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.


Navigation/Query Panel:
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 [...,...].
Gene Rank Value Type description Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 1873 to 1922 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
network_comparison
green
235 Measured neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Subtracted 9649.61 1403.89 11053.5
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided 5181.2 1.23728 6410.58
Ranked 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Subtracted 243.944 24.251 268.195
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Divided 227.357 1.11785 254.15
Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Subtracted 41502.9 10666.1 30836.8
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Divided 42411.6 1.31573 55802.1
Rooted dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Subtracted 95.0526 9.732 85.3206
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Divided 137.446 1.13758 120.823
236 Measured nitrogen fixation cluster-like. [refseq;acc:nm_014301] Subtracted 9649.61 1403.89 11053.5
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Divided 4723.53 1.23392 5828.46
Ranked histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Subtracted 252.644 24.224 228.42
pp3111 protein. [refseq;acc:nm_022156] Divided 227.357 1.11785 254.15
Squared mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Subtracted 41502.9 10666.1 30836.8
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Divided 42411.6 1.31573 55802.1
Rooted melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 137.446 1.13758 120.823
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Subtracted 95.0526 9.732 85.3206
237 Measured star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 9649.61 1403.89 11053.5
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Divided 4567.04 1.23301 5631.2
Ranked mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Subtracted 242.011 24.169 266.18
syntaxin 18. [swissprot;acc:q9p2w9] Divided 227.357 1.11785 254.15
Squared metaxin 2. [swissprot;acc:o75431] Subtracted 41236 10571 51807
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Divided 42411.6 1.31573 55802.1
Rooted fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Subtracted 133.216 9.589 123.627
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 137.446 1.13758 120.823
238 Measured protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 27642.5 1.23182 22440.4
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Subtracted 9649.61 1403.89 11053.5
Ranked metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 24.156 228.356
rd protein. [swissprot;acc:p18615] Divided 227.357 1.11785 254.15
Squared golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Subtracted 42566.2 10419.1 52985.3
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Divided 42411.6 1.31573 55802.1
Rooted melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 137.446 1.13758 120.823
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Subtracted 56.3709 9.524 65.8949
239 Measured carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided 7711.38 1.23071 6265.8
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Subtracted 9649.61 1403.89 11053.5
Ranked dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 243.817 24.145 267.962
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Divided 227.357 1.11785 254.15
Squared adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Subtracted 36563.7 10407.4 46971.1
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Divided 42411.6 1.31573 55802.1
Rooted mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 55.646 9.5074 65.1534
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 137.446 1.13758 120.823
240 Measured mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 7711.36 1.23071 6265.79
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Subtracted 9649.61 1403.89 11053.5
Ranked androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Divided 227.357 1.11785 254.15
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 24.093 228.297
Squared 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] Divided 42411.6 1.31573 55802.1
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Subtracted 58831 10246.8 48584.2
Rooted max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 55.6486 9.4992 65.1478
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 137.446 1.13758 120.823
241 Measured 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] Subtracted 9649.61 1403.89 11053.5
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Divided 7711.31 1.23071 6265.76

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/