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

Results: HTML CSV LaTeX

Showing element 401 to 450 of 6456 in total

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

Rank	description	Network Comparison Type	red	network_comparison	green
201	60s ribosomal protein l11. [swissprot;acc:p39026]	Subtracted	241.828	25.518	267.346
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Divided	240.133	1.13601	211.382
202	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Subtracted	240.758	25.321	266.079
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Divided	201.478	1.13553	228.784
203	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Subtracted	240.758	25.32	266.078
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Divided	201.515	1.13516	228.752
204	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). [swissprot;acc:p17655]	Subtracted	268.632	25.044	243.588
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Divided	201.515	1.13516	228.752
205	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Subtracted	268.635	25.043	243.592
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Divided	228.1	1.13501	200.968
206	40s ribosomal protein s15a. [swissprot;acc:p39027]	Subtracted	241.411	25.003	266.414
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Divided	228.085	1.13472	201.006
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

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.