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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Gene Value Type Rank description Filtered Interaction Map Network Comparison Type network_comparison green red
Results: HTML CSV LaTeX Showing element 601 to 650 of 14920 in total
Value Type  : Measured
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
description
Filtered
network_comparison
green
red
301 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1 1.20078 11466 13768.2
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 0 1.10405 149.371 135.294
302 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 1 1.19999 7073.65 5894.75
303 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 1.1998 18560.4 22268.8
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 0 1.10256 863.886 952.488
304 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 1 1.19958 5824.52 4855.46
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] 0 1.10224 5469.68 4962.34
305 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 1 1.19912 4624.15 3856.29
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] 0 1.10224 5469.68 4962.34
306 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 1.10211 1547.2 1705.19
pnas-18. [sptrembl;acc:q9bzu3] 1 1.19903 11409.6 13680.5
307 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 0 1.10183 3775.43 4159.87
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 1 1.19892 14824.9 12365.2
308 neurocalcin delta. [swissprot;acc:p29554] 0 1.10136 773.218 702.055
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 1 1.19878 5966.44 4977.09
309 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 1.19855 5966.14 4977.8
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 0 1.10104 2081.91 1890.86
310 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 1.10075 4320.09 4755.32
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] 1 1.19736 5878.79 4909.79
311 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 1.19734 5964.58 4981.52
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 0 1.09994 2833.94 3117.17
312 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 1.0998 3800.29 3455.43
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 1 1.19622 5500.48 4598.21
313 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 0 1.09921 6739.34 6131.07
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 1 1.1959 18098.7 21644.2
314 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 1.19583 18090 21632.5
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 0 1.09839 4827.7 5302.7
315 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 1.09796 1104.61 1212.82
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 1 1.19413 17896.5 21370.8
316 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 0 1.09714 576 525
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 1 1.19413 17896.5 21370.8
317 adiponectin receptor 2. [refseq;acc:nm_024551] 1.19329 3762.56 3153.1
my016 protein. [sptrembl;acc:q9h3k6] 0 1.09579 1615.47 1770.21
318 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 1.19318 40795.8 34190.9
protein cgi-147. [swissprot;acc:q9y3e5] 0 1.09484 9192.38 8396.12
319 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 1.09483 1268.19 1388.45
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 1 1.19117 24908.5 20911
320 ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] 0 1.09452 156.3 142.802
321 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 1.09333 686.693 628.072
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 1 1.19117 24908.5 20911
322 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 0 1.09249 1771.04 1621.1
anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 1 1.19117 24908.5 20911
323 histone deacetylase 2 (hd2). [swissprot;acc:q92769] 0 1.09139 2244.06 2056.14
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 1 1.1907 5501.94 4620.76
324 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 1.18912 33457.6 28136.5
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 0 1.09059 2784.08 3036.29
325 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 1 1.18899 19235.4 16177.9
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 0 1.09059 2784.59 3036.85

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/