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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Network Comparison Type Value Type Interaction Map red network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 951 to 1000 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
476 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Divided 226.681 1.07527 210.814
Subtracted 15.867
477 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 220.183 15.832 236.015
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Divided 251.926 1.0741 234.547
478 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] Subtracted 220.171 15.808 235.979
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] Divided 228.051 1.07409 212.321
479 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Subtracted 220.172 15.808 235.98
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Divided 228.051 1.07409 212.321
480 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 1.07405 254.667
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Subtracted 220.172 15.808 235.98
481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Divided 237.109 1.07405 254.667
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Subtracted 220.171 15.808 235.979
482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Divided 237.109 1.07405 254.667
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Subtracted 220.161 15.789 235.95
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 237.109 1.07405 254.667
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 228.051 15.73 212.321
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Divided 237.109 1.07405 254.667
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 228.051 15.73 212.321
485 60s ribosomal protein l18. [swissprot;acc:q07020] Divided 237.109 1.07405 254.667
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Subtracted 231.276 15.649 215.627
486 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 248.866 15.579 233.287
mct-1 protein. [refseq;acc:nm_014060] Divided 226.313 1.07387 243.03
487 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Subtracted 238.529 15.57 254.099
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Divided 226.313 1.07387 243.03
488 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Subtracted 82.5916 15.4632 98.0548
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 225.026 1.07258 209.798
489 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Subtracted 82.5916 15.4632 98.0548
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 231.276 1.07257 215.627
490 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Subtracted 242.531 15.395 227.136
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Divided 220.183 1.0719 236.015
491 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 150.959 15.392 166.351
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Divided 251.83 1.07184 234.951
492 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted 150.982 15.39 166.372
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 220.171 1.0718 235.979
493 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] 220.172 235.98
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Subtracted 236.751 15.287 252.038
494 metaxin 2. [swissprot;acc:o75431] 219.537 15.256 234.793
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Divided 220.172 1.0718 235.98
495 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 220.171 235.979
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Subtracted 222.146 15.247 237.393
496 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 15.239 250.419
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Divided 250.938 1.07177 234.134
497 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514
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 225.026 15.228 209.798
498 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Divided 220.161 1.07172 235.95
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Subtracted 237.28 15.212 252.492
499 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Divided 231.496 1.0715 248.048
500 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 1.07127 240.673
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 237.28 15.212 252.492

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/