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 351 to 400 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
44 serpin b12. [swissprot;acc:q96p63] Ranked 0 14604.2 21138.6 1.44743
tigger transposable element derived 6. [refseq;acc:nm_030953] Squared 14.8773 83.3977 5.6057
45 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Rooted 8.79142 14.7392 1.67654
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared 1 129597 73157.5 1.77148
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1926.69 1056.02 1.82448
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Rooted 40.081 25.1546 1.59339
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Ranked 0 14592 21113.7 1.44694
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 1 204.641 161.051 1.27066
tigger transposable element derived 6. [refseq;acc:nm_030953] Measured 0 202.374 438.605 2.1673
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Squared 14.8569 83.2781 5.60535
46 60s ribosomal protein l37a. [swissprot;acc:p12751] Ranked 12941.7 18499.2 1.42943
apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 1 129597 73157.5 1.77148
deltex 2. [refseq;acc:nm_020892] Rooted 27.634 43.9629 1.5909
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 161.068 1.27053
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Rooted 0 12.53 7.48331 1.67439
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured 1 779.167 1390.33 1.78438
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Squared 0 14.8562 83.274 5.60534
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Measured 202.163 438.035 2.16674
47 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Ranked 12941.7 18499.2 1.42943
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Rooted 21.3967 34.6716 1.62042
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Measured 1 779.167 1390.33 1.78438
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted 27.7078 44.017 1.58861
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared 0 975.125 178.265 5.47009
gbp protein isoform a. [refseq;acc:nm_017870] Ranked 1 325.586 256.492 1.26938
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Measured 0 202.156 438.016 2.16672
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared 1 98517.9 56927.2 1.73059
48 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 0 870.482 403.196 2.15895
doc-1 related protein (doc-1r). [swissprot;acc:o75956] 1 779.167 1390.33 1.78438
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked 65.4586 83.0461 1.26868
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared 0 960.518 176.164 5.45241
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 1 6300.2 10703.5 1.69891
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Ranked 0 9830 6909 1.42278
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Rooted 1 27.7254 44.0299 1.58807
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 0 15.0533 9.31487 1.61605
49 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared 1 28994.2 17134.8 1.69212
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked 133 105 1.26667
brain protein 16. [refseq;acc:nm_016458] 0 6890.54 4854.99 1.41927
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Squared 8.10857 43.7473 5.39519
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted 1 27.7254 44.0299 1.58807
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Measured 779.167 1390.33 1.78438
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Rooted 0 14.1508 8.89106 1.59158
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Measured 72 151 2.09722
50 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked 1 133 105 1.26667
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 0 9249.73 13091.4 1.41533
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Rooted 11.0328 6.96286 1.58452
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 27.7254 44.0299 1.58807
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured 779.167 1390.33 1.78438
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Squared 0 10.974 2.38124 4.60852
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 1 28994.2 17134.8 1.69212
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] Measured 0 44 21 2.09524

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/