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

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Showing element 1332 to 1381 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison
167	FLNB	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]	Rooted	Subtracted	55.6161	66.7332	11.1171
	GAD1	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Ranked	Divided	209.299	249.187	1.19058
	MAGEA4	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured	Divided	23693.7	18263	1.29736
	MYO15A	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Measured	Subtracted	4489.19	2765.82	1723.37
	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Rooted	Divided	55.65	65.1448	1.17062
168	no value	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Ranked		82.5916	98.0548	1.18722
	no value	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Measured		23693.7	18263	1.29736
	BCL6B	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	Squared	Subtracted	69165.6	52992.1	16173.5
	CHD5	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Ranked	Subtracted	312	284	28
	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Squared	Divided	173408	242989	1.40126
	PYGM	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Measured	Subtracted	4489.19	2765.82	1723.37
	REV1	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Rooted	Subtracted	55.6161	66.7332	11.1171
	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Rooted	Divided	56.3709	65.8949	1.16895
169	no value	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Measured	Subtracted	4245.52	5942.75	1697.23
	ATG3	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Ranked	Divided	82.5916	98.0548	1.18722
	CDK2AP1	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	Ranked	Subtracted	312	284	28
	COPS3	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Rooted	Divided	62.762	53.7761	1.1671
	MAGEA10	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Measured	Divided	23693.7	18263	1.29736
	PASK	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148]	Squared	Subtracted	69165	52991.7	16173.3
	PRMT1	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Rooted	Subtracted	55.6161	66.7332	11.1171
	SYMPK	symplekin. [swissprot;acc:q92797]	Squared	Divided	124118	88668.8	1.39979
170	no value	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Measured	Subtracted	4247.86	5941.88	1694.02
	B9D1	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	Rooted	Divided	53.4993	45.9227	1.16499
	BCL6	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	Squared	Subtracted	69165	52991.7	16173.3
	CTPS2	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	Squared	Divided	96730.5	69286.7	1.39609
	MAGEB4	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured	Divided	23693.7	18263	1.29736
	PRMT8	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Rooted	Subtracted	55.6161	66.7332	11.1171
	PRPF40B	huntingtin interacting protein c. [refseq;acc:nm_012272]	Ranked	Subtracted	227.971	200.417	27.554
	TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Ranked	Divided	227.199	192.715	1.17894
171	CTPS	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	Squared		96602.7	69211.2	1.39577
	LASS2	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Rooted		61.6639	71.7355	1.16333
	MAGED2	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Measured		23693.7	18263	1.29736
	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Measured	Subtracted	4117.67	5801.04	1683.37
	SNAI2	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Squared		69165	52991.7	16173.3
	SNRP70	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Rooted		55.6161	66.7332	11.1171
	TIAL1	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Ranked	Divided	227.202	192.823	1.17829
	TRPC4	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Ranked	Subtracted	201.478	228.784	27.306
172	no value	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Rooted		55.6161	66.7332	11.1171
	no value	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	Measured		4556.78	2945.26	1611.52
	CSTF2T	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	Squared	Divided	121579	87259.3	1.39331
	CTBP1	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	Squared	Subtracted	69123.3	52967	16156.3
	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Rooted	Divided	56.7592	65.9889	1.16261
	TBC1D10A	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Ranked	Subtracted	201.515	228.752	27.237
	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Ranked	Divided	174.667	205.556	1.17685
	TRO	trophinin. [swissprot;acc:q12816]	Measured	Divided	23693.7	18263	1.29736
173	no value	methyltransferase like 2. [refseq;acc:nm_018396]	Squared	Subtracted	71576.8	56326.7	15250.1
	BCAR3	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Measured	Divided	4579.34	5940.64	1.29727
	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Rooted	Divided	145.551	168.796	1.1597
	PPP2R2D	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Measured	Subtracted	4556.79	2945.28	1611.51
	PSEN2	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Rooted	Subtracted	37.3005	48.4141	11.1136

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
- Hugo is the HGNC identifier if it exists
- 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/