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 Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 825 to 874 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
52 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared Subtracted 1 173408 242989 69581
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 120.823 16.623
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] Divided 0 16.3095 25.3969 1.55718
neuralized-like. [refseq;acc:nm_004210] 1 27.9107 44.1656 1.58239
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 28994.2 17134.8 1.69212
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked Subtracted 350 290 60
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Squared Divided 0 1.22698 5.39669 4.39835
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] Measured Subtracted 2230.13 1729.7 500.43
53 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted Divided 11.844 18.0183 1.5213
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Ranked Subtracted 7230 10771 3541
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] Measured Divided 1 779.167 1390.33 1.78438
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Rooted Subtracted 0 25.8353 33.3747 7.5394
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared 1 173408 242989 69581
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Measured Divided 0 420.365 861.814 2.05016
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] Ranked Subtracted 1 318.982 259.004 59.978
Rooted Divided 30.8986 46.4619 1.50369
necdin. [swissprot;acc:q99608] Subtracted 137.446 120.823 16.623
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 23326.5 19296.4 4030.1
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared Divided 28994.2 17134.8 1.69212
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 0 0.458225 0.104379 4.39001
transcription factor jun-b. [swissprot;acc:p17275] Ranked 1 201.144 158.868 1.26611
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 0 3284 4554.5 1.38688
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Squared Subtracted 25325.5 29804.9 4479.4
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] Measured 2230.13 1729.7 500.43
54 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 1 185.678 245.247 59.569
deltex 2. [refseq;acc:nm_020892] Measured Divided 1618.84 2651.88 1.63814
exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 23316 19288.8 4027.2
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 0 638.862 330.189 1.93484
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Rooted 14.8299 22.5463 1.52033
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared Subtracted 1 173408 242989 69581
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 219048 129762 1.68808
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Rooted Subtracted 137.446 120.823 16.623
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 0 52.3183 44.8382 7.4801
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Ranked 10793.5 14291.5 3498
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted Divided 1 40.0958 58.7986 1.46645
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Squared 0 295.992 69.1109 4.28286
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Subtracted 25325.5 29804.9 4479.4
syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked Divided 13884.4 19014.6 1.36949
transcription factor jun-d. [swissprot;acc:p17535] 1 200.941 158.941 1.26425
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] Measured Subtracted 0 2230.13 1729.7 500.43
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Divided 1 1629.21 2662.12 1.63399
Squared 0 468.221 113.017 4.14293
Rooted 24.4683 16.281 1.50287
glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075] Measured Subtracted 2230.13 1729.7 500.43
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked 1 185.678 245.247 59.569
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared Divided 219048 129762 1.68808
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 173408 242989 69581
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured Divided 0 630.942 327.517 1.92644
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Rooted Subtracted 1 137.446 120.823 16.623
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Ranked 0 22038 18578 3460

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/