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 Rank description Value Type Network Comparison Type red Interaction Map
Results: HTML CSV LaTeX Showing element 551 to 600 of 38536 in total
Filtered  : 0
Network Comparison Type  : Divided
network_comparison
green
Rank
description
Value Type
red
Interaction Map
1.01397 12032.8 734 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 11867 Low confidence
1.01402 22.0702 740 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted 21.7651
3174.79 454 transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Measured 3219.3 High confidence
1.01404 22.0706 739 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted 21.7651 Low confidence
1.01407 29.1131 738 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 29.5228
1.01408 22.0732 737 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 21.7668
11881.5 733 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Ranked 11716.5
1.01413 43.56 470 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Squared 42.9529 High confidence
779 Low confidence
1.01416 374.561 469 importin 4. [refseq;acc:nm_024658] 379.863 High confidence
1.01424 11525.9 732 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Ranked 11690 Low confidence
1.01428 16895.3 778 actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996] Squared 17136.5
1.01429 8.33665 736 pou domain, class 3, transcription factor 3 (brain-specific homeobox/pou domain protein 1) (brain-1) (brn-1 protein). [swissprot;acc:p20264] Rooted 8.45575
1.01435 10918.5 731 hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Ranked 11075.2
1.01438 1356.52 453 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Measured 1337.29 High confidence
1.01446 1521 466 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Ranked 1543
730 Low confidence
2079.25 728 forkhead box protein f1 (forkhead-related protein fkhl5) (forkhead- related transcription factor 1) (freac-1) (forkhead-related activator- 1). [swissprot;acc:q12946] Measured 2109.31
1.0145 10653.8 729 40s ribosomal protein s29. [swissprot;acc:p30054] Ranked 10808.3
1.01452 1904.79 726 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Measured 1877.52
2393.6 727 60s ribosomal protein l7. [swissprot;acc:p18124] 2359.34
1.01454 82.5719 735 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Rooted 81.3882
1.01455 9620.66 465 transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Ranked 9482.68 High confidence
1.01457 29.3554 734 60s ribosomal protein l7. [swissprot;acc:p18124] Rooted 28.9338 Low confidence
1.0146 14238.8 777 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Squared 14446.7
1.01465 12339.2 728 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Ranked 12161.1
1.01468 2267.94 776 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Squared 2301.24
1.0147 5278.14 727 dnaj homolog subfamily c member 5 (cysteine string protein) (csp). [swissprot;acc:q9h3z4] Ranked 5355.73
1.01471 30.5384 459 similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Rooted 30.9876 High confidence
1.01472 33.9164 733 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 34.4155 Low confidence
1.0148 2077.88 724 forkhead box protein d4 (forkhead-related protein fkhl9) (forkhead- related transcription factor 5) (freac-5) (myeloid factor-alpha). [swissprot;acc:q12950] Measured 2108.64
2171.71 725 microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 2140.04
1.01487 2077.61 723 forkhead box protein d4b (myeloid factor-gamma). [swissprot;acc:q8wxt5] 2108.51
16239.1 775 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Squared 16480.5
1.01489 2071.38 722 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Measured 2040.98
1.01491 2077.47 721 forkhead box protein d4-like 1. [swissprot;acc:q9nu39] 2108.44
25771.2 774 aldo-keto reductase loopadr; aldo-keto reductase related protein. [refseq;acc:nm_031436] Squared 25392.6
1.01492 1011.6 773 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 1026.69
1.01494 9928.08 464 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Ranked 10076.4 High confidence
1.01496 1504.85 452 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Measured 1527.36
25766.5 771 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] Squared 25386.6 Low confidence
25766.9 772 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] 25387.1
1.01501 10665.3 726 sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Ranked 10507.6
1.01502 10529.4 724 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 10373.6
10529.7 725 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 10373.9
10530.4 723 60s ribosomal protein l12. [swissprot;acc:p30050] 10374.6
1.01509 12252.7 722 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 12070.5
1.01517 2076.43 720 forkhead box protein l1 (forkhead-related protein fkhl11) (forkhead- related transcription factor 7) (freac-7). [swissprot;acc:q12952] Measured 2107.93
1.01521 31.9514 732 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Rooted 32.4375
1.01528 22.9607 731 histone deacetylase 2 (hd2). [swissprot;acc:q92769] 23.3116

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/