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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Gene Rank Network Comparison Type description Value Type Interaction Map green red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1873 to 1922 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
Value Type
green
red
network_comparison
235 Divided melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Rooted 120.823 137.446 1.13758
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Squared 55802.1 42411.6 1.31573
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Ranked 254.15 227.357 1.11785
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Measured 6410.58 5181.2 1.23728
Subtracted 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Ranked 268.195 243.944 24.251
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Rooted 85.3206 95.0526 9.732
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Squared 30836.8 41502.9 10666.1
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Measured 11053.5 9649.61 1403.89
236 Divided melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Rooted 120.823 137.446 1.13758
pp3111 protein. [refseq;acc:nm_022156] Ranked 254.15 227.357 1.11785
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Measured 5828.46 4723.53 1.23392
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Squared 55802.1 42411.6 1.31573
Subtracted histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Ranked 228.42 252.644 24.224
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Squared 30836.8 41502.9 10666.1
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Rooted 85.3206 95.0526 9.732
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Measured 11053.5 9649.61 1403.89
237 Divided melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Rooted 120.823 137.446 1.13758
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Squared 55802.1 42411.6 1.31573
syntaxin 18. [swissprot;acc:q9p2w9] Ranked 254.15 227.357 1.11785
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Measured 5631.2 4567.04 1.23301
Subtracted fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Rooted 123.627 133.216 9.589
metaxin 2. [swissprot;acc:o75431] Squared 51807 41236 10571
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Ranked 266.18 242.011 24.169
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Measured 11053.5 9649.61 1403.89
238 Divided melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Rooted 120.823 137.446 1.13758
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Squared 55802.1 42411.6 1.31573
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Measured 22440.4 27642.5 1.23182
rd protein. [swissprot;acc:p18615] Ranked 254.15 227.357 1.11785
Subtracted golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Squared 52985.3 42566.2 10419.1
metastasis-associated protein mta1. [swissprot;acc:q13330] Ranked 228.356 252.512 24.156
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Rooted 65.8949 56.3709 9.524
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Measured 11053.5 9649.61 1403.89
239 Divided carboxypeptidase b precursor. [refseq;acc:nm_020361] 6265.8 7711.38 1.23071
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Ranked 254.15 227.357 1.11785
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Rooted 120.823 137.446 1.13758
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Squared 55802.1 42411.6 1.31573
Subtracted adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 46971.1 36563.7 10407.4
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Ranked 267.962 243.817 24.145
mad protein (max dimerizer). [swissprot;acc:q05195] Rooted 65.1534 55.646 9.5074
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Measured 11053.5 9649.61 1403.89
240 Divided androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Ranked 254.15 227.357 1.11785
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured 6265.79 7711.36 1.23071
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Rooted 120.823 137.446 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 55802.1 42411.6 1.31573
Subtracted 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] Ranked 228.297 252.39 24.093
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Rooted 65.1478 55.6486 9.4992
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Measured 11053.5 9649.61 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 48584.2 58831 10246.8
241 Divided atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Ranked 254.15 227.357 1.11785
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Rooted 120.823 137.446 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/