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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1818 to 1867 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
228 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Squared Divided 57913.5 76336.3 1.31811
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Rooted 137.446 120.823 1.13758
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Ranked Subtracted 244.126 268.604 24.478
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Rooted 95.0526 85.3206 9.732
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Measured Divided 9035 7279.6 1.24114
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Subtracted 6417.81 7852.52 1434.71
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 Divided 226.411 202.088 1.12036
229 60s ribosomal protein l3-like. [swissprot;acc:q92901] Subtracted 242.195 266.663 24.468
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Squared 45986 56776.1 10790.1
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Ranked Divided 226.401 202.094 1.12028
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 120.823 1.13758
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Squared 42411.6 55802.1 1.31573
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Measured 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted Subtracted 95.0526 85.3206 9.732
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Measured 10434.4 11846.2 1411.8
230 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Squared 45987 56777.1 10790.1
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Ranked Divided 239.35 267.915 1.11934
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Measured Subtracted 9649.61 11053.5 1403.89
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Rooted Subtracted 95.0526 85.3206 9.732
necdin. [swissprot;acc:q99608] Divided 137.446 120.823 1.13758
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Ranked Subtracted 242.694 267.017 24.323
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Squared Divided 42411.6 55802.1 1.31573
231 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Subtracted 45960.8 56749.6 10788.8
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Ranked Divided 239.336 267.881 1.11927
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Rooted 137.446 120.823 1.13758
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Measured 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted Subtracted 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] Squared Divided 42411.6 55802.1 1.31573
232 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Ranked Subtracted 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] Measured Divided 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] Squared Divided 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] Measured Subtracted 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] Ranked Divided 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] Measured Divided 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] Squared Subtracted 41502.9 30836.8 10666.1

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/