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 1094 to 1143 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
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	66.1063	74.1068	1.12102	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Ranked	241.373	267.352	1.10763	
274	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Squared	16120.1	20665.7	1.28198	
275	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Rooted	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	241.373	267.352	1.10763	
275	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Squared	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	3119.98	2579.49	1.20953	
276	60s ribosomal protein l32. [source:swissprot;acc:p02433]	Ranked	241.13	266.969	1.10716	
276	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Rooted	66.1046	74.0964	1.1209	
276	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Squared	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	3119.98	2579.49	1.20953	
277	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Ranked	241.849	267.642	1.10665	
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	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	65.9938	73.9449	1.12048	
277	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Squared	16120.1	20665.7	1.28198	
278	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Ranked	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	16120.1	20665.7	1.28198	
278	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Rooted	65.9938	73.9449	1.12048	
278	transcription factor lbx1. [source:swissprot;acc:p52954]	Measured	3119.98	2579.49	1.20953	
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Ranked	252.644	228.42	1.10605	
279	mosaic protein lgn. [source:swissprot;acc:p81274]	Measured	3119.98	2579.49	1.20953	
279	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Squared	15569.5	19953.6	1.28158	
279	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Rooted	66.0989	74.0609	1.12046	
280	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Rooted	57.9068	64.8562	1.12001	
280	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Ranked	252.512	228.356	1.10578	
280	musashi 1. [source:refseq;acc:nm_002442]	Squared	15569.5	19953.6	1.28158	
280	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	Measured	3119.98	2579.49	1.20953	
281	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Ranked	241.808	267.335	1.10557	
281	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	Measured	3119.98	2579.49	1.20953	
281	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Squared	15569.5	19953.6	1.28158	
281	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Rooted	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	252.39	228.297	1.10553	
282	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Measured	3119.98	2579.49	1.20953	
282	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Rooted	57.9819	64.9302	1.11984	
282	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Squared	59704	76460.4	1.28066	
283	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Ranked	241.828	267.346	1.10552	
283	deltex 2. [source:refseq;acc:nm_020892]	Squared	6627.24	8484.19	1.2802	
283	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887]	Rooted	57.9819	64.9302	1.11984	
283	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Measured	5221.28	6314.35	1.20935	
284	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Squared	59464	76120.8	1.28012	
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Ranked	224.657	203.235	1.10541	
284	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	Rooted	51.8647	46.3161	1.1198	
284	paxillin. [source:swissprot;acc:p49023]	Measured	5221.28	6314.35	1.20935	
285	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Rooted	48.4278	54.2262	1.11973	
285	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Squared	6680.89	8549.44	1.27969	
285	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Measured	23326.5	19296.4	1.20885	
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Ranked	224.647	203.242	1.10532	
286	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]	Ranked	224.633	203.251	1.1052	
286	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Measured	23316	19288.8	1.20878	
286	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	Rooted	51.8717	46.3287	1.11965	

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/