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 1236 to 1285 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
309 SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Ranked 242.153 266.673 1.10126
310 no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Rooted 95.0526 85.3206 1.11406
CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Squared 28901.4 36762.1 1.27198
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] Measured 4909.79 5878.79 1.19736
SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Ranked 242.153 266.673 1.10126
311 AGPAT4 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Squared 30566.4 38866.5 1.27154
DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Measured 4981.52 5964.58 1.19734
EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Ranked 242.627 267.151 1.10108
MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted 95.0526 85.3206 1.11406
312 no value methyltransferase like 2. [refseq;acc:nm_018396] Squared 71576.8 56326.7 1.27074
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Measured 4598.21 5500.48 1.19622
MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Rooted 95.0526 85.3206 1.11406
RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Ranked 242.195 266.663 1.10103
313 DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Squared 71576.8 56326.7 1.27074
MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted 95.0526 85.3206 1.11406
PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured 21644.2 18098.7 1.1959
RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Ranked 232.473 211.207 1.10069
314 FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared 71576.8 56326.7 1.27074
METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Ranked 244.126 268.604 1.10027
MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Rooted 95.0526 85.3206 1.11406
PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Measured 21632.5 18090 1.19583
315 METAP2 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] Ranked 244.126 268.604 1.10027
MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Rooted 95.0526 85.3206 1.11406
PCSK5 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] Squared 71576.8 56326.7 1.27074
RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Measured 21370.8 17896.5 1.19413
316 no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Rooted 95.0526 85.3206 1.11406
EIF1 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Ranked 242.694 267.017 1.10022
PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Measured 21370.8 17896.5 1.19413
WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Squared 28918.3 36746 1.27068
317 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Ranked 224.445 204.044 1.09998
ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Measured 3153.1 3762.56 1.19329
MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Rooted 95.0526 85.3206 1.11406
NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Squared 33982.3 43159.1 1.27005
318 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Measured 34190.9 40795.8 1.19318
MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Ranked 242.011 266.18 1.09987
MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Rooted 95.0526 85.3206 1.11406
TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Squared 46739.9 59134.5 1.26518
319 NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Rooted 49.0663 54.4978 1.1107
PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Squared 46739.9 59134.5 1.26518
RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] Ranked 240.73 264.729 1.09969
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Measured 20911 24908.5 1.19117
320 no value 40s ribosomal protein s29. [swissprot;acc:p30054] Rooted 50.2784 45.294 1.11005
CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Ranked 241.892 265.96 1.0995
EPHX1 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Squared 87971.9 69563.1 1.26463
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured 20911 24908.5 1.19117
321 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Ranked 241.892 265.959 1.09949
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Rooted 55.9231 62.0565 1.10968
NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Squared 33526 42390.2 1.2644
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Measured 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]

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/