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 Rank Value Type description Interaction Map Filtered Network Comparison Type green red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 38536 in total
Network Comparison Type  : Divided
Rank
Value Type
description
Interaction Map
Filtered
green
red
network_comparison
29 Measured potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 0 434.911 111.278 3.90833
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Low confidence 1 3739.84 3121.28 1.19818
Ranked cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 170.557 203.115 1.19089
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] High confidence 0 11625 7395 1.57201
solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246] Low confidence 8687.07 12129.6 1.39628
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] High confidence 1 243.678 187.458 1.29991
Squared chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 457.521 143.692 3.18404
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Low confidence 0 0.355148 3.41692 9.62112
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 1 61881.5 82347.8 1.33073
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] High confidence 0 141.427 5.18438 27.2794
Rooted cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Low confidence 1 56.7071 48.8531 1.16077
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 0 6.85565 11.9583 1.7443
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] High confidence 7.34614 17.7955 2.42243
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 1 43.1914 26.0288 1.65937
30 Measured bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 43509.4 36474.3 1.19288
dystrophin. [swissprot;acc:p11532] High confidence 0 111.739 427.217 3.82335
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 1 895.633 1834.59 2.04837
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Low confidence 0 35.5 105.5 2.97183
Ranked alpha 2 globin. [refseq;acc:nm_000517] 15987.1 11486.2 1.39185
bcl2-related ovarian killer. [refseq;acc:nm_032515] 1 223.235 265.638 1.18995
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] High confidence 0 11625 7395 1.57201
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 1 243.678 187.457 1.29991
Squared cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 457.521 143.692 3.18404
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Low confidence 61881.5 82347.8 1.33073
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 0 0.355148 3.41692 9.62112
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 141.944 6.25494 22.6931
Rooted cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Low confidence 1 56.7253 48.8781 1.16055
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] High confidence 43.1914 26.0288 1.65937
protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] Low confidence 0 7.5 13.0622 1.74163
ptd016 protein. [refseq;acc:nm_016125] High confidence 12.5698 5.47723 2.29492
31 Measured dok-like protein. [refseq;acc:nm_024872] 0.00001 35 3500000
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 895.697 1834.63 2.04827
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Low confidence 0 35.5 105.5 2.97183
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 1 43503.3 36469.3 1.19287
Ranked deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 48.8186 57.395 1.17568
hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] 0 15984.3 11485.6 1.39168
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] High confidence 5266.67 8082.33 1.53462
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 1 243.677 187.458 1.2999
Squared beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 25146.6 9924.76 2.53372
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 0 103.726 5.54059 18.7211
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Low confidence 1 61881.5 82347.8 1.33073
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 0 0.355148 3.41692 9.62112
Rooted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1 168.796 145.551 1.1597
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] High confidence 0 27.8029 12.1655 2.28539
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 1 43.1914 26.0288 1.65937
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Low confidence 0 12.7411 7.3589 1.73139
32 Measured cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] High confidence 184 598 3.25
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 1 895.893 1834.73 2.04793
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Low confidence 0 35.5 105.5 2.97183
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 43368.8 36360.3 1.19275

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/