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 network_comparison green
Results: HTML CSV LaTeX Showing element 2613 to 2662 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
network_comparison
green
2613 adp-ribosylation factor-like protein 1. [swissprot;acc:p40616] 215.497 1.0014 215.799
2614 transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206] 202.821 1.00139 202.54
2615 transcription factor relb (i-rel). [swissprot;acc:q01201]
2616 nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]
2617 coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
2618 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] 190.166 1.00138 190.429
2619 swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] 220.024 1.00137 219.722
2620 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] 215.615 215.91
2621 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 224.891 1.00135 225.195
2622 zinc finger protein 258. [refseq;acc:nm_145310]
2623 zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]
2624 zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]
2625 wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] 204.304 204.028
2626 actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142] 224.891 225.195
2627 conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]
2628 similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
2629 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
2630 zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]
2631 actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
2632 arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]
2633 nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]
2634 actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]
2635 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 166.612 1.00132 166.393
2636 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 195.635 1.00128 195.384
2637 small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 187.075 1.00126 186.84
2638 junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] 204.911 1.00125 205.168
2639 myosin viia. [swissprot;acc:q13402] 220.658 1.00123 220.386
2640 ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567]
2641 ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459]
2642 topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] 194.097 1.00119 194.328
2643 acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
2644 atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]
2645 probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]
2646 tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] 213.169 1.00116 213.417
2647 s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] 212.496 212.25
2648 sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] 213.169 213.417
2649 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 213.63 1.00114 213.874
2650 kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685] 217.188 1.00113 216.942
2651 nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] 201.37 1.00111 201.594
2652 nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] 201.451 1.0011 201.673
2653 nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] 201.452 201.674
2654 nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653]
2655 b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] 201.445 201.667
2656 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] 217.179 1.00109 216.943
2657 channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] 216.934 1.00108 216.7
2658 presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] 216.933
2659 presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796]
2660 presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] 216.937 216.704
2661 proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 204.768 1.00107 204.549
2662 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]

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
- 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/