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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 3558 to 3607 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
223	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	Measured	Divided	0	750.981	650.724	1.15407
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Measured	Subtracted		1225.09	1079.36	145.73
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Ranked	Subtracted		14257.4	13134.5	1122.9
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted	Divided	1	137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Ranked		1	112	126	1.125
	pnas-18. [sptrembl;acc:q9bzu3]	Ranked		0	12602.7	13939.6	1.10608
	septin 6. [swissprot;acc:q14141]	Rooted	Subtracted	1	113.169	123.23	10.061
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Ranked	Subtracted	1	242.153	266.673	24.52
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Squared	Divided	0	952.068	697.024	1.3659
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Squared	Divided	1	40982.6	54272.3	1.32428
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	Measured	Subtracted	1	6417.18	7859.59	1442.41
224	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	Ranked		0	14930.6	16053	1122.4
	60s ribosomal protein l23a. [swissprot;acc:p29316]	Rooted		0	22.6514	25.1571	2.5057
	60s ribosomal protein l34. [swissprot;acc:p49207]	Ranked		1	242.153	266.673	24.52
	60s ribosomal protein l7. [swissprot;acc:p18124]	Measured	Divided	0	1915.27	2206.07	1.15183
	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Rooted			26.1198	23.1206	1.12972
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Ranked			9815.6	8889.93	1.10413
	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Squared			399.199	542.77	1.35965
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Measured		1	41482.5	33356.5	1.24361
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Rooted	Subtracted		44.849	54.7964	9.9474
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Squared	Subtracted		46021.4	56813.2	10791.8
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Rooted	Divided		137.446	120.823	1.13758
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Measured	Subtracted	0	1225.09	1079.36	145.73
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Ranked	Divided	1	185.969	165.623	1.12285
	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	Measured	Subtracted		6417.18	7859.59	1442.41
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Squared	Divided		14943.9	19771.9	1.32307
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	Squared	Subtracted	0	295.992	69.1109	226.881
225	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Rooted	Divided		23.1768	26.17	1.12915
	40s ribosomal protein s29. [swissprot;acc:p30054]	Ranked	Divided		11035.3	9997.71	1.10378
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Rooted	Subtracted		22.6521	25.1534	2.5013
	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	Measured		1	6417.19	7859.51	1442.32
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Measured		0	1225.09	1079.36	145.73
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	Divided	1	137.446	120.823	1.13758
	metaxin 1. [swissprot;acc:q13505]	Squared			60401.6	79875.7	1.32241
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Measured			9035	7279.6	1.24114
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	Squared		0	399.199	542.77	1.35965
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Measured		0	8763	7608	1.15181
	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171]	Squared	Subtracted	1	45986	56776.1	10790.1
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Ranked		1	242.153	266.673	24.52
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]			0	8407.67	9516.92	1109.25
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]		Divided	1	226.471	201.769	1.12243
		Rooted	Subtracted	1	55.7423	65.6839	9.9416
	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	Squared	Subtracted	0	1021.12	1246	224.88
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Ranked	Divided	1	239.991	269.238	1.12187
	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Measured	Subtracted	1	6417.31	7858.12	1440.81
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Measured	Divided	0	658.544	758.411	1.15165
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	Squared	Subtracted		13550.9	13764.5	213.6
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Measured	Subtracted		1225.09	1079.37	145.72
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted	Divided	1	137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Measured	Divided	1	9035	7279.6	1.24114

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/