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 2175 to 2224 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
272	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	Rooted	1	66.1064	74.1074	1.12103
272	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	Ranked	0	7163.55	7759.61	1.08321
273	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Squared	0	4224.07	5253.37	1.24367
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]	Ranked	1	241.373	267.352	1.10763
	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	Measured		3199.4	3870.8	1.20985
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Squared		16120.1	20665.7	1.28198
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Rooted		66.1064	74.1074	1.12103
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Measured	0	1410.81	1582.65	1.1218
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Rooted		24.598	26.8697	1.09235
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Ranked		12748.1	11770.9	1.08302
274	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Squared		4214.44	5226.4	1.24012
	brain protein 16. [refseq;acc:nm_016458]	Measured		2155.75	2418.14	1.12172
	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Measured	1	3119.98	2579.49	1.20953
	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	Ranked	0	10432.4	11298.4	1.08301
	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]	Rooted	1	66.1063	74.1068	1.12102
	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	Ranked		241.373	267.352	1.10763
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Squared		16120.1	20665.7	1.28198
	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	Rooted	0	32.8979	30.1206	1.09221
275	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Rooted	1	66.1048	74.0977	1.12091
	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	Ranked	1	241.373	267.352	1.10763
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Ranked	0	10783	11674.1	1.08264
	pnas-18. [sptrembl;acc:q9bzu3]	Squared	0	14643.9	11814.6	1.23947
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Squared	1	16120.1	20665.7	1.28198
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Measured	1	3119.98	2579.49	1.20953
	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]	Measured	0	717.401	804.725	1.12172
	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	Rooted	0	32.8937	30.117	1.0922
276	60s ribosomal protein l32. [swissprot;acc:p02433]	Ranked	1	241.13	266.969	1.10716
	60s ribosomal protein l9. [swissprot;acc:p32969]	Ranked	0	10741.6	9922.33	1.08257
	60s ribosomal protein l9. [swissprot;acc:p32969]	Rooted		26.3707	28.8011	1.09216
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Measured		10817.1	12125.1	1.12092
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared		14470.6	11676.7	1.23927
	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Rooted	1	66.1046	74.0964	1.1209
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Squared		16120.1	20665.7	1.28198
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Measured		3119.98	2579.49	1.20953
277	40s ribosomal protein s29. [swissprot;acc:p30054]	Ranked		241.849	267.642	1.10665
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Ranked	0	11096.8	10251.6	1.08245
	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Rooted		24.1033	22.0791	1.09168
	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	Measured		870.93	975.647	1.12024
	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	Squared		21885.1	17682.1	1.2377
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	Measured	1	3119.98	2579.49	1.20953
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Rooted		65.9938	73.9449	1.12048
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Squared		16120.1	20665.7	1.28198
278	40s ribosomal protein s11. [swissprot;acc:p04643]	Ranked		241.399	267.088	1.10642
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Ranked	0	11644	10763.4	1.08181
	bystin. [swissprot;acc:q13895]	Squared		26569.7	32857.7	1.23666
	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	Rooted		34.0153	31.1803	1.09092
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Squared	1	16120.1	20665.7	1.28198
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Rooted	1	65.9938	73.9449	1.12048
	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]	Measured	0	2162.33	1932	1.11922
	transcription factor lbx1. [swissprot;acc:p52954]	Measured	1	3119.98	2579.49	1.20953

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/