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 Rank red 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
Rank
red
0.81 1242.41 Measured hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367] Low confidence 833 1243.22
0.8237 30.3649 Rooted brain protein 16. [refseq;acc:nm_016458] 622 31.1886
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 450 0
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 395 93.5322
0.8321 30.6602 transcription factor tel-2 (ets-related protein tel2) (tel related ets factor). [swissprot;acc:q9y603] Low confidence 621 31.4923
0.8349 61.8357 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] High confidence 394 62.6706
0.8418 22.1303 pr-domain zinc finger protein 16 (transcription factor mel1). [swissprot;acc:q9haz2] Low confidence 620 22.9721
0.8517 10.7395 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] 619 11.5912
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 449 0.852071
0.85277 8.90701 Rooted ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] 392 8.05424
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 618 15.9015
0.8578 21.3142 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 617 22.172
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] 616 24.5595
0.8626 26.2481 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 615 25.3855
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 391 20.9428
0.868 11.8854 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 390 12.7534
0.8712 16.3116 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 389 15.4404
0.8724 25.3903 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Low confidence 614 26.2627
0.875765 0.365145 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] High confidence 448 1.24091
0.876 130.866 Rooted cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] 388 131.742
0.8796 30.7905 eukaryotic initiation factor 4a-like nuk-34. [swissprot;acc:p38919] Low confidence 613 29.9109
0.8834 17.6702 tera protein. [refseq;acc:nm_021238] 612 18.5536
0.8843 24.7479 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 611 25.6322
0.886 17.1712 zinc finger imprinted 2. [swissprot;acc:q9nzv7] 610 18.0572
0.8881 31.8153 signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 609 32.7034
0.8905 17.1797 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 608 18.0702
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] 607 18.0716
0.8932 40.2337 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 606 39.3405
0.8941 27.1011 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 605 27.9952
0.9 13844.1 Ranked protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 836 13845
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] 604 23.4374
0.9128 27.2883 dna-crosslink repair gene snm1. [refseq;acc:nm_014881] 602 28.2011
t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283] 603
0.9161 33.096 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 601 32.1799
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 387 78.4729
Low confidence 600
0.9241 68.7756 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] 599 67.8515
0.926159 1.06249 Squared ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760] 803 0.136331
0.9331 18.9799 Rooted alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 598 19.913
0.9334 25.0878 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 597 26.0212
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] 596 26.4018
0.9422 68.5228 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] 595 67.5806
0.95 111.493 high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] High confidence 386 110.543
0.951 34.2093 paired box protein pax-9. [swissprot;acc:p55771] Low confidence 594 33.2583
111.576 nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] High confidence 385 110.625
0.955 111.754 high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 384 110.799
0.956 111.772 dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] 383 110.816
111.817 high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] 382 110.861

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/