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	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

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	green	red	network_comparison
201	60s ribosomal protein l11. [swissprot;acc:p39026]	Subtracted	267.346	241.828	25.518
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Divided	211.382	240.133	1.13601
202	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Subtracted	266.079	240.758	25.321
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Divided	228.784	201.478	1.13553
203	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Subtracted	266.078	240.758	25.32
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Divided	228.752	201.515	1.13516
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	243.588	268.632	25.044
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Divided	228.752	201.515	1.13516
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	243.592	268.635	25.043
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Divided	200.968	228.1	1.13501
206	40s ribosomal protein s15a. [swissprot;acc:p39027]	Subtracted	266.414	241.411	25.003
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Divided	201.006	228.085	1.13472
207	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Subtracted	212.363	237.312	24.949
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Divided	252.234	285.684	1.13261
208	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Subtracted	265.717	240.782	24.935
	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	252.234	285.684	1.13261
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	265.717	240.782	24.935
	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	252.234	285.684	1.13261
210	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
	rna-binding protein. [refseq;acc:nm_019027]	Subtracted	212.41	237.302	24.892
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	252.234	285.684	1.13261
212	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
	ns1-associated protein 1. [refseq;acc:nm_006372]	Subtracted	212.41	237.302	24.892
213	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Divided	186.95	210.693	1.127
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		170.192	191.644	1.12605
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	Subtracted	266.12	241.282	24.838
215	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]		212.457	237.292	24.835
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Divided	126	112	1.125
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	201.769	226.471	24.702
217	60s ribosomal protein l26. [swissprot;acc:q02877]		267.008	242.326	24.682
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Divided	126	112	1.125
218	60s ribosomal protein l35. [swissprot;acc:p42766]	Subtracted	266.999	242.333	24.666
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Divided	126	112	1.125
219	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Subtracted	266.986	242.339	24.647
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Divided	126	112	1.125
220	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Subtracted	266.986	242.339	24.647
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Divided	126	112	1.125
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Subtracted	267.151	242.627	24.524
222	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		266.673	242.153	24.52
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Divided	126	112	1.125
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Subtracted	266.673	242.153	24.52
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	165.623	185.969	1.12285
225	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Subtracted	266.673	242.153	24.52
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Divided	201.769	226.471	1.12243

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.