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 2580 to 2629 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
323 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Rooted 0 27.5028 29.1579 1.06018
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Measured 2056.14 2244.06 1.09139
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Squared 1 33514.4 42370.8 1.26426
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Ranked 0 17387.1 16427.3 1.05843
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Measured 1 4620.76 5501.94 1.1907
324 40s ribosomal protein s23. [swissprot;acc:p39028] Ranked 243.944 268.195 1.09941
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Squared 0 1742.44 1500.84 1.16098
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured 1 28136.5 33457.6 1.18912
fad synthetase. [refseq;acc:nm_025207] Rooted 50.3803 45.4193 1.10923
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Squared 34527.9 43507.9 1.26008
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Rooted 0 27.5028 29.1579 1.06018
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Ranked 17387.1 16427.3 1.05843
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Measured 3036.29 2784.08 1.09059
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Ranked 1 243.944 268.195 1.09941
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Rooted 50.3803 45.4193 1.10923
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared 34506.3 43476 1.25994
mstp028 protein. [refseq;acc:nm_031954] Ranked 0 7965.66 7528.21 1.05811
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured 1 16177.9 19235.4 1.18899
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] Rooted 0 16.5182 17.4854 1.05855
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Measured 3036.85 2784.59 1.09059
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] Squared 1742.44 1500.84 1.16098
326 60s ribosomal protein l5. [swissprot;acc:p46777] Ranked 1 241.899 265.924 1.09932
anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Squared 69124.3 54897.4 1.25915
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Rooted 0 83.9673 88.8829 1.05854
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Measured 1 3432.96 4081.21 1.18883
chromodomain y-like protein 2. [refseq;acc:nm_152342] 0 3053.31 2799.81 1.09054
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Ranked 11948.4 11295.6 1.05779
germ cell-less. [refseq;acc:nm_022471] Squared 3567.33 3084.18 1.15665
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Rooted 1 50.3803 45.4193 1.10923
327 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Ranked 0 9897.29 10466.5 1.05751
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Squared 178.482 205.335 1.15045
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Rooted 1 50.3803 45.4193 1.10923
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Measured 0 175.644 161.091 1.09034
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Ranked 1 243.817 267.962 1.09903
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Squared 16424.1 20645.8 1.25704
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Rooted 0 23.6959 25.0734 1.05813
septin 10 isoform 1. [refseq;acc:nm_144710] Measured 1 16067.4 19094.4 1.18839
328 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Squared 0 6747.71 5878.56 1.14785
60s ribosomal protein l12. [swissprot;acc:p30050] Measured 1657.78 1805.05 1.08884
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Ranked 1 258.437 235.183 1.09888
brain protein 44. [swissprot;acc:o95563] Measured 15999.1 19007.1 1.18801
histone h4. [swissprot;acc:p02304] Rooted 0 98.5525 104.126 1.05655
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Squared 1 16442.8 20662.7 1.25664
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Rooted 50.3803 45.4193 1.10923
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Ranked 0 10897 11520 1.05717
329 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Squared 195397 170319 1.14724
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Rooted 1 50.3803 45.4193 1.10923
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Measured 0 1658.07 1805.36 1.08883
metaxin 2. [swissprot;acc:o75431] Squared 1 41236 51807 1.25635
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Ranked 312 284 1.09859

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/