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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2180 to 2229 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
273	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Measured	Divided	3199.4	3870.8	1.20985	
273	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. [source:refseq;acc:nm_001457]	Squared	Divided	16120.1	20665.7	1.28198	
273	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Rooted	Divided	66.1064	74.1074	1.12103	
273	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Measured	Subtracted	5181.2	6410.58	1229.38	
273	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Rooted	Subtracted	57.45	66.332	8.882	
274	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]	Squared	Subtracted	30807.7	39351.7	8544	
274	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	Ranked	Subtracted	242.744	266.07	23.326	
274	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	Measured	Divided	3119.98	2579.49	1.20953	
274	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Rooted	Subtracted	57.4586	66.3336	8.875	
274	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). [source:swissprot;acc:o75791]	Rooted	Divided	66.1063	74.1068	1.12102	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Ranked	Divided	241.373	267.352	1.10763	
274	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Squared	Divided	16120.1	20665.7	1.28198	
274	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Measured	Subtracted	5181.2	6410.58	1229.38	
275	40s ribosomal protein s5. [source:swissprot;acc:p46782]	Ranked	Subtracted	242.473	265.756	23.283	
275	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Rooted	Subtracted	41.8357	50.6469	8.8112	
275	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Rooted	Divided	66.1048	74.0977	1.12091	
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Ranked	Divided	241.373	267.352	1.10763	
275	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	Measured	Subtracted	10264.9	9043.51	1221.39	
275	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Squared	Divided	16120.1	20665.7	1.28198	
275	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	Measured	Divided	3119.98	2579.49	1.20953	
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	

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/