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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 1875 to 1924 of 12912 in total 
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	Value Type	red	green	network_comparison	
469	nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	Squared	23531.7	28371.6	1.20568	
469	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	Measured	3831.17	4388.74	1.14554	
470	block of proliferation 1. [source:swissprot;acc:q14137]	Measured	3796.24	4348.59	1.1455	
470	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Ranked	248.152	267.226	1.07686	
470	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	Rooted	60.0148	65.6429	1.09378	
470	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	Squared	10418.3	8641.84	1.20557	
471	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Ranked	248.152	267.226	1.07686	
471	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [source:swissprot;acc:p53778]	Measured	9649.61	11053.5	1.14549	
471	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [source:swissprot;acc:p07205]	Squared	28188.7	33982.7	1.20554	
471	vav-2 protein. [source:swissprot;acc:p52735]	Rooted	66.088	72.2597	1.09339	
472	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [source:swissprot;acc:p09104]	Squared	28190.4	33984.1	1.20552	
472	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	Measured	9649.61	11053.5	1.14549	
472	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Ranked	248.152	267.226	1.07686	
472	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	Rooted	50.3767	46.0753	1.09336	
473	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [source:swissprot;acc:p13929]	Squared	28190.4	33984.1	1.20552	
473	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	Ranked	225.661	209.651	1.07637	
473	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Rooted	62.574	68.4128	1.09331	
473	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [source:swissprot;acc:q9h3h5]	Measured	9649.61	11053.5	1.14549	
474	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [source:swissprot;acc:p06733]	Squared	28190.4	33984.1	1.20552	
474	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Rooted	62.574	68.4128	1.09331	
474	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [source:swissprot;acc:p16389]	Ranked	226.789	210.818	1.07576	
474	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [source:swissprot;acc:q96qb1]	Measured	9649.61	11053.5	1.14549	
475	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Rooted	62.574	68.4128	1.09331	
475	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [source:swissprot;acc:p49137]	Measured	9649.61	11053.5	1.14549	
475	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [source:swissprot;acc:p00558]	Squared	28192	33985.3	1.20549	
475	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [source:swissprot;acc:q09470]	Ranked	226.727	210.816	1.07547	
476	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [source:swissprot;acc:q15825]	Measured	9649.61	11053.5	1.14549	
476	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [source:swissprot;acc:p22459]	Ranked	226.681	210.814	1.07527	
476	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Rooted	62.574	68.4128	1.09331	
476	vav proto-oncogene. [source:swissprot;acc:p15498]	Squared	31223.8	37614.3	1.20467	
477	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Rooted	62.574	68.4128	1.09331	
477	nitrogen fixation cluster-like. [source:refseq;acc:nm_014301]	Measured	9649.61	11053.5	1.14549	
477	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Ranked	251.926	234.547	1.0741	
477	vav-3 protein. [source:swissprot;acc:q9ukw4]	Squared	31248.8	37623.4	1.204	
478	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	Rooted	50.6084	55.2961	1.09263	
478	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Squared	16318.4	19645.8	1.2039	
478	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [source:swissprot;acc:q9y3m8]	Measured	9649.61	11053.5	1.14549	
478	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Ranked	228.051	212.321	1.07409	
479	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	Rooted	50.6084	55.2961	1.09263	
479	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Ranked	228.051	212.321	1.07409	
479	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [source:swissprot;acc:q92502]	Measured	9649.61	11053.5	1.14549	
479	translation initiation factor if-2. [source:swissprot;acc:o60841]	Squared	24031.6	28929.7	1.20382	
480	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Rooted	50.6084	55.2961	1.09263	
480	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [source:swissprot;acc:q15822]	Measured	9649.61	11053.5	1.14549	
480	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	Ranked	237.109	254.667	1.07405	
480	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	Squared	26874.6	32347.4	1.20364	
481	histone h2b. [source:refseq;acc:nm_175055]	Rooted	50.6084	55.2961	1.09263	
481	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [source:refseq;acc:nm_004635]	Measured	9649.61	11053.5	1.14549	
481	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	Ranked	237.109	254.667	1.07405	
481	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Squared	16335.9	19660.7	1.20353	

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/