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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Gene Rank Value Type Network Comparison Type description Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 651 to 700 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
green
network_comparison
326 Divided atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 3432.96 4081.21 1.18883
Subtracted protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] 11773 10733.2 1039.8
327 Divided septin 10 isoform 1. [refseq;acc:nm_144710] 16067.4 19094.4 1.18839
Subtracted peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] 11773 10733.2 1039.8
328 Divided brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 1.18801
Subtracted udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] 11773 10733.2 1039.8
329 Divided septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 15999.1 19007.1 1.18801
Subtracted cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 11773 10733.2 1039.8
330 Divided septin 6. [swissprot;acc:q14141] 15959.9 18957.1 1.1878
Subtracted cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 11773 10733.2 1039.8
331 Divided pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 20287.2 17083.8 1.18751
Subtracted estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 10246.1 11285.8 1039.7
332 Divided pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 5051.16 5975.51 1.183
Subtracted vav-2 protein. [swissprot;acc:p52735] 6660.02 7697.78 1037.76
333 Divided nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 5039.63 5961.83 1.18299
Subtracted deltex 2. [refseq;acc:nm_020892] 1618.84 2651.88 1033.04
334 Divided septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 14924.4 17655.2 1.18298
Subtracted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 1629.21 2662.12 1032.91
335 Divided probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 3494.31 4129.6 1.18181
Subtracted t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 1631.67 2664.55 1032.88
336 Divided dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 3751.3 4431.34 1.18128
Subtracted kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1631.67 2664.55 1032.88
337 Divided homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 20446.1 24136.4 1.18049
Subtracted kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1631.67 2664.55 1032.88
338 Divided homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 1.18049
Subtracted kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1631.67 2664.55 1032.88
339 Divided homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 20446.1 24136.4 1.18049
Subtracted neuralized-like. [refseq;acc:nm_004210] 1657.68 2690.25 1032.57
340 Divided homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 20446.1 24136.4 1.18049
Subtracted signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] 11743.3 10712.3 1031
341 Divided homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 20446.1 24136.4 1.18049
Subtracted serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 4916.8 3888.18 1028.62
342 Divided homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 20446.1 24136.4 1.18049
Subtracted steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] 10230.1 11256.2 1026.1
343 Divided homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 20446.1 24136.4 1.18049
Subtracted tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 4991.48 6014.08 1022.6
344 Divided homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 20446.1 24136.4 1.18049
Subtracted ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 9921.43 10941.2 1019.77
345 Divided retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 20446.1 24136.4 1.18049
Subtracted voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 4068.78 5082.18 1013.4
346 Divided septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 14229.2 16780.7 1.17931
Subtracted voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 4068.78 5082.18 1013.4
347 Divided enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 4991.02 5885.09 1.17914
Subtracted voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 4068.82 5082.21 1013.39
348 Divided splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 4991.02 5885.09 1.17914
Subtracted voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 4068.91 5082.27 1013.36
349 Divided putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 4714.85 5554.38 1.17806
Subtracted sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 3349.9 4362.61 1012.71
350 Divided sedlin. [swissprot;acc:o14582] 17396.9 20483.9 1.17745
Subtracted voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 4074.83 5086.49 1011.66

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/