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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 [...,...].
Rank Value Type Gene description Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 14872 to 14921 of 29840 in total
Filtered  : 1
Interaction Map  : High confidence
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
1357 Rooted nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Divided 65.1521 67.8158 1.04088
1358 Measured sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] Subtracted 5655.85 6120.62 464.77
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Divided 5657.71 6103.54 1.0788
Ranked geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] Subtracted 225.039 229.573 4.534
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Divided 214.987 210.359 1.022
Squared importin 8; ran-binding protein 8. [refseq;acc:nm_006390] 24948.9 28072.6 1.1252
inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] Subtracted 23913 26757.8 2844.8
Rooted intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Divided 60.4911 58.1154 1.04088
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] Subtracted 63.5941 66.1672 2.5731
1359 Measured dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Divided 5657.71 6103.54 1.0788
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Subtracted 5779.83 6244.56 464.73
Ranked fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] 225.039 229.573 4.534
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Divided 228.642 223.726 1.02197
Squared brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 24948.9 28072.6 1.1252
uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Subtracted 23913 26757.8 2844.8
Rooted hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Divided 60.4911 58.1154 1.04088
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Subtracted 63.5941 66.1672 2.5731
1360 Measured calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] Divided 5657.72 6103.52 1.07879
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] Subtracted 6192.38 6656.34 463.96
Ranked mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] 225.039 229.573 4.534
tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Divided 223.89 228.805 1.02195
Squared hsgcn1 (fragment). [sptrembl;acc:q99736] 24948.9 28072.6 1.1252
myosin vi. [swissprot;acc:q9um54] Subtracted 23913 26757.8 2844.8
Rooted alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] 62.4303 65.0019 2.5716
cgthba protein (-14 gene protein). [swissprot;acc:q12980] Divided 60.4911 58.1154 1.04088
1361 Measured calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] 5657.72 6103.52 1.07879
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Subtracted 5675.96 6136.47 460.51
Ranked fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] 225.039 229.573 4.534
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Divided 214.971 210.354 1.02195
Squared brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 24948.9 28072.6 1.1252
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Subtracted 20836.6 23679.5 2842.9
Rooted hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Divided 60.4911 58.1154 1.04088
sipl protein. [refseq;acc:nm_018269] Subtracted 66.3152 68.8865 2.5713
1362 Measured deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 6146.36 6606.21 459.85
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Divided 6322.75 6820.5 1.07872
Ranked fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Subtracted 225.039 229.573 4.534
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Divided 228.644 223.736 1.02194
Squared brain protein 16. [refseq;acc:nm_016458] Subtracted 26202.2 29043.8 2841.6
zinc finger protein t86. [swissprot;acc:o00488] Divided 16283.6 18321.8 1.12517
Rooted 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 61.5231 64.0358 1.04084
dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] Subtracted 62.4314 65.0015 2.5701
1363 Measured nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Divided 6322.75 6820.5 1.07872
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Subtracted 6343.76 6803.44 459.68
Ranked camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Divided 218.591 213.899 1.02194
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Subtracted 168.989 164.46 4.529
Squared hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] Divided 17915.5 20153.8 1.12494
jm1 protein. [refseq;acc:nm_014008] Subtracted 27139.1 29980.5 2841.4
Rooted elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] 62.4314 65.0015 2.5701
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Divided 65.1444 67.8042 1.04083
1364 Measured dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] Subtracted 5685.77 6145.43 459.66

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/