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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 725 to 774 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
363 SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Subtracted 233.539 253.197 19.658
SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Divided 231.481 211.131 1.09639
364 CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Subtracted 233.539 253.197 19.658
POLR2B dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Divided 243.208 266.617 1.09625
365 FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Subtracted 233.539 253.197 19.658
MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Divided 242.744 266.07 1.09609
366 CD209 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Subtracted 233.539 253.197 19.658
RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Divided 242.473 265.756 1.09602
367 DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Subtracted 218.827 238.407 19.58
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Divided 234.146 256.627 1.09601
368 DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Subtracted 218.827 238.407 19.58
PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Divided 242.66 265.715 1.09501
369 MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 1.09475
POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Subtracted 239.977 259.525 19.548
370 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 218.818 238.358 19.54
NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Divided 242.159 265.104 1.09475
371 RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 186.52 170.42 1.09447
SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Subtracted 186.172 166.661 19.511
372 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided 186.52 170.42 1.09447
POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Subtracted 239.709 259.038 19.329
373 DCTN5 dynactin 4. [refseq;acc:nm_032486] 233.142 252.253 19.111
MRPL11 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Divided 242.37 265.255 1.09442
374 CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Subtracted 248.152 267.226 19.074
TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Divided 267.208 244.168 1.09436
375 ADCY6 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Subtracted 248.152 267.226 19.074
POLR3A dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Divided 242.686 265.516 1.09407
376 ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Subtracted 248.152 267.226 19.074
DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Divided 257.017 234.945 1.09395
377 LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Subtracted 248.152 267.226 19.074
POLR1A dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Divided 242.691 265.481 1.09391
378 FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Subtracted 248.152 267.226 19.074
RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] Divided 242.593 265.365 1.09387
379 AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 241.509 264.163 1.0938
LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Subtracted 248.152 267.226 19.074
380 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Divided 242.109 264.79 1.09368
LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Subtracted 248.152 267.226 19.074
381 SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051]
TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Divided 200.586 183.423 1.09357
382 DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Subtracted 253.852 234.808 19.044
TAF7L 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
383 RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 217.739 1.09242
TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Subtracted 236.245 255.113 18.868
384 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 227.575 208.756 18.819
E2F1 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 E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Subtracted 227.575 208.756 18.819
386 RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Divided 242.238 264.11 1.09029
RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] Subtracted 238.986 257.784 18.798
387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Divided 242.238 264.11 1.09029
ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 56.6768 75.3531 18.6763

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
- Hugo is the HGNC identifier if it exists
- 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/