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 732 to 781 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
366 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Low confidence 207.433 199.944 1.03746
367 heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] High confidence 234.146 256.627 1.09601
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Low confidence 206.945 199.503 1.0373
368 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] 219.655 211.763 1.03727
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] High confidence 242.66 265.715 1.09501
369 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 1.09475
mad protein (max dimerizer). [swissprot;acc:q05195] Low confidence 205.943 198.554 1.03721
370 af-4 protein (proto-oncogene af4) (fel protein). [swissprot;acc:p51825] 219.597 211.722 1.0372
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] High confidence 242.159 265.104 1.09475
371 fragile x mental retardation 2 protein (protein fmr-2) (fmr2p) (ox19 protein) (fragile x e mental retardation syndrome protein). [swissprot;acc:p51816] Low confidence 219.599 211.723 1.0372
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] High confidence 186.52 170.42 1.09447
372 laf-4 protein (lymphoid nuclear protein related to af4). [swissprot;acc:p51826] Low confidence 219.598 211.722 1.0372
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] High confidence 186.52 170.42 1.09447
373 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 242.37 265.255 1.09442
all1 fused gene from 5q31. [refseq;acc:nm_014423] Low confidence 219.598 211.722 1.0372
374 excision repair protein ercc-6 (cockayne syndrome protein csb). [swissprot;acc:q03468] 210.34 202.797 1.03719
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] High confidence 267.208 244.168 1.09436
375 dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 242.686 265.516 1.09407
spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] Low confidence 219.556 211.692 1.03715
376 nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] 209.328 201.83
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] High confidence 257.017 234.945 1.09395
377 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 242.691 265.481 1.09391
l-lactate dehydrogenase a-like (ec 1.1.1.27). [swissprot;acc:q9byz2] Low confidence 205.928 198.554 1.03714
378 60s ribosomal protein l30. [swissprot;acc:p04645] High confidence 242.593 265.365 1.09387
l-lactate dehydrogenase c chain (ec 1.1.1.27) (ldh-c) (ldh testis subunit) (ldh-x). [swissprot;acc:p07864] Low confidence 205.928 198.554 1.03714
379 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] High confidence 241.509 264.163 1.0938
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] Low confidence 205.928 198.554 1.03714
380 l-lactate dehydrogenase b chain (ec 1.1.1.27) (ldh-b) (ldh heart subunit) (ldh-h). [swissprot;acc:p07195]
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] High confidence 242.109 264.79 1.09368
381 clip-associating protein 1; drosophila 'multiple asters' (mast)-like homolog 1. [refseq;acc:nm_015282] Low confidence 205.928 198.554 1.03714
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] High confidence 200.586 183.423 1.09357
382 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Low confidence 205.926 198.554 1.03713
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] High confidence 200.791 183.66 1.09328
383 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Low confidence 205.921 198.554 1.0371
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] High confidence 237.862 217.739 1.09242
384 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Low confidence 205.918 198.554 1.03709
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] High confidence 266.421 244.236 1.09083
385 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Low confidence 201.176 193.984 1.03708
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] High confidence 266.421 244.236 1.09083
386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Low confidence 205.821 198.494 1.03691
387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] High confidence 242.238 264.11 1.09029
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Low confidence 200.057 192.938 1.0369
388 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 200.049 192.942 1.03683
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 227.575 208.756 1.09015
389 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Low confidence 200.049 192.942 1.03683
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] High confidence 227.575 208.756 1.09015
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
solute carrier family 35, member e2. [refseq;acc:nm_182838] Low confidence 203.647 211.144 1.03681
391 40s ribosomal protein s16. [swissprot;acc:p17008] High confidence 241.828 263.62 1.09011

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/