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

Results: HTML CSV LaTeX

Showing element 780 to 829 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	red	green	network_comparison
195	Rooted	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	59.6399	51.9242	1.1486
196	Measured	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	17738.5	13995.7	1.26742
	Ranked	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	263.215	231.407	1.13745
	Squared	calsyntenin-1 precursor. [swissprot;acc:o94985]	71062.4	95488.9	1.34373
	Rooted	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]	59.6399	51.9242	1.1486
197	Measured	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	17738.5	13995.7	1.26742
	Ranked	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	263.215	231.407	1.13745
	Squared	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	71062.4	95488.9	1.34373
	Rooted	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	59.6399	51.9242	1.1486
198	Measured	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	17710.9	13977.7	1.26708
	Ranked	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	263.191	231.394	1.13741
	Squared	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	71062.2	95488.6	1.34373
	Rooted	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	59.6399	51.9242	1.1486
199	Measured	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	4916.8	3888.18	1.26455
	Ranked	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	242.735	276.059	1.13729
	Squared	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	71062.2	95488.6	1.34373
	Rooted	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	61.2893	70.3856	1.14842
200	Measured	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	4808.79	6074.21	1.26315
	Ranked	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	242.718	276.018	1.1372
	Squared	gk001 protein. [refseq;acc:nm_020198]	71062.2	95488.6	1.34373
	Rooted	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	61.2893	70.3856	1.14842
201	Measured	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	4810.22	6075.04	1.26294
	Ranked	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	240.133	211.382	1.13601
	Squared	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	71033.4	95440.2	1.3436
	Rooted	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	61.2893	70.3856	1.14842
202	Measured	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	4812.01	6076.09	1.26269
	Ranked	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	201.478	228.784	1.13553
	Squared	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	71030.1	95434.8	1.34358
	Rooted	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	57.3527	65.7973	1.14724
203	Measured	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	11757.8	9352.11	1.25723
	Ranked	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	201.515	228.752	1.13516
	Squared	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	20988.2	15632.1	1.34263
	Rooted	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	46.3291	53.1063	1.14628
204	Measured	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	4512.19	5655.52	1.25339
	Ranked	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	201.515	228.752	1.13516
	Squared	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	12326.4	16522.9	1.34045
	Rooted	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	55.8956	63.9636	1.14434
205	Measured	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	4512.19	5655.52	1.25339
	Ranked	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	228.1	200.968	1.13501
	Squared	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	12326.4	16522.9	1.34045
	Rooted	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	55.8956	63.9636	1.14434
206	Measured	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	5720.25	4577.5	1.24965
	Ranked	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	228.085	201.006	1.13472
	Squared	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	12326.4	16522.9	1.34045
	Rooted	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	140.508	122.878	1.14348
207	Measured	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	4771.21	5961.43	1.24946
	Ranked	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	285.684	252.234	1.13261
	Squared	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	70525.9	52678.7	1.33879
	Rooted	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	140.508	122.878	1.14348
208	Measured	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	4068.78	5082.18	1.24907

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.