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 Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 963 to 1012 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Divided 254.667 237.109 1.07405
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Subtracted 235.95 220.161 15.789
483 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Divided 254.667 237.109 1.07405
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Subtracted 212.321 228.051 15.73
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Divided 254.667 237.109 1.07405
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 212.321 228.051 15.73
485 60s ribosomal protein l18. [swissprot;acc:q07020] Divided 254.667 237.109 1.07405
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Subtracted 215.627 231.276 15.649
486 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 233.287 248.866 15.579
mct-1 protein. [refseq;acc:nm_014060] Divided 243.03 226.313 1.07387
487 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Subtracted 254.099 238.529 15.57
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Divided 243.03 226.313 1.07387
488 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Subtracted 98.0548 82.5916 15.4632
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Divided 209.798 225.026 1.07258
489 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Subtracted 98.0548 82.5916 15.4632
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 215.627 231.276 1.07257
490 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Subtracted 227.136 242.531 15.395
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Divided 236.015 220.183 1.0719
491 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 166.351 150.959 15.392
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Divided 234.951 251.83 1.07184
492 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted 166.372 150.982 15.39
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Divided 235.979 220.171 1.0718
493 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] 235.98 220.172
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Subtracted 252.038 236.751 15.287
494 metaxin 2. [swissprot;acc:o75431] 234.793 219.537 15.256
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Divided 235.98 220.172 1.0718
495 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 235.979 220.171
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Subtracted 237.393 222.146 15.247
496 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 250.419 235.18 15.239
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Divided 234.134 250.938 1.07177
497 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 234.514 251.344
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Subtracted 209.798 225.026 15.228
498 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Divided 235.95 220.161 1.07172
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Subtracted 252.492 237.28 15.212
499 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Divided 248.048 231.496 1.0715
500 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 240.673 224.662 1.07127
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 252.492 237.28 15.212
501 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Divided 255.68 238.704 1.07112
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Subtracted 252.492 237.28 15.212
502 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Divided 255.68 238.704 1.07112
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Subtracted 252.492 237.28 15.212
503 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Divided 255.68 238.704 1.07112
504 homeobox protein barh-like 2. [swissprot;acc:q9umq3] Subtracted 252.492 237.28 15.212
oligophrenin 1. [swissprot;acc:o60890] Divided 255.68 238.704 1.07112
505 ad24 protein. [refseq;acc:nm_022451] 234.672 251.334 1.071
zinc finger protein t86. [swissprot;acc:o00488] Subtracted 231.796 246.805 15.009
506 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 230.07 215.237 14.833
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Divided 240.476 224.535 1.071

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/