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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Filtered Rank Gene green Value Type description Network Comparison Type network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 77072 in total
Filtered  : 0
Rank
green
Value Type
description
Network Comparison Type
network_comparison
Interaction Map
red
66 6909 Ranked nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Subtracted 2921 High confidence 9830
8270.5 blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] 3019.5 Low confidence 11290
10030.4 kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Divided 1.26584 7923.89
13809 Measured fibrillin 3. [refseq;acc:nm_032447] Subtracted 437 High confidence 14246
15180 Ranked heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Divided 1.32449 11461
57580.1 Squared ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Subtracted 3752.9 Low confidence 61333
67 12.9538 Rooted alpha 2 globin. [refseq;acc:nm_000517] Divided 1.41698 18.3553
14.4058 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted 6.50517 High confidence 7.90063
15.2519 Squared tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Divided 3.33542 Low confidence 50.8715
15.3166 Rooted isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 1.39177 High confidence 11.0051
21.1366 tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105] Subtracted 4.681 Low confidence 16.4556
142.417 Measured 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Divided 1.89769 270.264
190.865 Squared filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 3.1865 High confidence 608.191
898 Measured 1.78508 1603
1971.25 similar to zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [refseq;acc:nm_145233] Subtracted 383.14 Low confidence 2354.39
3763.18 Squared udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 2360.1 High confidence 6123.28
4320.09 Measured purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 435.23 4755.32
10324.5 Ranked protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 2996 Low confidence 13320.5
11823.3 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 2890.74 High confidence 8932.56
14291.5 presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Divided 1.32408 10793.5
14697.6 dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 1.26309 Low confidence 11636.2
21426.5 Squared solute carrier family 2, facilitated glucose transporter, member 11 (glucose transporter type 11) (glucose transporter type 10). [swissprot;acc:q9byw1] Subtracted 3746.5 17680
68 0.00001 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 3136000 High confidence 31.36
8.63381 Rooted alpha crystallin a chain. [swissprot;acc:p02489] 1.38766 6.22183
12.9627 hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] 1.41651 Low confidence 18.3618
15.1833 Squared 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 3.33538 50.642
18.9308 Rooted glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Subtracted 4.6319 14.2989
87.2238 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 6.3871 High confidence 93.6109
351.772 Measured protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Divided 1.76802 198.964
734 nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483] 1.86294 Low confidence 394
1971.25 zinc finger protein 222. [swissprot;acc:q9uk12] Subtracted 383.14 2354.39
3763.18 Squared udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 2360.1 High confidence 6123.28
6019.79 Measured folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 432.87 6452.66
9824.6 Ranked repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Divided 1.25899 Low confidence 7803.58
11823.3 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 1.32362 High confidence 8932.56
12378.5 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Subtracted 2929.23 Low confidence 9449.27
17098 40s ribosomal protein s26. [swissprot;acc:p02383] 2828.3 High confidence 14269.7
21397.2 Squared solute carrier family 2, facilitated glucose transporter, member 5 (glucose transporter type 5, small intestine) (fructose transporter). [swissprot;acc:p22732] 3739.5 Low confidence 17657.7
69 12.9659 Rooted myoglobin. [swissprot;acc:p02144] Divided 1.41635 18.3642
13.5207 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 1.38596 High confidence 18.7392
17.6725 tigger transposable element derived 6. [refseq;acc:nm_030953] Subtracted 4.612 Low confidence 13.0605
18.0183 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 6.1743 High confidence 11.844
50.7408 Squared protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Divided 3.12432 16.2406
70.5 Measured tubulointerstitial nephritis antigen. [refseq;acc:nm_014464] 1.82979 Low confidence 129
139 phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Subtracted 431 High confidence 570
253.857 Squared tolloid-like 1. [refseq;acc:nm_012464] Divided 3.26573 Low confidence 77.7335
1971.21 Measured zinc finger protein 223. [swissprot;acc:q9uk11] Subtracted 383.13 2354.34
2804 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Divided 1.7602 High confidence 1593
3763.18 Squared udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] Subtracted 2360.1 6123.28
6909 Ranked nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 2921 Low confidence 9830

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/