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 730 to 779 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
365 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 0 7769.96 8139.71 1.04759
366 40s ribosomal protein s5. [swissprot;acc:p46782] 1 242.473 265.756 1.09602
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 0 8614.89 9017.27 1.04671
367 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 13801.7 13185.9 1.0467
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] 1 234.146 256.627 1.09601
368 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 0 16679.2 15940.6 1.04633
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 1 242.66 265.715 1.09501
369 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 0 18849.7 19704.7 1.04536
60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 1 242.159 265.104 1.09475
370 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] 0 13652.7 13061 1.0453
371 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 1 186.52 170.42 1.09447
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] 0 13247.9 12674.2 1.04527
372 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 11869.9 12402.7 1.04489
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 1 186.52 170.42 1.09447
373 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 242.37 265.255 1.09442
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] 0 10598.2 11061.5 1.04371
374 calcyphosine. [swissprot;acc:q13938] 9874.54 9478.1 1.04183
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 1 267.208 244.168 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
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] 0 14247.6 13686.9 1.04097
376 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 1 257.017 234.945 1.09395
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 0 10284.9 10695.6 1.03993
377 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 1 242.691 265.481 1.09391
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] 0 14512.3 13958.2 1.0397
378 60s ribosomal protein l30. [swissprot;acc:p04645] 1 242.593 265.365 1.09387
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] 0 19713.5 18962.5 1.0396
379 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 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
380 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 0 9566.15 9936.37 1.0387
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 1 242.109 264.79 1.09368
381 ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 0 9565.54 9935.19 1.03864
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 1 200.586 183.423 1.09357
382 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 0 10449 10061.8 1.03848
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] 1 200.791 183.66 1.09328
383 chromodomain y-like protein 2. [refseq;acc:nm_152342] 0 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
384 bystin. [swissprot;acc:q13895] 0 10833.3 11244.5 1.03796
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] 1 266.421 244.236 1.09083
385 testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 0 10302.7 10686.7 1.03727
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 1 266.421 244.236 1.09083
386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 0 10303.7 10687.4 1.03724
387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 1 242.238 264.11 1.09029
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] 0 10481.8 10869.5 1.03699
388 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] 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
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 1 227.575 208.756 1.09015
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 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/