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 1875 to 1924 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
235 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Squared Subtracted 41502.9 30836.8 10666.1
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Rooted Divided 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Measured Subtracted 9649.61 11053.5 1403.89
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Squared Divided 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] Ranked Subtracted 252.644 228.42 24.224
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Rooted Divided 137.446 120.823 1.13758
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Squared Subtracted 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] Ranked Divided 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] Rooted Subtracted 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] Squared Subtracted 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
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Squared Divided 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 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Squared Subtracted 42566.2 52985.3 10419.1
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Rooted Divided 137.446 120.823 1.13758
metastasis-associated protein mta1. [swissprot;acc:q13330] Ranked Subtracted 252.512 228.356 24.156
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Squared Divided 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
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Rooted Subtracted 56.3709 65.8949 9.524
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Measured 9649.61 11053.5 1403.89
239 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Squared 36563.7 46971.1 10407.4
carboxypeptidase b precursor. [refseq;acc:nm_020361] Measured Divided 7711.38 6265.8 1.23071
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Ranked Subtracted 243.817 267.962 24.145
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Divided 227.357 254.15 1.11785
mad protein (max dimerizer). [swissprot;acc:q05195] Rooted Subtracted 55.646 65.1534 9.5074
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 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
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Measured Subtracted 9649.61 11053.5 1403.89
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Ranked Divided 227.357 254.15 1.11785
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Subtracted 252.39 228.297 24.093
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured Divided 7711.36 6265.79 1.23071
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Rooted Subtracted 55.6486 65.1478 9.4992
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 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
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Measured Subtracted 9649.61 11053.5 1403.89
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Squared 58831 48584.2 10246.8
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Ranked Divided 227.357 254.15 1.11785
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Subtracted 241.892 265.96 24.068
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Rooted 55.6495 65.1458 9.4963
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Divided 137.446 120.823 1.13758

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/