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 Interaction Map Filtered Network Comparison Type green red network_comparison
Results: HTML CSV LaTeX Showing element 2632 to 2681 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Interaction Map
Filtered
green
red
network_comparison
710 rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Low confidence 1 8158.36 7822.22 1.04297
711 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] 8182.77 8534.3 1.04296
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 0 5607.7 5699.32 1.01634
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] High confidence 1 5944.25 5317.78 1.11781
712 double c2-like domains, beta. [refseq;acc:nm_003585] Low confidence 0 2017.07 2049.53 1.01609
mitogen-activated protein kinase kinase kinase 3 (ec 2.7.1.-) (mapk/erk kinase kinase 3) (mek kinase 3) (mekk 3). [swissprot;acc:q99759] 1 8636.93 8281.14 1.04296
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] High confidence 5944.25 5317.78 1.11781
713 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Low confidence 7586.18 7273.8 1.04295
synaptotagmin iii (sytiii). [swissprot;acc:q9bqg1] 0 2021.15 2053.54 1.01603
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] High confidence 1 4465.61 3996.81 1.11729
714 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Low confidence 0 2058.14 2090.86 1.0159
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] High confidence 1 5834.57 5222.71 1.11715
sam and sh3 domain containing 1. [refseq;acc:nm_015278] Low confidence 8183.02 8534.42 1.04294
715 dendritic cell protein. [refseq;acc:nm_006360] High confidence 7364.55 6593.17 1.117
mitogen-activated protein kinase kinase kinase 2 (ec 2.7.1.-) (mapk/erk kinase kinase 2) (mek kinase 2) (mekk 2). [swissprot;acc:q9y2u5] Low confidence 8635.76 8280.29 1.04293
th1-like; th1 drosophila homolog; th1-like (drosophila homolog); negative elongation factor proteins c and d. [refseq;acc:nm_016397] 0 9504.83 9654.03 1.0157
716 diaphanous protein homolog 1 (diaphanous-related formin 1) (drf1). [swissprot;acc:o60610] 1 8431.08 8084.21 1.04291
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] 0 3156.83 3108.28 1.01562
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] High confidence 1 7364.55 6593.17 1.117
717 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
forkhead box protein c2 (forkhead-related protein fkhl14) (mesenchyme fork head protein 1) (mfh-1 protein) (transcription factor fkh-14). [swissprot;acc:q99958] Low confidence 0 2074.73 2107.1 1.0156
sestrin 3. [swissprot;acc:p58005] 1 8453.94 8106.21 1.0429
718 cpz gene product. [refseq;acc:nm_003652] High confidence 7364.55 6593.17 1.117
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Low confidence 0 1906.74 1877.89 1.01536
sestrin 2 (hi95). [swissprot;acc:p58004] 1 8453.96 8106.17 1.0429
719 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] High confidence 7364.55 6593.17 1.117
flotillin-1. [swissprot;acc:o75955] Low confidence 8453.92 8106.26 1.04289
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 0 2827.2 2784.62 1.01529
720 atp-dependent helicase ddx8 (rna helicase hrh1) (deah-box protein 8). [swissprot;acc:q14562] 1 8286.99 7946.35 1.04287
forkhead box protein l1 (forkhead-related protein fkhl11) (forkhead- related transcription factor 7) (freac-7). [swissprot;acc:q12952] 0 2076.43 2107.93 1.01517
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] High confidence 1 7364.55 6593.17 1.117
721 forkhead box protein d4-like 1. [swissprot;acc:q9nu39] Low confidence 0 2077.47 2108.44 1.01491
oxysterol-binding protein 1. [swissprot;acc:p22059] 1 8962.95 8594.6 1.04286
syntaxin 7. [swissprot;acc:o15400] High confidence 6233.52 5580.97 1.11692
722 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 9002.33 8061.05 1.11677
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Low confidence 0 2071.38 2040.98 1.01489
sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 1 8453.87 8106.39 1.04286
723 forkhead box protein d4b (myeloid factor-gamma). [swissprot;acc:q8wxt5] 0 2077.61 2108.51 1.01487
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] High confidence 1 8996.46 8056.09 1.11673
oxysterol-binding protein 2 (oxysterol binding protein-related protein 4) (osbp-related protein 4) (orp-4). [swissprot;acc:q969r2] Low confidence 8958.94 8591.36 1.04278
724 forkhead box protein d4 (forkhead-related protein fkhl9) (forkhead- related transcription factor 5) (freac-5) (myeloid factor-alpha). [swissprot;acc:q12950] 0 2077.88 2108.64 1.0148
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] High confidence 1 6012.82 5384.41 1.11671
rest corepressor. [refseq;acc:nm_015156] Low confidence 9149.63 8774.84 1.04271
725 iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] 8228.85 7892.07 1.04267
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 0 2171.71 2140.04 1.0148
phenylalanine-trna synthetase. [refseq;acc:nm_006567] High confidence 1 6012.82 5384.41 1.11671
726 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 7064.13 6327.86 1.11635
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Low confidence 8477.45 8130.72 1.04264
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 0 1904.79 1877.52 1.01452
727 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 1 8803.2 8443.4 1.04261

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/