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 1513 to 1562 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
379 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Divided 0 11228.4 10806 1.03909
adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 1 241.509 264.163 1.0938
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Subtracted 0 11794.7 11375.4 419.3
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 1 248.152 267.226 19.074
380 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Divided 0 9566.15 9936.37 1.0387
bystin. [swissprot;acc:q13895] Subtracted 10833.3 11244.5 411.2
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 1 248.152 267.226 19.074
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Divided 242.109 264.79 1.09368
381 ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 0 9565.54 9935.19 1.03864
thymic stromal co-transporter. [refseq;acc:nm_033051] Subtracted 1 248.152 267.226 19.074
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Divided 200.586 183.423 1.09357
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Subtracted 0 10284.9 10695.6 410.7
382 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Divided 10449 10061.8 1.03848
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Subtracted 1 253.852 234.808 19.044
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] Divided 200.791 183.66 1.09328
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Subtracted 0 13607.6 13202 405.6
383 chromodomain y-like protein 2. [refseq;acc:nm_152342] Divided 10273.1 10665.1 1.03816
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 1 237.862 217.739 1.09242
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Subtracted 0 13571.2 13166.3 404.9
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 1 236.245 255.113 18.868
384 bystin. [swissprot;acc:q13895] Divided 0 10833.3 11244.5 1.03796
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Subtracted 8614.89 9017.27 402.38
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 1 227.575 208.756 18.819
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] Divided 266.421 244.236 1.09083
385 small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Subtracted 227.575 208.756 18.819
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Divided 0 10302.7 10686.7 1.03727
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Subtracted 12305.9 11904.9 401
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided 1 266.421 244.236 1.09083
386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
40s ribosomal protein s9. [swissprot;acc:p46781] Subtracted 238.986 257.784 18.798
calcyphosine. [swissprot;acc:q13938] 0 9874.54 9478.1 396.44
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Divided 10303.7 10687.4 1.03724
387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 1 242.238 264.11 1.09029
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Subtracted 0 12115.7 12508.3 392.6
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 1 56.6768 75.3531 18.6763
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Divided 0 10481.8 10869.5 1.03699
388 chromodomain y-like protein 2. [refseq;acc:nm_152342] Subtracted 10273.1 10665.1 392
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 1 56.7244 75.3948 18.6704
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Divided 0 9953.39 10320.9 1.03692
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 1 227.575 208.756 1.09015
389 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 0 11794.7 11375.4 1.03686
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 1 56.7252 75.3954 18.6702
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Divided 227.575 208.756 1.09015
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Subtracted 0 10481.8 10869.5 387.7
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Divided 1 241.828 263.62 1.09011
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Subtracted 0 10449 10061.8 387.2
alpha-nac protein. [sptrembl;acc:q9h009] Divided 14204.4 14724.5 1.03662
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 1 56.7841 75.447 18.6629
391 40s ribosomal protein s16. [swissprot;acc:p17008] Divided 241.828 263.62 1.09011
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 0 14223.9 14738.5 1.03618

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/