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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 201 to 250 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Interaction Map
Filtered
red
green
network_comparison
51 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Low confidence 1 7563.09 8732.2 1.15458
histone-lysine n-methyltransferase, h3 lysine-79 specific (ec 2.1.1.43) (histone h3-k79 methyltransferase) (h3-k79-hmtase) (dot1-like protein). [swissprot;acc:q8tek3] 0 195 88 2.21591
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence 1 779.167 1390.33 1.78438
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 0 184.422 88.5622 2.0824
52 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 1 779.167 1390.33 1.78438
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Low confidence 13195.9 11486.4 1.14883
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] High confidence 0 999.28 481.725 2.07438
fos39347_1. [sptrembl;acc:o75863] Low confidence 247.692 112.523 2.20126
53 bcl2-related ovarian killer. [refseq;acc:nm_032515] 1 4955.33 5659.35 1.14207
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] High confidence 779.167 1390.33 1.78438
dj254p11.1 (novel protein similar to rna polymerase ii elongation factor siii, subunit p15). [sptrembl;acc:q9h575] Low confidence 0 247.16 112.931 2.18859
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] High confidence 420.365 861.814 2.05016
54 deltex 2. [refseq;acc:nm_020892] 1 1618.84 2651.88 1.63814
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 0 638.862 330.189 1.93484
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] Low confidence 78.06 170.038 2.1783
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 1 13203.5 15033.4 1.13859
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] High confidence 1629.21 2662.12 1.63399
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 0 630.942 327.517 1.92644
selenoprotein t. [swissprot;acc:q9nzj3] Low confidence 174.52 379.277 2.17326
septin 10 isoform 1. [refseq;acc:nm_144710] 1 13081.2 14872.6 1.13694
56 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 15464.1 17572.7 1.13635
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] High confidence 1631.67 2664.55 1.63302
tigger transposable element derived 6. [refseq;acc:nm_030953] Low confidence 0 202.374 438.605 2.1673
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] High confidence 271.484 142.981 1.89874
57 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 270.264 142.417 1.89769
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 1 15464.1 17572.7 1.13635
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 1631.67 2664.55 1.63302
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Low confidence 0 202.163 438.035 2.16674
58 40s ribosomal protein s26. [swissprot;acc:p02383] High confidence 150.741 81.2233 1.85588
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 1 15464.1 17572.7 1.13635
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 1631.67 2664.55 1.63302
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Low confidence 0 202.156 438.016 2.16672
59 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] High confidence 150.673 279.24 1.85328
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 1 15464.1 17572.7 1.13635
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 1631.67 2664.55 1.63302
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Low confidence 0 147.107 315.505 2.14473
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 1 4489.19 2765.82 1.6231
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 0 47.4756 87.5499 1.8441
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 1 15464.1 17572.7 1.13635
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] 0 147.143 315.567 2.14463
61 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] High confidence 324.442 593.094 1.82804
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 4489.19 2765.82 1.6231
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Low confidence 15464.1 17572.7 1.13635
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 0 72 151 2.09722
62 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 2082 4356 2.09222
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] High confidence 210.767 384.407 1.82385
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 4489.19 2765.82 1.6231
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 15464.1 17572.7 1.13635
63 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942] 0 154.208 75.6508 2.03842

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/