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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 325 to 374 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
41 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Squared Divided 144912 81155 1.78562
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Ranked 322 253 1.27273
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Rooted Subtracted 60.8365 77.7233 16.8868
trophinin. [swissprot;acc:q12816] Measured 23693.7 18263 5430.7
42 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared 211446 137422 74024
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured 21785.2 16426.1 5359.1
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Divided 1857.32 958.237 1.93827
Rooted 40.225 24.7051 1.62821
jun dimerization protein. [refseq;acc:nm_130469] Subtracted 60.8365 77.7233 16.8868
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared Divided 144911 81154.7 1.78561
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked 204.641 160.957 1.2714
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] Subtracted 332.874 267.246 65.628
43 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Measured 21785.2 16426.1 5359.1
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared Divided 144876 81136.5 1.78558
fos-related antigen 2. [swissprot;acc:p15408] Rooted Subtracted 60.8675 77.7168 16.8493
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Divided 40.6302 25.4452 1.59677
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Measured 1881.02 1027.36 1.83093
jun dimerization protein. [refseq;acc:nm_130469] Ranked 204.641 160.957 1.2714
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Subtracted 332.874 267.246 65.628
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Squared 110342 184298 73956
44 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured 28136.5 33457.6 5321.1
fos-related antigen 2. [swissprot;acc:p15408] Ranked Divided 204.641 161.046 1.2707
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 1.78117
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted 40.5691 25.4263 1.59556
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Measured 1931.34 1057.39 1.82652
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked Subtracted 332.874 267.246 65.628
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Squared 110342 184298 73956
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 16.8473
45 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 60.875 77.7152 16.8402
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared Divided 129597 73157.5 1.77148
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1926.69 1056.02 1.82448
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Rooted 40.081 25.1546 1.59339
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Ranked Subtracted 332.874 267.246 65.628
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Squared 110342 184298 73956
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked Divided 204.641 161.051 1.27066
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Measured Subtracted 27642.5 22440.4 5202.1
46 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared Divided 129597 73157.5 1.77148
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] Measured Subtracted 24896.4 20431.7 4464.7
deltex 2. [refseq;acc:nm_020892] Rooted Divided 27.634 43.9629 1.5909
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 161.068 1.27053
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Rooted Subtracted 137.446 120.823 16.623
neuralized-like. [refseq;acc:nm_004210] Ranked 332.326 266.948 65.378
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured Divided 779.167 1390.33 1.78438
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared Subtracted 210445 136779 73666
47 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured Divided 779.167 1390.33 1.78438
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 27.7078 44.017 1.58861
exocyst complex component sec5. [swissprot;acc:q96kp1] Squared Subtracted 210335 136716 73619
gbp protein isoform a. [refseq;acc:nm_017870] Ranked Divided 325.586 256.492 1.26938
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Rooted Subtracted 137.446 120.823 16.623
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked 350 290 60

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/