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 green Value Type description Interaction Map Network Comparison Type red Rank Gene
Results: HTML CSV LaTeX Showing element 451 to 500 of 77072 in total
Filtered  : 0
Network Comparison Type  : Subtracted
network_comparison
green
Value Type
description
Interaction Map
red
Rank
0.81 1242.41 Measured hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367] Low confidence 1243.22 833
0.8237 30.3649 Rooted brain protein 16. [refseq;acc:nm_016458] 31.1886 622
0.823905 0.823905 Squared guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] High confidence 0 450
Low confidence 804
0.8251 92.7071 Rooted probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] High confidence 93.5322 395
0.8321 30.6602 transcription factor tel-2 (ets-related protein tel2) (tel related ets factor). [swissprot;acc:q9y603] Low confidence 31.4923 621
0.8349 61.8357 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] High confidence 62.6706 394
0.8418 22.1303 pr-domain zinc finger protein 16 (transcription factor mel1). [swissprot;acc:q9haz2] Low confidence 22.9721 620
0.8517 10.7395 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] 11.5912 619
0.852071 0 Squared similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] High confidence 0.852071 449
0.85277 8.90701 Rooted ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] 8.05424 392
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] 393
0.8528 16.7543 syntaxin 10 (syn10). [swissprot;acc:o60499] Low confidence 15.9015 618
0.8578 21.3142 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 22.172 617
0.8615 23.698 peptidyl-prolyl cis-trans isomerase a (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin a) (cyclosporin a-binding protein). [swissprot;acc:p05092] 24.5595 616
0.8626 26.2481 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 25.3855 615
0.8635 21.8063 protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] High confidence 20.9428 391
0.868 11.8854 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 12.7534 390
0.8712 16.3116 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 15.4404 389
0.8724 25.3903 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Low confidence 26.2627 614
0.875765 0.365145 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] High confidence 1.24091 448
0.876 130.866 Rooted cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] 131.742 388
0.8796 30.7905 eukaryotic initiation factor 4a-like nuk-34. [swissprot;acc:p38919] Low confidence 29.9109 613
0.8834 17.6702 tera protein. [refseq;acc:nm_021238] 18.5536 612
0.8843 24.7479 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 25.6322 611
0.886 17.1712 zinc finger imprinted 2. [swissprot;acc:q9nzv7] 18.0572 610
0.8881 31.8153 signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 32.7034 609
0.8905 17.1797 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 18.0702 608
0.8909 17.1807 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 18.0716 607
0.8932 40.2337 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 39.3405 606
0.8941 27.1011 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 27.9952 605
0.9 13844.1 Ranked protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 13845 836
0.9013 24.3387 Rooted polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 23.4374 604
0.9128 27.2883 dna-crosslink repair gene snm1. [refseq;acc:nm_014881] 28.2011 602
t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283] 603
0.9161 33.096 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 32.1799 601
0.9185 79.3914 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] High confidence 78.4729 387
Low confidence 600
0.9241 68.7756 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] 67.8515 599
0.926159 1.06249 Squared ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760] 0.136331 803
0.9331 18.9799 Rooted alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 19.913 598
0.9334 25.0878 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 26.0212 597
0.9381 27.3399 ubiquitin and ribosomal protein s27a precursor; ubiquitin carboxyl extension protein 80; 40s ribosomal protein s27a; ubiquitin; ubiquitin-cep80. [refseq;acc:nm_002954] 26.4018 596
0.9422 68.5228 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] 67.5806 595
0.95 111.493 high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] High confidence 110.543 386
0.951 34.2093 paired box protein pax-9. [swissprot;acc:p55771] Low confidence 33.2583 594
111.576 nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] High confidence 110.625 385
0.955 111.754 high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 110.799 384
0.956 111.772 dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] 110.816 383
111.817 high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] 110.861 382

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/