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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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2680 to 2729 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
335 Rooted histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Subtracted 52.7146 60.0088 7.2942
336 Measured dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Divided 3751.3 4431.34 1.18128
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Subtracted 1631.67 2664.55 1032.88
Ranked 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] Divided 312 284 1.09859
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Subtracted 241.045 261.874 20.829
Squared acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 36109.8 42811.6 6701.8
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Divided 46785.7 58383.2 1.24789
Rooted 60s ribosomal protein l11. [swissprot;acc:p39026] 50.3167 45.4063 1.10814
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Subtracted 59.4073 66.7002 7.2929
337 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 20446.1 24136.4 1.18049
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Subtracted 1631.67 2664.55 1032.88
Ranked 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 243.583 267.527 1.0983
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Subtracted 200.691 179.88 20.811
Squared human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Divided 46785.7 58383.2 1.24789
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted 28895.6 35572.8 6677.2
Rooted carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided 77.5801 70.0182 1.108
paxillin. [swissprot;acc:p49023] Subtracted 59.4073 66.7002 7.2929
338 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided 20446.1 24136.4 1.18049
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Subtracted 1631.67 2664.55 1032.88
Ranked 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 243.583 267.528 1.0983
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 200.691 179.88 20.811
Squared importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] 28895.6 35572.8 6677.2
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Divided 46785.7 58383.2 1.24789
Rooted mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 77.58 70.0181 1.108
metastasis-associated protein mta1. [swissprot;acc:q13330] Subtracted 52.7557 60.035 7.2793
339 Measured homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Divided 20446.1 24136.4 1.18049
neuralized-like. [refseq;acc:nm_004210] Subtracted 1657.68 2690.25 1032.57
Ranked dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Divided 243.583 267.527 1.0983
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Subtracted 200.691 179.88 20.811
Squared human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Divided 46785.7 58383.2 1.24789
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Subtracted 28895.6 35572.8 6677.2
Rooted chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 52.7936 60.0592 7.2656
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Divided 77.5797 70.0179 1.108
340 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 20446.1 24136.4 1.18049
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Subtracted 11743.3 10712.3 1031
Ranked 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 260.544 20.794
myelin gene expression factor 2. [refseq;acc:nm_016132] Divided 235.383 258.476 1.09811
Squared ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 32117 40054 1.24713
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Subtracted 28895.6 35572.8 6677.2
Rooted nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Divided 58.4926 64.8047 1.10791
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted 45.7414 52.932 7.1906
341 Measured homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Divided 20446.1 24136.4 1.18049
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Subtracted 4916.8 3888.18 1028.62
Ranked 60s ribosomal protein l9. [swissprot;acc:p32969] Divided 240.243 263.798 1.09805
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Subtracted 240.788 261.416 20.628
Squared acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 31646.1 38288.7 6642.6
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Divided 32056.4 39965.8 1.24673
Rooted lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] 51.9812 57.5858 1.10782
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Subtracted 120.033 112.905 7.128
342 Measured homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Divided 20446.1 24136.4 1.18049

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/