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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 682 to 731 of 66312 in total
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
Interaction Map
red
green
network_comparison
43 JUND Rooted transcription factor jun-d. [swissprot;acc:p17535] Subtracted Low confidence 67.1245 75.5619 8.4374
KHDRBS3 Ranked kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 332.874 267.246 65.628
MAGEA4 Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided Low confidence 82347.8 61881.5 1.33073
MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Subtracted 20466.3
MFAP4 Ranked microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 242.742 217.217 25.525
MYO5B Squared myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence 110342 184298 73956
RGS12 Ranked regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Divided Low confidence 247.768 219.841 1.12703
44 no value Squared melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 82347.8 61881.5 1.33073
Rooted protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 55.7075 63.2842 1.13601
DNASE2B Measured deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Subtracted High confidence 28136.5 33457.6 5321.1
FOSB Rooted protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 60.8692 77.7165 16.8473
FOSL2 Ranked fos-related antigen 2. [swissprot;acc:p15408] Divided 204.641 161.046 1.2707
GABARAP Squared gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 139741 78454.6 1.78117
GNB1 Measured guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1931.34 1057.39 1.82652
GNB4 Rooted guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 40.5691 25.4263 1.59556
JUNB transcription factor jun-b. [swissprot;acc:p17275] Subtracted Low confidence 67.118 75.5523 8.4343
JUND Measured transcription factor jun-d. [swissprot;acc:p17535] Divided 6614.51 7680.25 1.16112
KHDRBS1 Ranked kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Subtracted High confidence 332.874 267.246 65.628
MAGEB6B Squared melanoma antigen, family b, 6. [refseq;acc:nm_173523] Low confidence 82347.8 61881.5 20466.3
MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence 110342 184298 73956
NFE2L2 Measured nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] Low confidence 8313.02 9645.34 1332.32
PPP1R14A Ranked protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Divided 242.742 217.217 1.11751
PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Subtracted 25.525
45 no value Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided High confidence 129597 73157.5 1.77148
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Subtracted Low confidence 82347.8 61881.5 20466.3
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] High confidence 110342 184298 73956
BACH2 Measured transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Low confidence 8313.02 9645.34 1332.32
FCN2 Ranked ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 242.742 217.217 25.525
FOS Rooted proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided 66.5831 75.4064 1.13252
FOSB Ranked protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence 204.641 161.051 1.27066
FOSL1 Rooted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted 60.875 77.7152 16.8402
GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Divided 40.081 25.1546 1.59339
GNB4 Measured guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 1926.69 1056.02 1.82448
JUNB transcription factor jun-b. [swissprot;acc:p17275] Low confidence 6613.42 7678.76 1.16109
KHDRBS2 Ranked kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Subtracted High confidence 332.874 267.246 65.628
MAGEA10 Squared melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided Low confidence 82347.8 61881.5 1.33073
MFAP4 Ranked microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 242.742 217.217 1.11751
PPP1R7 Measured protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Subtracted High confidence 27642.5 22440.4 5202.1
RGS12 Rooted regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Low confidence 54.8296 63.2347 8.4051
46 no value Ranked protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 242.742 217.217 25.525
Rooted atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 75.6323 67.6572 7.9751
jun dimerization protein. [refseq;acc:nm_130469] Divided 66.5831 75.4064 1.13252
ATG3 Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] High confidence 129597 73157.5 1.77148
BACH1 Measured transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Low confidence 8313.02 9645.34 1.16027
CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Subtracted High confidence 24896.4 20431.7 4464.7
DTX2 Rooted deltex 2. [refseq;acc:nm_020892] Divided 27.634 43.9629 1.5909
FOSL1 Ranked fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 204.642 161.068 1.27053
MAGEA9 Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted Low confidence 82347.8 61881.5 20466.3
MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Divided 1.33073
MAGED4 Rooted melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Subtracted High confidence 137.446 120.823 16.623

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
- Hugo is the HGNC identifier if it exists
- 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/