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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1844 to 1893 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
red
green
network_comparison
231 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Divided Measured 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted Rooted 95.0526 85.3206 9.732
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Ranked 226.411 202.088 24.323
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Measured 9649.61 11053.5 1403.89
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Divided Squared 42411.6 55802.1 1.31573
232 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Subtracted Ranked 226.401 202.094 24.307
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Squared 41502.9 30836.8 10666.1
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Divided Measured 9035 7279.6 1.24114
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Rooted 137.446 120.823 1.13758
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Subtracted 95.0526 85.3206 9.732
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Divided Squared 42411.6 55802.1 1.31573
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Ranked 239.336 267.879 1.11926
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Subtracted Measured 9649.61 11053.5 1403.89
233 60s ribosomal protein l7. [swissprot;acc:p18124] Ranked 235.727 259.984 24.257
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Squared 41502.9 30836.8 10666.1
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Divided Ranked 239.32 267.842 1.11918
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Squared 42411.6 55802.1 1.31573
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 137.446 120.823 1.13758
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 95.0526 85.3206 9.732
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Divided Measured 9035 7279.6 1.24114
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Subtracted 9649.61 11053.5 1403.89
234 40s ribosomal protein s23. [swissprot;acc:p39028] Ranked 243.944 268.195 24.251
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided 287.41 256.835 1.11905
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Subtracted Squared 41502.9 30836.8 10666.1
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Measured 9649.61 11053.5 1403.89
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided Rooted 137.446 120.823 1.13758
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Subtracted 95.0526 85.3206 9.732
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Divided Squared 42411.6 55802.1 1.31573
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Measured 5181.2 6410.58 1.23728
235 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Subtracted Ranked 243.944 268.195 24.251
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Rooted 95.0526 85.3206 9.732
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Squared 41502.9 30836.8 10666.1
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Divided Rooted 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Subtracted Measured 9649.61 11053.5 1403.89
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Divided Squared 42411.6 55802.1 1.31573
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Ranked 227.357 254.15 1.11785
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Measured 5181.2 6410.58 1.23728
236 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Subtracted Ranked 252.644 228.42 24.224
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided Rooted 137.446 120.823 1.13758
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Subtracted Squared 41502.9 30836.8 10666.1
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Rooted 95.0526 85.3206 9.732
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Measured 9649.61 11053.5 1403.89
pp3111 protein. [refseq;acc:nm_022156] Divided Ranked 227.357 254.15 1.11785
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Measured 4723.53 5828.46 1.23392
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Squared 42411.6 55802.1 1.31573
237 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Subtracted Rooted 133.216 123.627 9.589
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 137.446 120.823 1.13758
metaxin 2. [swissprot;acc:o75431] Subtracted Squared 41236 51807 10571
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Ranked 242.011 266.18 24.169
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Measured 9649.61 11053.5 1403.89

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/