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 1251 to 1300 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
313 PPP1R2 Measured protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 21644.2 18098.7 1.1959
RRM2B Ranked ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 232.473 211.207 1.10069
314 FZR1 Squared fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 71576.8 56326.7 1.27074
METAP1 Ranked methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 268.604 1.10027
MYH3 Rooted myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 95.0526 85.3206 1.11406
PPP1R2P9 Measured type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 21632.5 18090 1.19583
315 METAP2 Ranked methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] 244.126 268.604 1.10027
MYH1 Rooted myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 95.0526 85.3206 1.11406
PCSK5 Squared proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] 71576.8 56326.7 1.27074
RRS1 Measured ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 21370.8 17896.5 1.19413
316 no value Rooted myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 95.0526 85.3206 1.11406
EIF1 Ranked protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 242.694 267.017 1.10022
PPP1CA Measured serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 21370.8 17896.5 1.19413
WASL Squared neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 28918.3 36746 1.27068
317 no value Ranked splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 224.445 204.044 1.09998
ADIPOR2 Measured adiponectin receptor 2. [refseq;acc:nm_024551] 3153.1 3762.56 1.19329
MYH7B Rooted dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 95.0526 85.3206 1.11406
NME3 Squared nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 33982.3 43159.1 1.27005
318 no value Measured nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 34190.9 40795.8 1.19318
MRPL3 Ranked mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 242.011 266.18 1.09987
MYH13 Rooted myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 95.0526 85.3206 1.11406
TOMM20 Squared mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 46739.9 59134.5 1.26518
319 NIP7 Rooted saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 49.0663 54.4978 1.1107
PEX19 Squared peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 46739.9 59134.5 1.26518
RPL19 Ranked 60s ribosomal protein l19. [swissprot;acc:p14118] 240.73 264.729 1.09969
RRAGA Measured ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 20911 24908.5 1.19117
320 no value Rooted 40s ribosomal protein s29. [swissprot;acc:p30054] 50.2784 45.294 1.11005
CDH1 Ranked epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 241.892 265.96 1.0995
EPHX1 Squared epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] 87971.9 69563.1 1.26463
RRAGC Measured ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 20911 24908.5 1.19117
321 no value Ranked c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 241.892 265.959 1.09949
Rooted u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 55.9231 62.0565 1.10968
NME2P1 Squared putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 33526 42390.2 1.2644
RRAGB Measured ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 20911 24908.5 1.19117
322 ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
DNASE2B Ranked deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 86.7483 78.8995 1.09948
GIPC1 Rooted rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 60.594 67.2244 1.10942
NME2 Squared nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] 33522.8 42384.8 1.26436
323 no value Ranked 60s ribosomal protein l23a. [swissprot;acc:p29316] 241.884 265.945 1.09947
Squared nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] 33514.4 42370.8 1.26426
LSM4 Measured u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 4620.76 5501.94 1.1907
PCYT1A Rooted cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 50.3803 45.4193 1.10923
324 DNASE2B Measured deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 28136.5 33457.6 1.18912
FLAD1 Rooted fad synthetase. [refseq;acc:nm_025207] 50.3803 45.4193 1.10923
HARS2 Squared histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 34527.9 43507.9 1.26008
RPS23 Ranked 40s ribosomal protein s23. [swissprot;acc:p39028] 243.944 268.195 1.09941
325 no value Rooted bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 50.3803 45.4193 1.10923
HARS Squared histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 34506.3 43476 1.25994
MRPS12 Ranked 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 243.944 268.195 1.09941
SEPT8 Measured septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 16177.9 19235.4 1.18899

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/