MK5 Microarray Data

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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Gene	Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 413 to 462 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	network_comparison	green
207	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Subtracted	237.312	24.949	212.363
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Divided	285.684	1.13261	252.234
208	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Subtracted	240.782	24.935	265.717
	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). [swissprot;acc:p34991]	Divided	285.684	1.13261	252.234
209	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	Subtracted	240.782	24.935	265.717
	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. [refseq;acc:nm_018315]	Divided	285.684	1.13261	252.234
210	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
	rna-binding protein. [refseq;acc:nm_019027]	Subtracted	237.302	24.892	212.41
211	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Divided	285.684	1.13261	252.234
212	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
	ns1-associated protein 1. [refseq;acc:nm_006372]	Subtracted	237.302	24.892	212.41
213	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Divided	210.693	1.127	186.95
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		191.644	1.12605	170.192
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	Subtracted	241.282	24.838	266.12
215	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]		237.292	24.835	212.457
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Divided	112	1.125	126
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Subtracted	226.471	24.702	201.769
217	60s ribosomal protein l26. [swissprot;acc:q02877]		242.326	24.682	267.008
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Divided	112	1.125	126
218	60s ribosomal protein l35. [swissprot;acc:p42766]	Subtracted	242.333	24.666	266.999
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Divided	112	1.125	126
219	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Subtracted	242.339	24.647	266.986
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Divided	112	1.125	126
220	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Subtracted	242.339	24.647	266.986
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Divided	112	1.125	126
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Subtracted	242.627	24.524	267.151
222	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		242.153	24.52	266.673
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Divided	112	1.125	126
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Subtracted	242.153	24.52	266.673
224	60s ribosomal protein l34. [swissprot;acc:p49207]
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Divided	185.969	1.12285	165.623
225	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Subtracted	242.153	24.52	266.673
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Divided	226.471	1.12243	201.769
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]		239.991	1.12187	269.238
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Subtracted	242.153	24.52	266.673
227	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]		244.126	24.478	268.604
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Divided	239.99	1.12186	269.234
228	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Subtracted	244.126	24.478	268.604
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Divided	226.411	1.12036	202.088
229	60s ribosomal protein l3-like. [swissprot;acc:q92901]	Subtracted	242.195	24.468	266.663
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Divided	226.401	1.12028	202.094
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]		239.35	1.11934	267.915
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Subtracted	242.694	24.323	267.017
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Divided	239.336	1.11927	267.881
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Subtracted	226.411	24.323	202.088

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.