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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1150 to 1199 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
288 CPSF3 Measured cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 23422.4 19380.3 1.20857
CSRP3 Rooted lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 51.8789 46.3416 1.11949
KHDRBS1 Squared kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 6693.64 8564.94 1.27956
289 no value Ranked hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 272.781 246.892 1.10486
KHDRBS2 Squared kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 6693.64 8564.94 1.27956
LSM6 Measured u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 4682.88 5646.19 1.20571
PRPF31 Rooted pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 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 Squared 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 15734.4 20126.8 1.27916
RRM2 Ranked ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 231.969 210.064 1.10428
TFIP11 Measured tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 4991.48 6014.08 1.20487
291 no value Rooted ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 113.983 101.979 1.11771
CLEC3B Squared tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 59016.1 75486.9 1.27909
NFYB Ranked 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] 251.679 228.037 1.10368
UBAC1 Measured putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 36927.5 1.20481
292 LSM6 Rooted u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 56.48 63.119 1.11755
NEURL Squared neuralized-like. [refseq;acc:nm_004210] 6828.26 8728.66 1.27831
NUBP1 Measured nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 4641.09 5588.75 1.20419
RPS15A Ranked 40s ribosomal protein s15a. [swissprot;acc:p39027] 241.411 266.414 1.10357
293 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 240.782 265.717 1.10356
KYNU Squared kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 35991.8 46002.9 1.27815
NUBP2 Measured nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 4641.09 5588.75 1.20419
TRPC4 Rooted short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 63.0715 56.4506 1.11729
294 AGPAT2 Squared 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] 30826.5 39383.9 1.2776
BCCIP Ranked 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] 240.782 265.717 1.10356
CSTF3 Measured cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 22515.5 18702.6 1.20387
DVL1 Rooted segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 59.0296 65.951 1.11725
295 no value Squared 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] 30807.7 39351.7 1.27733
DVL2 Rooted segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 59.029 65.9421 1.11711
RGL1 Measured ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 13261.9 11017.8 1.20368
SCYE1 Ranked multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 223.273 202.423 1.103
296 MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 241.282 266.12 1.10294
SF3A2 Measured splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 4911.81 5909.18 1.20306
TBC1D10A Rooted ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 63.0663 56.4667 1.11688
WAS Squared wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 28878.8 36783.5 1.27372
297 no value Ranked 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 259.984 1.1029
KLF5 Measured 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] 4911.81 5909.18 1.20306
RPS6KC1 Squared ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 14247.4 18142.1 1.27336
TRPC5 Rooted short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 63.0663 56.4667 1.11688
298 no value Measured u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 4633.92 5572.85 1.20262
Squared ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 14247.4 18142.1 1.27336
CAPN2 Ranked 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] 268.632 243.588 1.10281
SART1 Rooted 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] 57.6823 64.4212 1.11683
299 no value Measured ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 4914.27 5907.12 1.20203
CAPN1 Ranked calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 268.635 243.592 1.10281
CRK Squared proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 28896.2 36767 1.27238
DVL3 Rooted segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 59.026 65.8955 1.11638
300 ABL2 Squared tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 28896.2 36767 1.27238
MKI67IP Rooted mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 48.1584 53.7378 1.11586
PITRM1 Ranked metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 150.959 166.351 1.10196

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/