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	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 244 to 293 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
122	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	Divided	269.248	327.642	1.21688
123	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]		269.23	327.601	1.21681
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Subtracted	227.032	193.056	33.976
124	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	Divided	208.52	171.595	1.21519
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Subtracted	285.684	252.234	33.45
125	high-mobility group 20a. [refseq;acc:nm_018200]	Divided	208.588	171.778	1.21429
	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]	Subtracted	285.684	252.234	33.45
126	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Divided	94	114	1.21277
	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]	Subtracted	285.684	252.234	33.45
127	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Divided	94	114	1.21277
128	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Subtracted	285.684	252.234	33.45
129	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Divided	94	114	1.21277
130	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	Subtracted	242.735	276.059	33.324
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Divided	94	114	1.21277
131	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Subtracted	242.718	276.018	33.3
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Divided	294.053	242.562	1.21228
132	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Subtracted	229.406	196.695	32.711
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	350	290	1.2069
133	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Subtracted	226.887	194.72	32.167
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	350	290	1.2069
134	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Subtracted	226.884	194.79	32.094
135	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	350	290	1.2069
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Subtracted	263.215	231.407	31.808
136	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Divided	350	290	1.2069
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Subtracted	263.215	231.407	31.808
137	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]		263.191	231.394	31.797
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	350	290	1.2069
138	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Subtracted	174.667	205.556	30.889
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Divided	194.372	234.204	1.20493
139	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]		271.752	225.68	1.20415
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Subtracted	287.41	256.835	30.575
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]		228.306	198.011	30.295
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Divided	59	49	1.20408
141	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Subtracted	239.991	269.238	29.247
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Divided	59	49	1.20408
142	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Subtracted	239.99	269.234	29.244
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Divided	59	49	1.20408
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Subtracted	240.133	211.382	28.751
144	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]		239.35	267.915	28.565
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Divided	265.686	319.651	1.20312
145	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Subtracted	239.336	267.881	28.545
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Divided	265.639	319.546	1.20293
146	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]		265.632	319.531	1.20291
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Subtracted	239.336	267.879	28.543
147	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]		239.32	267.842	28.522

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.