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 175 to 224 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	199.949	234.187	1.17123	
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	275.754	235.908	1.1689	
177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	229.406	196.695	1.1663	
178	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	226.887	194.72	1.1652	
179	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	226.884	194.79	1.16476	
180	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	256.228	298.438	1.16474	
181	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	229.818	267.265	1.16294	
182	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	277.546	240.461	1.15422	
183	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	228.306	198.011	1.153	
184	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	274.027	237.79	1.15239	
185	adiponectin receptor 2. [source:refseq;acc:nm_024551]	281.582	246.371	1.14292	
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]	226.582	198.444	1.14179	
187	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	226.582	198.444	1.14179	
188	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	226.582	198.444	1.14179	
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	226.582	198.444	1.14179	
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	226.582	198.444	1.14179	
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	226.582	198.444	1.14179	
192	musashi 2 isoform a. [source:refseq;acc:nm_138962]	227.491	199.458	1.14055	
193	musashi 1. [source:refseq;acc:nm_002442]	227.491	199.458	1.14055	
194	nuclear protein ukp68. [source:refseq;acc:nm_024824]	227.491	199.458	1.14055	
195	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	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]	263.215	231.407	1.13745	
197	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	263.215	231.407	1.13745	
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	263.191	231.394	1.13741	
199	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	242.735	276.059	1.13729	
200	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	242.718	276.018	1.1372	
201	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	240.133	211.382	1.13601	
202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	201.478	228.784	1.13553	
203	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	201.515	228.752	1.13516	
204	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	201.515	228.752	1.13516	
205	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	228.1	200.968	1.13501	
206	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	228.085	201.006	1.13472	
207	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	285.684	252.234	1.13261	
208	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]	285.684	252.234	1.13261	
209	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]	285.684	252.234	1.13261	
210	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	285.684	252.234	1.13261	
211	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	285.684	252.234	1.13261	
212	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	285.684	252.234	1.13261	
213	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	210.693	186.95	1.127	
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	191.644	170.192	1.12605	
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	112	126	1.125	
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	112	126	1.125	
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	112	126	1.125	
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	112	126	1.125	
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	112	126	1.125	
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	112	126	1.125	
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	112	126	1.125	
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	112	126	1.125	
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	112	126	1.125	
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	185.969	165.623	1.12285	

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/