Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 1525 to 1574 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
191	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	Ranked	0	18809.5	16764.2	1.122
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Measured	1	4638.1	5923.4	1.27712
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Squared	0	40674.4	28034.4	1.45087
	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]	Rooted	0	32.4121	28.377	1.1422
192	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Measured	1	17757.5	14008	1.26767
	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Squared	1	71387.4	96033.4	1.34524
	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Squared	0	3480.56	5039.04	1.44777
	musashi 2 isoform a. [refseq;acc:nm_138962]	Ranked	1	227.491	199.458	1.14055
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Measured	0	1965.47	2389.69	1.21584
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Rooted	1	53.6107	61.5862	1.14877
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Ranked	0	12715.9	11333.2	1.122
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	Rooted		32.4121	28.377	1.1422
193	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	Squared		3338.97	4832.12	1.44719
	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Squared	1	71386.9	96032.5	1.34524
	musashi 1. [refseq;acc:nm_002442]	Ranked		227.491	199.458	1.14055
	nostrin. [refseq;acc:nm_052946]	Rooted		59.6399	51.9242	1.1486
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	0	23818.1	19621.3	1.21389
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Rooted	0	29.5635	33.7491	1.14158
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Measured	1	17756.5	14007.3	1.26766
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Ranked	0	10899.5	12217.4	1.12091
194	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Squared	1	71346.6	95965.1	1.34505
	cyclin g2. [swissprot;acc:q16589]	Measured		17738.6	13995.7	1.26743
	eap30 subunit of ell complex. [refseq;acc:nm_007241]	Rooted		59.6399	51.9242	1.1486
	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	Squared	0	668.421	962.098	1.43936
	kappa b-ras 1. [refseq;acc:nm_020345]	Ranked		12657.7	11299.1	1.12024
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Rooted		23.871	20.9159	1.14128
	nuclear protein ukp68. [refseq;acc:nm_024824]	Ranked	1	227.491	199.458	1.14055
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Measured	0	125.5	103.5	1.21256
195	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Measured		23	19	1.21053
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Squared		479.423	335.966	1.427
	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Measured	1	17738.5	13995.6	1.26743
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Ranked	1	227.971	200.417	1.13748
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Rooted	0	23.8722	20.933	1.14041
	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	Rooted	1	59.6399	51.9242	1.1486
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Ranked	0	13942.8	15586.4	1.11788
	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Squared	1	71062.4	95488.9	1.34373
196	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]		0	479.099	335.74	1.42699
	calsyntenin-1 precursor. [swissprot;acc:o94985]		1	71062.4	95488.9	1.34373
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Ranked		263.215	231.407	1.13745
	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]	Rooted		59.6399	51.9242	1.1486
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Rooted	0	23.8722	20.9332	1.1404
	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]	Measured	1	17738.5	13995.7	1.26742
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Ranked	0	11064.2	9897.84	1.11784
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Measured		465.37	562.085	1.20782
197	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Squared		479.099	335.74	1.42699
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Measured		2145.97	1784.22	1.20275
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Ranked	1	263.215	231.407	1.13745
	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	Rooted	1	59.6399	51.9242	1.1486
	importin 4. [refseq;acc:nm_024658]	Ranked	0	12337.6	13788.9	1.11763
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Rooted	0	23.8722	20.9331	1.1404

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.

- http://analysis.yellowcouch.org/