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 1151 to 1200 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
288 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
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted 51.8789 46.3416 1.11949
289 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Ranked 272.781 246.892 1.10486
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
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 57.4274 64.2609 1.11899
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Measured 4682.88 5646.19 1.20571
290 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
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Rooted 75.6323 67.6572 1.11788
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Ranked 231.969 210.064 1.10428
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Measured 4991.48 6014.08 1.20487
291 nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Ranked 251.679 228.037 1.10368
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Measured 44490.5 36927.5 1.20481
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Squared 59016.1 75486.9 1.27909
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Rooted 113.983 101.979 1.11771
292 40s ribosomal protein s15a. [swissprot;acc:p39027] Ranked 241.411 266.414 1.10357
neuralized-like. [refseq;acc:nm_004210] Squared 6828.26 8728.66 1.27831
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Measured 4641.09 5588.75 1.20419
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Rooted 56.48 63.119 1.11755
293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Ranked 240.782 265.717 1.10356
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Squared 35991.8 46002.9 1.27815
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Measured 4641.09 5588.75 1.20419
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Rooted 63.0715 56.4506 1.11729
294 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Squared 30826.5 39383.9 1.2776
brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Ranked 240.782 265.717 1.10356
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Measured 22515.5 18702.6 1.20387
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted 59.0296 65.951 1.11725
295 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Squared 30807.7 39351.7 1.27733
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Ranked 223.273 202.423 1.103
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Measured 13261.9 11017.8 1.20368
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted 59.029 65.9421 1.11711
296 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 63.0663 56.4667 1.11688
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Ranked 241.282 266.12 1.10294
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured 4911.81 5909.18 1.20306
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared 28878.8 36783.5 1.27372
297 60s ribosomal protein l7. [swissprot;acc:p18124] Ranked 235.727 259.984 1.1029
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] Measured 4911.81 5909.18 1.20306
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Squared 14247.4 18142.1 1.27336
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Rooted 63.0663 56.4667 1.11688
298 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Ranked 268.632 243.588 1.10281
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Squared 14247.4 18142.1 1.27336
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] Rooted 57.6823 64.4212 1.11683
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Measured 4633.92 5572.85 1.20262
299 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 4914.27 5907.12 1.20203
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Ranked 268.635 243.592 1.10281
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared 28896.2 36767 1.27238
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted 59.026 65.8955 1.11638
300 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Ranked 150.959 166.351 1.10196
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Rooted 48.1584 53.7378 1.11586
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Squared 28896.2 36767 1.27238
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Measured 4914.27 5907.12 1.20203

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/