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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1112 to 1161 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
278 RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Ranked 241.399 267.088 1.10642
279 GPSM2 mosaic protein lgn. [swissprot;acc:p81274] Measured 3119.98 2579.49 1.20953
MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Squared 15569.5 19953.6 1.28158
RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Ranked 252.644 228.42 1.10605
WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Rooted 66.0989 74.0609 1.12046
280 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 57.9068 64.8562 1.12001
MSI1 musashi 1. [refseq;acc:nm_002442] Squared 15569.5 19953.6 1.28158
MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Ranked 252.512 228.356 1.10578
RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Measured 3119.98 2579.49 1.20953
281 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Ranked 241.808 267.335 1.10557
GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Measured 3119.98 2579.49 1.20953
SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Rooted 57.9068 64.8562 1.12001
ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Squared 15569.5 19953.6 1.28158
282 CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 59704 76460.4 1.28066
RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Measured 3119.98 2579.49 1.20953
RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Ranked 252.39 228.297 1.10553
SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Rooted 57.9819 64.9302 1.11984
283 DTX2 deltex 2. [refseq;acc:nm_020892] Squared 6627.24 8484.19 1.2802
KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Rooted 57.9819 64.9302 1.11984
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Measured 5221.28 6314.35 1.20935
RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Ranked 241.828 267.346 1.10552
284 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 224.657 203.235 1.10541
CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Squared 59464 76120.8 1.28012
CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Rooted 51.8647 46.3161 1.1198
PXN paxillin. [swissprot;acc:p49023] Measured 5221.28 6314.35 1.20935
285 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked 224.647 203.242 1.10532
DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Rooted 48.4278 54.2262 1.11973
DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Squared 6680.89 8549.44 1.27969
PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 23326.5 19296.4 1.20885
286 CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Rooted 51.8717 46.3287 1.11965
EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Measured 23316 19288.8 1.20878
NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Ranked 224.633 203.251 1.1052
PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Squared 6693.64 8564.94 1.27956
287 KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]
PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 23303.1 19279.5 1.2087
RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked 240.758 266.079 1.10517
SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Rooted 51.8714 46.3281 1.11965
288 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked 240.758 266.078 1.10517
CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Measured 23422.4 19380.3 1.20857
CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted 51.8789 46.3416 1.11949
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Squared 6693.64 8564.94 1.27956
289 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Ranked 272.781 246.892 1.10486
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Squared 6693.64 8564.94 1.27956
LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Measured 4682.88 5646.19 1.20571
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 57.4274 64.2609 1.11899
290 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 75.6323 67.6572 1.11788
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Squared 15734.4 20126.8 1.27916
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Ranked 231.969 210.064 1.10428
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Measured 4991.48 6014.08 1.20487
291 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Rooted 113.983 101.979 1.11771

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/