	1.14055	
193	PAPSS1	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	
194	POR	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Subtracted	241.373	267.352	25.979	
194	ZC3H14	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Divided	227.491	199.458	1.14055	
195	PCYT1B	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	PRPF40B	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Divided	227.971	200.417	1.13748	
196		hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Subtracted	272.781	246.892	25.889	
196	FOXP4	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	
197	FOXP1	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Divided	263.215	231.407	1.13745	
197	SNORA7A	60s ribosomal protein l32. [source:swissprot;acc:p02433]	Subtracted	241.13	266.969	25.839	
198		40s ribosomal protein s29. [source:swissprot;acc:p30054]	Subtracted	241.849	267.642	25.793	
198	FOXP3	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Divided	263.191	231.394	1.13741	
199	EGFL8	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	Divided	242.735	276.059	1.13729	
199	RPS11	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Subtracted	241.399	267.088	25.689	
200		60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Subtracted	241.808	267.335	25.527	
200	EGFL7	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	Divided	242.718	276.018	1.1372	
201	RPL11	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Subtracted	241.828	267.346	25.518	
201	SF4	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Divided	240.133	211.382	1.13601	
202	RPS4Y2	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Subtracted	240.758	266.079	25.321	
202	TRPC4	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Divided	201.478	228.784	1.13553	
203		40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Subtracted	240.758	266.078	25.32	
203	TBC1D10A	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Divided	201.515	228.752	1.13516	
204	CAPN2	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [source:swissprot;acc:p17655]	Subtracted	268.632	243.588	25.044	
204	TRPC5	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Divided	201.515	228.752	1.13516	
205	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	Subtracted	268.635	243.592	25.043	
205	LUC7L2	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Divided	228.1	200.968	1.13501	
206	LUC7L	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Divided	228.085	201.006	1.13472	
206	RPS15A	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	Subtracted	241.411	266.414	25.003	
207	EIF4G3	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Subtracted	237.312	212.363	24.949	
207	PSEN2	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	Divided	285.684	252.234	1.13261	
208		60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	Subtracted	240.782	265.717	24.935	
208	SKP1A	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [source:swissprot;acc:p34991]	Divided	285.684	252.234	1.13261	
209	BCCIP	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [source:refseq;acc:nm_016567]	Subtracted	240.782	265.717	24.935	
209	FBXW7	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315]	Divided	285.684	252.234	1.13261	
210		rna-binding protein. [source:refseq;acc:nm_019027]	Subtracted	237.302	212.41	24.892	
210	CUL2	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Divided	285.684	252.234	1.13261	
211		apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Subtracted	237.302	212.41	24.892	
211	PSEN1	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Divided	285.684	252.234	1.13261	
212	CUL1	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Divided	285.684	252.234	1.13261	
212	SYNCRIP	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Subtracted	237.302	212.41	24.892	

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/