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 736 to 785 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
368 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] High confidence 5082.66 5959.99 1.17261
369 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 3583.56 4194.95 1.17061
solute carrier family 26 member 6 (pendrin-like protein 1) (pendrin l1). [swissprot;acc:q9bxs9] Low confidence 8452.93 8910.99 1.05419
370 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 7708.02 8125.74
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] High confidence 4108.15 4808.93 1.17058
371 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] 5067.02 5926.46 1.16961
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Low confidence 8551.15 9014.39 1.05417
372 au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698] 7799.23 8221.54 1.05415
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] High confidence 5067 5926.17 1.16956
373 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 5066.99 5926.1 1.16955
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Low confidence 7633.63 8043.87 1.05374
374 prefoldin subunit 1. [swissprot;acc:o60925]
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] High confidence 5066.93 5925.38 1.16942
375 secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Low confidence 7633.63 8043.87 1.05374
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] High confidence 4700.42 5492.63 1.16854
376 44050 protein. [refseq;acc:nm_178832] 17385.9 14889.2 1.16769
choline dehydrogenase. [refseq;acc:nm_018397] Low confidence 7633.63 8043.87 1.05374
377 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 8724.99 9193.69 1.05372
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] High confidence 17385.9 14889.2 1.16769
378 ceramide glucosyltransferase (ec 2.4.1.80) (glucosylceramide synthase) (gcs) (udp-glucose:n-acylsphingosine d-glucosyltransferase) (glct-1). [swissprot;acc:q16739] Low confidence 8722.84 9190.81 1.05365
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] High confidence 12471.7 14561.7 1.16758
379 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Low confidence 7625.7 8034.6 1.05362
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] High confidence 6704.44 7811.45 1.16512
380 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 12998.5 15138.2 1.16461
dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] Low confidence 6760.17 7122.67 1.05362
381 c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835]
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] High confidence 5246.01 6109.31 1.16456
382 histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Low confidence 8721.03 9188.39 1.05359
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] High confidence 4533.74 5279.4 1.16447
383 hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Low confidence 7115.47 7496.56 1.05356
384 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] High confidence 4533.74 5279.4 1.16447
iroquois-class homeodomain protein irx-3 (iroquois homeobox protein 3) (fragment). [swissprot;acc:p78415] Low confidence 8964.52 9443.02 1.05338
385 iroquois-class homeodomain protein irx-1 (iroquois homeobox protein 1) (fragment). [swissprot;acc:p78414] 8964.32 9442.82
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] High confidence 4533.74 5279.4 1.16447
386 60s ribosomal protein l8. [swissprot;acc:p25120]
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Low confidence 8159.45 8594.89 1.05337
387 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] High confidence 4533.74 5279.4 1.16447
iroquois-class homeodomain protein irx-5 (iroquois homeobox protein 5) (irx-2a). [swissprot;acc:p78411] Low confidence 8966.17 9444.64 1.05336
388 iroquois-class homeodomain protein irx-2 (iroquois homeobox protein 2) (fragment). [swissprot;acc:q9bzi1] 8966.8 9445.26
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] High confidence 4533.74 5279.4 1.16447
389 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Low confidence 8159.97 8595.12 1.05333
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] High confidence 4533.74 5279.4 1.16447
390 rw1 protein (fragment). [swissprot;acc:q92545]
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Low confidence 6983.51 7354.87 1.05318
391 tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] High confidence 3658.76 3144.39 1.16358
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Low confidence 8552.2 9004.53 1.05289
392 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] High confidence 3641.89 4236.95 1.16339
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Low confidence 7781.34 8192.41 1.05283
393 cryptochrome 1 (photolyase-like). [refseq;acc:nm_004075] 8673.83 9132.05

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/