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 description Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 451 to 500 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
network_comparison
green
113 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Subtracted Low confidence 224.763 14.197 210.566
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] High confidence 194.372 39.832 234.204
114 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 58 14 44
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] High confidence 229.818 37.447 267.265
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Divided Low confidence 197.779 1.07182 211.983
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 332.874 1.24557 267.246
115 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Low confidence 197.779 1.07182 211.983
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Subtracted High confidence 277.546 37.085 240.461
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 332.874 1.24557 267.246
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Subtracted Low confidence 58 14 44
116 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Divided High confidence 268.565 1.24545 334.483
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Subtracted 208.52 36.925 171.595
testican-3 precursor. [swissprot;acc:q9bq16] Low confidence 220.395 13.994 234.389
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Divided 204.161 1.07008 190.791
117 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] 226.395 1.06935 211.713
high-mobility group 20a. [refseq;acc:nm_018200] Subtracted High confidence 208.588 36.81 171.778
neuralized-like. [refseq;acc:nm_004210] Divided 332.326 1.24491 266.948
striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Subtracted Low confidence 225.495 13.966 211.529
118 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Divided High confidence 284.753 1.24382 228.934
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Subtracted 274.027 36.237 237.79
protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Divided Low confidence 226.395 1.06935 211.713
testican-1 precursor (spock protein). [swissprot;acc:q08629] Subtracted 220.254 13.857 234.111
119 adiponectin receptor 2. [refseq;acc:nm_024551] High confidence 281.582 35.211 246.371
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 318.982 1.23157 259.004
natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 225.666 1.06897 211.107
testican-2 precursor. [swissprot;acc:q92563] Subtracted 220.222 13.825 234.047
120 nanos (fragment). [sptrembl;acc:q8wy41] 203.66 13.819 217.479
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] High confidence 227.199 34.484 192.715
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 269.278 1.21699 327.709
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence 203.016 1.0687 189.965
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] High confidence 269.254 1.2169 327.655
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted 227.202 34.379 192.823
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Divided Low confidence 203.007 1.06854 189.985
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Subtracted 203.914 13.725 190.189
122 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] High confidence 199.949 34.238 234.187
nanos (fragment). [sptrembl;acc:q8wy41] Divided Low confidence 203.66 1.06785 217.479
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] High confidence 269.248 1.21688 327.642
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Subtracted Low confidence 204.161 13.37 190.791
123 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided High confidence 269.23 1.21681 327.601
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Low confidence 202.96 1.06768 190.094
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted High confidence 227.032 33.976 193.056
striatin. [swissprot;acc:o43815] Low confidence 214.085 13.289 200.796
124 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 220.268 13.271 206.997
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided High confidence 208.52 1.21519 171.595
natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 224.763 1.06742 210.566
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted High confidence 285.684 33.45 252.234
125 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Divided Low confidence 213.243 1.0674 227.616
high-mobility group 20a. [refseq;acc:nm_018200] High confidence 208.588 1.21429 171.778
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Subtracted Low confidence 220.268 13.271 206.997
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] High confidence 285.684 33.45 252.234

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/