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 1400 to 1449 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
175 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Squared Divided 112820 157033 1.39189
176 bet3 homolog. [swissprot;acc:o43617]
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted Subtracted 37.3005 48.4141 11.1136
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Ranked Divided 275.754 235.908 1.1689
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Subtracted 271.016 244.167 26.849
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Measured 10235.2 11830.8 1595.6
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Divided 4456.93 5773.67 1.29544
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Rooted 145.551 168.796 1.1597
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Squared Subtracted 71576.8 56326.7 15250.1
177 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 9924.76 25146.6 15221.8
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked Divided 229.406 196.695 1.1663
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured Subtracted 4110.14 5694.99 1584.85
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 4457.06 5773.63 1.29539
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Rooted 145.551 168.796 1.1597
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted 37.3005 48.4141 11.1136
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Squared Divided 78383 108483 1.38401
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked Subtracted 241.07 267.88 26.81
178 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared 9924.76 25146.6 15221.8
carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided 25326.4 18354.1 1.37988
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Rooted Subtracted 37.3005 48.4141 11.1136
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Ranked 241.07 267.88 26.81
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 226.887 194.72 1.1652
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Measured 21591.5 27904.5 1.29238
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Subtracted 10908.6 12491.8 1583.2
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Rooted Divided 45.7414 52.932 1.1572
179 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Measured Subtracted 4266.04 5843.51 1577.47
huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted 55.0737 66.0298 10.9561
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Ranked Divided 226.884 194.79 1.16476
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Squared 25326.3 18354.1 1.37987
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Measured 21591.5 27904.5 1.29238
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Rooted 50.272 43.4634 1.15665
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Ranked Subtracted 227.357 254.15 26.793
spermatogenesis associated 6. [refseq;acc:nm_019073] Squared 9924.76 25146.6 15221.8
180 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Measured 10872.4 12447 1574.6
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Rooted Divided 50.2801 43.4779 1.15645
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 88.4361 77.5112 10.9249
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Measured Divided 21591.5 27904.5 1.29238
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Squared 25326.2 18354.1 1.37987
pp3111 protein. [refseq;acc:nm_022156] Ranked Subtracted 227.357 254.15 26.793
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Divided 256.228 298.438 1.16474
181 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Rooted Subtracted 88.4266 77.5047 10.9219
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided 57.4432 66.3307 1.15472
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Measured 4068.56 5252.6 1.29102
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Squared 55630.4 76083.7 1.36766
musashi 2 isoform a. [refseq;acc:nm_138962] Measured Subtracted 4241.57 5810.79 1569.22
syntaxin 18. [swissprot;acc:q9p2w9] Ranked 227.357 254.15 26.793
transcription factor iib. [refseq;acc:nm_013242] Squared 64739.9 50300.6 14439.3
182 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Rooted 47.6504 36.9304 10.72

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/