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 2200 to 2249 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
275	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	Squared	Subtracted	59331.2	67833.7	8502.5	
276	60s ribosomal protein l32. [source:swissprot;acc:p02433]	Ranked	Divided	241.13	266.969	1.10716	
276	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Ranked	Subtracted	258.437	235.183	23.254	
276	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Rooted	Subtracted	128.909	120.173	8.736	
276	gbp protein isoform a. [source:refseq;acc:nm_017870]	Measured	Subtracted	699.76	1894.39	1194.63	
276	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Rooted	Divided	66.1046	74.0964	1.1209	
276	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Squared	Divided	16120.1	20665.7	1.28198	
276	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	Measured	Divided	3119.98	2579.49	1.20953	
276	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Squared	Subtracted	33100.3	41520.6	8420.3	
277	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Ranked	Divided	241.849	267.642	1.10665	
277	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	Ranked	Subtracted	239.277	262.434	23.157	
277	cerebral cell adhesion molecule. [source:refseq;acc:nm_016174]	Squared	Subtracted	62198.5	70599.4	8400.9	
277	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Measured	Subtracted	8600.02	9792.49	1192.47	
277	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [source:swissprot;acc:o76081]	Measured	Divided	3119.98	2579.49	1.20953	
277	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Rooted	Divided	65.9938	73.9449	1.12048	
277	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Rooted	Subtracted	104.459	113.143	8.684	
277	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Squared	Divided	16120.1	20665.7	1.28198	
278	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Ranked	Divided	241.399	267.088	1.10642	
278	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Squared	Divided	16120.1	20665.7	1.28198	
278	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [source:swissprot;acc:p55060]	Squared	Subtracted	34018.3	42373	8354.7	
278	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	Ranked	Subtracted	235.383	258.476	23.093	
278	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Measured	Subtracted	8600.02	9792.49	1192.47	
278	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Rooted	Divided	65.9938	73.9449	1.12048	
278	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Rooted	Subtracted	57.3527	65.7973	8.4446	
278	transcription factor lbx1. [source:swissprot;acc:p52954]	Measured	Divided	3119.98	2579.49	1.20953	
279	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]	Squared	Subtracted	30596.2	38919.9	8323.7	
279	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Rooted	Subtracted	42.0574	50.4237	8.3663	
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Ranked	Divided	252.644	228.42	1.10605	
279	mosaic protein lgn. [source:swissprot;acc:p81274]	Measured	Divided	3119.98	2579.49	1.20953	
279	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Squared	Divided	15569.5	19953.6	1.28158	
279	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Rooted	Divided	66.0989	74.0609	1.12046	
279	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Measured	Subtracted	4771.21	5961.43	1190.22	
279	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	Ranked	Subtracted	242.66	265.715	23.055	
280	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Squared	Subtracted	30566.4	38866.5	8300.1	
280	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Rooted	Divided	57.9068	64.8562	1.12001	
280	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Rooted	Subtracted	42.0577	50.424	8.3663	
280	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Ranked	Divided	252.512	228.356	1.10578	
280	musashi 1. [source:refseq;acc:nm_002442]	Squared	Divided	15569.5	19953.6	1.28158	
280	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Measured	Subtracted	677.5	1865.5	1188	
280	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	Measured	Divided	3119.98	2579.49	1.20953	
280	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Ranked	Subtracted	267.208	244.168	23.04	
281	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	Ranked	Subtracted	242.159	265.104	22.945	
281	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Ranked	Divided	241.808	267.335	1.10557	
281	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Rooted	Subtracted	42.0684	50.4323	8.3639	
281	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	Measured	Divided	3119.98	2579.49	1.20953	
281	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Measured	Subtracted	677.5	1865.5	1188	
281	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Squared	Divided	15569.5	19953.6	1.28158	
281	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	Squared	Subtracted	52623.3	44380.3	8243	
281	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Rooted	Divided	57.9068	64.8562	1.12001	
282	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	Ranked	Divided	252.39	228.297	1.10553	

Legend:
- Rank is the rank after comparing the two networks
- 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/