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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 951 to 1000 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
476 KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Divided 226.681 210.814 1.07527
Subtracted 15.867
477 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 220.183 236.015 15.832
NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Divided 251.926 234.547 1.0741
478 BRF1 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] 228.051 212.321 1.07409
PAK2 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 220.171 235.979 15.808
479 COG5 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
NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Divided 228.051 212.321 1.07409
480 NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Subtracted 220.172 235.98 15.808
481 NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Divided 237.109 254.667 1.07405
PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Subtracted 220.171 235.979 15.808
482 ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] 220.161 235.95 15.789
HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Divided 237.109 254.667 1.07405
483 BRF1 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 228.051 212.321 15.73
RUNX2 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 237.109 254.667 1.07405
484 HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 228.051 212.321 15.73
485 PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 231.276 215.627 15.649
RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] Divided 237.109 254.667 1.07405
486 EIF6 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Subtracted 248.866 233.287 15.579
MCTS1 mct-1 protein. [refseq;acc:nm_014060] Divided 226.313 243.03 1.07387
487 MDH2 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Subtracted 238.529 254.099 15.57
MRPL22 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Divided 226.313 243.03 1.07387
488 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Subtracted 82.5916 98.0548 15.4632
SART1 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 225.026 209.798 1.07258
489 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Subtracted 82.5916 98.0548 15.4632
PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 231.276 215.627 1.07257
490 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 220.183 236.015 1.0719
SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Subtracted 242.531 227.136 15.395
491 GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Divided 251.83 234.951 1.07184
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 150.959 166.351 15.392
492 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 150.982 166.372 15.39
PAK2 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 220.171 235.979 1.0718
493 COG5 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
ZNRD1 zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Subtracted 236.751 252.038 15.287
494 MTX2 metaxin 2. [swissprot;acc:o75431] 219.537 234.793 15.256
PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Divided 220.172 235.98 1.0718
495 PAK3 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
YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Subtracted 222.146 237.393 15.247
496 no value dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 15.239
PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Divided 250.938 234.134 1.07177
497 EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514
SART1 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 225.026 209.798 15.228
498 ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Divided 220.161 235.95 1.07172
TLX3 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Subtracted 237.28 252.492 15.212
499 BARX1 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
TPI1 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Divided 231.496 248.048 1.0715
500 ING2 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 240.673 1.07127
OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 237.28 252.492 15.212

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
- Hugo is the HGNC identifier if it exists
- 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/