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 5158 to 5207 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
323 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Squared Subtracted 0 229.508 283.721 54.213
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Rooted Divided 27.5028 29.1579 1.06018
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Measured Subtracted 1 10247.8 11289 1041.2
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Divided 0 2056.14 2244.06 1.09139
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Squared Subtracted 1 25326.3 18354.1 6972.2
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] Divided 33514.4 42370.8 1.26426
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Ranked Subtracted 0 12320.2 13018.5 698.3
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Rooted 1 125.493 117.944 7.549
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Ranked Divided 0 17387.1 16427.3 1.05843
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Rooted Subtracted 11.7534 10.3214 1.432
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Measured Divided 1 4620.76 5501.94 1.1907
324 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Ranked Subtracted 242.238 264.11 21.872
40s ribosomal protein s23. [swissprot;acc:p39028] Divided 243.944 268.195 1.09941
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Squared Subtracted 0 105.615 53.4024 52.2126
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Divided 1742.44 1500.84 1.16098
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] Ranked Subtracted 7101.79 6406.18 695.61
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured Divided 1 28136.5 33457.6 1.18912
fad synthetase. [refseq;acc:nm_025207] Rooted 50.3803 45.4193 1.10923
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Subtracted 0 22.112 20.6871 1.4249
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Squared Divided 1 34527.9 43507.9 1.26008
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured Subtracted 0 6323 6254.09 68.91
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Rooted Divided 27.5028 29.1579 1.06018
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Squared Subtracted 1 25326.2 18354.1 6972.1
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Measured 11773.7 10733.8 1039.9
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Ranked Divided 0 17387.1 16427.3 1.05843
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Measured 3036.29 2784.08 1.09059
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Rooted Subtracted 1 125.447 117.906 7.541
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Ranked Divided 243.944 268.195 1.09941
60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Subtracted 241.828 263.62 21.792
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 Divided 50.3803 45.4193 1.10923
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Measured Subtracted 0 375.322 306.933 68.389
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 1 8362.81 9402.7 1039.89
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted 100.684 108.135 7.451
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared Divided 34506.3 43476 1.25994
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Subtracted 0 290.82 239.342 51.478
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Rooted 12.8935 14.3151 1.4216
mesoderm induction early response 1. [refseq;acc:nm_020948] Ranked 3609 4302.5 693.5
mstp028 protein. [refseq;acc:nm_031954] Divided 7965.66 7528.21 1.05811
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared Subtracted 1 19321 12542.6 6778.4
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Divided 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 40s ribosomal protein s16. [swissprot;acc:p17008] Ranked Subtracted 1 241.828 263.62 21.792
60s ribosomal protein l5. [swissprot;acc:p46777] Divided 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
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Subtracted 0 375.07 306.727 68.343
chromodomain y-like protein 2. [refseq;acc:nm_152342] Divided 3053.31 2799.81 1.09054

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/