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 418 to 467 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
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]	Divided	285.684	252.234	1.13261	
210	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Divided	285.684	252.234	1.13261	
210	rna-binding protein. [source:refseq;acc:nm_019027]	Subtracted	237.302	212.41	24.892	
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	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Divided	285.684	252.234	1.13261	
212	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Divided	285.684	252.234	1.13261	
212	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Subtracted	237.302	212.41	24.892	
213	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Subtracted	237.302	212.41	24.892	
213	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Divided	210.693	186.95	1.127	
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Divided	191.644	170.192	1.12605	
214	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	Subtracted	241.282	266.12	24.838	
215	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Subtracted	237.292	212.457	24.835	
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Divided	112	126	1.125	
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Divided	112	126	1.125	
216	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Subtracted	226.471	201.769	24.702	
217	60s ribosomal protein l26. [source:swissprot;acc:q02877]	Subtracted	242.326	267.008	24.682	
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Divided	112	126	1.125	
218	60s ribosomal protein l35. [source:swissprot;acc:p42766]	Subtracted	242.333	266.999	24.666	
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Divided	112	126	1.125	
219	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Subtracted	242.339	266.986	24.647	
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Divided	112	126	1.125	
220	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	Subtracted	242.339	266.986	24.647	
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Divided	112	126	1.125	
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Divided	112	126	1.125	
221	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Subtracted	242.627	267.151	24.524	
222	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	Subtracted	242.153	266.673	24.52	
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Divided	112	126	1.125	
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Divided	112	126	1.125	
223	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	Subtracted	242.153	266.673	24.52	
224	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Subtracted	242.153	266.673	24.52	
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	Divided	185.969	165.623	1.12285	
225	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Subtracted	242.153	266.673	24.52	
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Divided	226.471	201.769	1.12243	
226	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Divided	239.991	269.238	1.12187	
226	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Subtracted	242.153	266.673	24.52	
227	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	Subtracted	244.126	268.604	24.478	
227	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Divided	239.99	269.234	1.12186	
228	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	Subtracted	244.126	268.604	24.478	
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	Divided	226.411	202.088	1.12036	
229	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Subtracted	242.195	266.663	24.468	
229	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Divided	226.401	202.094	1.12028	
230	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	Divided	239.35	267.915	1.11934	
230	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	Subtracted	242.694	267.017	24.323	
231	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Divided	239.336	267.881	1.11927	
231	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	Subtracted	226.411	202.088	24.323	
232	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Subtracted	226.401	202.094	24.307	
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	Divided	239.336	267.879	1.11926	
233	60s ribosomal protein l7. [source:swissprot;acc:p18124]	Subtracted	235.727	259.984	24.257	
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	Divided	239.32	267.842	1.11918	
234	40s ribosomal protein s23. [source:swissprot;acc:p39028]	Subtracted	243.944	268.195	24.251	

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/