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 9664 to 9713 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2416 ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Rooted 57.6219 58.4734 1.01478
2417 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Measured 3598.55 3467.65 1.03775
mstp028 protein. [refseq;acc:nm_031954] Squared 27928.1 29734 1.06466
nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426] Rooted 57.6219 58.4734 1.01478
upf0183 protein. [swissprot;acc:q9bsu1] Ranked 218.2 218.984 1.00359
2418 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Measured 4857.03 5039.78 1.03763
antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008] Ranked 218.2 218.984 1.00359
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Squared 19990.2 21282.2 1.06463
ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] Rooted 57.6219 58.4734 1.01478
2419 dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992]
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Squared 27935.5 29738.4 1.06454
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Measured 4857.03 5039.78 1.03763
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Ranked 218.2 218.984 1.00359
2420 squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508]
survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] Rooted 57.6219 58.4734 1.01478
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Measured 4857.03 5039.78 1.03763
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Squared 27939.6 29740.9 1.06447
2421 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] Ranked 210.205 209.454 1.00359
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Measured 7355.46 7088.93 1.0376
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Squared 27940.4 29741.3 1.06446
probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6] Rooted 57.6219 58.4734 1.01478
2422 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Measured 7355.46 7088.93 1.0376
lim/homeobox protein lhx4. [swissprot;acc:q969g2] Squared 39931 37536.3 1.0638
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Ranked 218.2 218.984 1.00359
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Rooted 57.626 58.4722 1.01468
2423 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Measured 7355.46 7088.93 1.0376
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Ranked 220.682 221.471 1.00358
lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Squared 39916.6 37528.7 1.06363
transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Rooted 57.6285 58.4715 1.01463
2424 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] 70.8372 71.869 1.01457
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Measured 7355.46 7088.93 1.0376
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Ranked 220.682 221.472 1.00358
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Squared 39916.7 37528.7 1.06363
2425 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Ranked 220.682 221.472 1.00358
lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] Squared 39904.4 37522.2 1.06349
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Measured 7355.46 7088.93 1.0376
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Rooted 58.8509 59.701 1.01444
2426 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] Squared 27135.1 28847.4 1.0631
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Rooted 60.4888 61.358 1.01437
mesoderm induction early response 1. [refseq;acc:nm_020948] Ranked 212.374 211.618 1.00357
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Measured 6123.47 6351.84 1.03729
2427 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Squared 20171.2 21443.4 1.06307
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Measured 5333.6 5531.41 1.03709
Rooted 59.9715 59.1233 1.01435
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Ranked 212.374 211.618 1.00357
2428 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 192.871 193.555 1.00355
ba207c16.2 (fragment). [sptrembl;acc:q9nql7] Rooted 67.052 68.0131 1.01433
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Measured 7243.19 7509.81 1.03681
phosducin-like protein (phlp). [swissprot;acc:q13371] Squared 20163.2 21432.5 1.06295
2429 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Rooted 60.43 61.2917 1.01426

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/