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 Value Type Network Comparison Type Gene Rank Interaction Map description network_comparison green red
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 77072 in total
Filtered  : 0
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
Interaction Map
description
network_comparison
green
red
496 Low confidence udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 1.05948 12162 12885.4
497 High confidence sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 1.00186 13718.2 13692.7
Low confidence udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] 1.05948 12160.8 12884.1
498 High confidence adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 1.00161 10248.3 10231.8
Low confidence udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 1.05928 12143.1 12862.9
499 High confidence inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 1.00123 9069.58 9080.73
Low confidence udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] 1.05908 12128.8 12845.4
500 High confidence huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 1 394 394
Low confidence udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] 1.05908 12129.6 12846.2
501 High confidence homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 1 0.00001 0.00001
Low confidence 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 1.0588 11352.1 10721.7
502 High confidence brca1 associated protein. [refseq;acc:nm_006768] 1 0.00001 0.00001
Low confidence pnas-18. [sptrembl;acc:q9bzu3] 1.05859 12793.5 12085.4
503 neurofibromin (neurofibromatosis-related protein nf-1) [contains: neurofibromin truncated]. [swissprot;acc:p21359] 11516.1 10878.7
504 ero1-like. [refseq;acc:nm_014584] 1.05849 10148.1 9587.31
505 importin 9. [refseq;acc:nm_018085] 1.05845 10602 10016.5
506 mstp028 protein. [refseq;acc:nm_031954] 1.05811 7528.21 7965.66
507 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] 1.05772 12524.9 11841.4
508 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1.05744 12764 12070.7
509 cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] 1.05731 11175.5 11816
510 methyltransferase like 2. [refseq;acc:nm_018396] 1.05727 12508.3 11830.8
511 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 1.05681 10716 11324.8
512 helicase ski2w (helicase-like protein) (hlp). [swissprot;acc:q15477] 1.05604 11116.2 10526.3
513 cg4853 gene product. [refseq;acc:nm_145313] 1.05597 14671.5 13893.9
514 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 1.05594 11580 10966.5
515 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 1.0554 12290.5 11645.4
516 ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 1.0553 11832.5 11212.4
517 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 1.055 12854.2 12184.1
518 espin. [refseq;acc:nm_031475] 1.0548 14545.8 13790.1
519 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 1.05438 12486.3 11842.3
520 dna topoisomerase i (ec 5.99.1.2). [swissprot;acc:p11387] 1.05416 10982.6 10418.3
521 60s ribosomal protein l39. [swissprot;acc:p02404] 1.05384 12300.8 11672.4
522 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 1.05351 11120.5 10555.7
523 chromodomain-helicase-dna-binding protein 1 (chd-1). [swissprot;acc:o14646] 1.05348 11561.3 10974.4
524 40s ribosomal protein s26. [swissprot;acc:p02383] 1.05312 11262.9 10694.8
525 importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 1.05259 10573.9 11130
526 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] 1.05238 12688.2 13352.8
527 germ cell-less. [refseq;acc:nm_022471] 1.05157 10823.5 11381.7
528 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 1.05154 9334.3 9815.39
529 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 1.05139 7957.08 8366.02
530 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 1.05121 12338.8 11737.7
531 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 1.05117 12338.9 11738.2
532 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 1.05098 11193.3 10650.3
533 zinc finger imprinted 2. [swissprot;acc:q9nzv7] 1.05079 12339.6 11743.2
534 my016 protein. [sptrembl;acc:q9h3k6] 1.0506 9729.69 10222
535 cytochrome c oxidase subunit viia-l related protein, mitochondrial precursor. [swissprot;acc:o60397] 10671.1 11211.1
536 huntingtin interacting protein c. [refseq;acc:nm_012272] 1.05002 10582.2 11111.5
537 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 1.0499 12637.1 12036.5
538 cytochrome c oxidase polypeptide viia-heart, mitochondrial precursor (ec 1.9.3.1) (cytochrome c oxidase subunit viia-h) (cox viia-m). [swissprot;acc:p24310] 1.04974 10710.2 11242.9
539 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] 1.04969 11143.6 11697.3

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/