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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Filtered network_comparison Gene green red Value Type Interaction Map Network Comparison Type Rank description
Results: HTML CSV LaTeX Showing element 101 to 150 of 77072 in total
Filtered  : 0
Network Comparison Type  : Subtracted
network_comparison
green
red
Value Type
Interaction Map
Rank
description
0.0698 22.0046 21.9348 Rooted Low confidence 814 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]
0.070296 0.615621 0.545325 Squared High confidence 472 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
473 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
474 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
475 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
476 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
477 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
478 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
479 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
480 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
481 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
482 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
483 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
484 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
485 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
486 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
487 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
488 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
0.0725 20.7123 20.6398 Rooted 485 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]
Low confidence 813
0.073 25.822 25.895 812 forkhead box protein l1 (forkhead-related protein fkhl11) (forkhead- related transcription factor 7) (freac-7). [swissprot;acc:q12952]
0.0766864 0 0.0766864 Squared High confidence 471 rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
0.0766864 0 470 phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]
0.08 1589.95 1589.87 Measured Low confidence 836 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]
0.0843 34.4874 34.4031 Rooted 811 60s acidic ribosomal protein p1. [swissprot;acc:p05386]
0.0856 25.8046 25.8902 810 forkhead box protein c2 (forkhead-related protein fkhl14) (mesenchyme fork head protein 1) (mfh-1 protein) (transcription factor fkh-14). [swissprot;acc:q99958]
0.0857 22.4903 22.576 High confidence 484 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]
0.0902 24.1232 24.2134 483 thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]
0.0922 23.2443 23.1521 Low confidence 809 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]
0.0932 37.263 37.1698 808 ptk9l protein tyrosine kinase 9-like (a6-related protein); protein tyrosine kinase 9-like (a6-related protein). [refseq;acc:nm_007284]
0.0934 22.8556 22.949 807 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]
0.0949 26.5172 26.4223 High confidence 482 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]
0.0976 21.1631 21.0655 Low confidence 806 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]
0.0989 22.1318 22.2307 805 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]
0.1095 31.3293 31.2198 804 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]
0.1185 30.5097 30.3912 803 phospholipase b. [refseq;acc:nm_153021]
0.1191 8.33665 8.45575 802 pou domain, class 3, transcription factor 3 (brain-specific homeobox/pou domain protein 1) (brain-1) (brn-1 protein). [swissprot;acc:p20264]
0.125 19.0561 19.1811 801 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]
0.1261 25.2796 25.4057 800 ectonucleoside triphosphate diphosphohydrolase 6 (ec 3.6.1.6) (ntpdase6) (cd39 antigen-like 2). [swissprot;acc:o75354]
0.1279 21.5465 21.4186 799 40s ribosomal protein s3a. [swissprot;acc:p49241]
0.1293 39.8405 39.9698 798 dnaj homolog subfamily c member 5 (cysteine string protein) (csp). [swissprot;acc:q9h3z4]
0.134 18.8095 18.6755 High confidence 481 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]
0.1345 23.2445 23.11 Low confidence 797 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]
0.13698 7.53683 7.39985 796 rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
0.1376 25.3841 25.5217 795 timeless homolog. [refseq;acc:nm_003920]
0.140962 0.140962 0 Squared 829 jumonji protein. [swissprot;acc:q92833]
0.141747 0.426714 0.284967 High confidence 469 suppressor of actin 1. [refseq;acc:nm_014016]
0.144 29.9367 29.7927 Rooted Low confidence 794 solute carrier family 35, member e2. [refseq;acc:nm_182838]
0.1471 25.6728 25.8199 793 aldo-keto reductase family 1 member c2 (ec 1.1.1.-) (trans-1,2- dihydrobenzene-1,2-diol dehydrogenase) (ec 1.3.1.20) (chlordecone reductase homolog hakrd) (dihydrodiol dehydrogenase/bile acid-binding protein) (dd/babp) (dihydrodiol dehydrogenase 2) (dd2). [swissprot;acc:p52895]
0.1473 25.6723 25.8196 792 aldo-keto reductase family 1 member c4 (ec 1.1.1.-) (chlordecone reductase) (ec 1.1.1.225) (cdr) (3-alpha-hydroxysteroid dehydrogenase) (ec 1.1.1.50) (3-alpha-hsd) (dihydrodiol dehydrogenase 4) (dd4) (hakra). [swissprot;acc:p17516]

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/