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 912 to 961 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
228 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 1.12036
229 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 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
230 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Ranked 239.35 267.915 1.11934
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Measured 9035 7279.6 1.24114
necdin. [swissprot;acc:q99608] Rooted 137.446 120.823 1.13758
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Squared 42411.6 55802.1 1.31573
231 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Ranked 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
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 42411.6 55802.1 1.31573
232 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Measured 9035 7279.6 1.24114
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Rooted 137.446 120.823 1.13758
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 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
233 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 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, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Measured 9035 7279.6 1.24114
234 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Ranked 287.41 256.835 1.11905
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Rooted 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 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 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Rooted 137.446 120.823 1.13758
nitrogen fixation cluster-like. [refseq;acc:nm_014301] 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 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Rooted 137.446 120.823 1.13758
pp3111 protein. [refseq;acc:nm_022156] 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 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Rooted 137.446 120.823 1.13758
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Squared 42411.6 55802.1 1.31573
syntaxin 18. [swissprot;acc:q9p2w9] Ranked 227.357 254.15 1.11785
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Measured 4567.04 5631.2 1.23301
238 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Rooted 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Squared 42411.6 55802.1 1.31573
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Measured 27642.5 22440.4 1.23182
rd protein. [swissprot;acc:p18615] Ranked 227.357 254.15 1.11785
239 carboxypeptidase b precursor. [refseq;acc:nm_020361] Measured 7711.38 6265.8 1.23071
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Ranked 227.357 254.15 1.11785
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Rooted 137.446 120.823 1.13758
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Squared 42411.6 55802.1 1.31573
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Ranked 227.357 254.15 1.11785
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured 7711.36 6265.79 1.23071
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Rooted 137.446 120.823 1.13758
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Squared 42411.6 55802.1 1.31573
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Ranked 227.357 254.15 1.11785

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/