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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2680 to 2729 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
335 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Squared 1 30651.3 38253.3 1.24802
336 60s ribosomal protein l11. [swissprot;acc:p39026] Rooted 50.3167 45.4063 1.10814
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 0 20.5317 19.4823 1.05386
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] Ranked 1 312 284 1.09859
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Measured 0 1766.66 1908.13 1.08008
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 1 3751.3 4431.34 1.18128
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Squared 46785.7 58383.2 1.24789
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 0 3680.43 3222.6 1.14207
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Ranked 8125.5 7697.5 1.0556
337 60s ribosomal protein l12. [swissprot;acc:p30050] 1 243.583 267.527 1.0983
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] Measured 0 2039.07 2194.52 1.07624
carboxypeptidase b precursor. [refseq;acc:nm_020361] Rooted 1 77.5801 70.0182 1.108
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 0 56.92 59.965 1.0535
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Ranked 12953.2 12273.2 1.05541
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 1 20446.1 24136.4 1.18049
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Squared 46785.7 58383.2 1.24789
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 0 3680.39 3222.57 1.14207
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Ranked 1 243.583 267.528 1.0983
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Measured 20446.1 24136.4 1.18049
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Ranked 0 11149.7 10571.4 1.0547
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Squared 3680.31 3222.51 1.14206
lamin b2. [swissprot;acc:q03252] Measured 579.262 538.704 1.07529
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Rooted 1 77.58 70.0181 1.108
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 0 9.92736 9.42407 1.0534
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] Squared 1 46785.7 58383.2 1.24789
339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Ranked 243.583 267.527 1.0983
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Measured 0 996.883 1070.03 1.07338
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Rooted 29.6274 31.1837 1.05253
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Measured 1 20446.1 24136.4 1.18049
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Squared 46785.7 58383.2 1.24789
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 0 3680.04 3222.31 1.14205
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Rooted 1 77.5797 70.0179 1.108
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Ranked 0 10344.1 10903.3 1.05406
340 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Measured 559.333 600 1.07271
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked 11372.3 10792.3 1.05374
histone h2b.d (h2b/d). [swissprot;acc:q99877] Rooted 29.6283 31.1839 1.0525
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Measured 1 20446.1 24136.4 1.18049
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Squared 0 3680.04 3222.31 1.14205
myelin gene expression factor 2. [refseq;acc:nm_016132] Ranked 1 235.383 258.476 1.09811
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Rooted 58.4926 64.8047 1.10791
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Squared 32117 40054 1.24713
341 60s ribosomal protein l9. [swissprot;acc:p32969] Ranked 240.243 263.798 1.09805
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 0 8702.94 9169.98 1.05366
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Measured 6452.66 6019.79 1.07191
histone h2b.s (h2b/s). [swissprot;acc:p57053] Rooted 29.6311 31.1846 1.05243
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured 1 20446.1 24136.4 1.18049
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Squared 0 3679.97 3222.25 1.14205
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Rooted 1 51.9812 57.5858 1.10782
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared 32056.4 39965.8 1.24673
342 40s ribosomal protein s20. [swissprot;acc:p17075] Ranked 243.5 267.21 1.09737

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/