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 925 to 974 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
463 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Divided 238.921 257.327 1.07704
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Subtracted 223.648 207.62 16.028
464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Divided 210.578 226.764 1.07686
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Subtracted 223.648 207.62 16.028
465 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 240.673 16.011
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Divided 248.152 267.226 1.07686
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Subtracted 225.661 209.651 16.01
467 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Divided 248.152 267.226 1.07686
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Subtracted 248.56 232.579 15.981
468 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 237.627 253.604 15.977
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Divided 248.152 267.226 1.07686
469 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Subtracted 226.789 210.818 15.971
470 inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] 224.535 240.476 15.941
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Divided 248.152 267.226 1.07686
471 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
zinc finger-like protein 9. [refseq;acc:nm_033414] Subtracted 250.942 235.004 15.938
472 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
thymic stromal co-transporter. [refseq;acc:nm_033051] Divided 248.152 267.226 1.07686
473 guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Subtracted 250.942 235.004 15.938
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 225.661 209.651 1.07637
474 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Subtracted 226.727 210.816 15.911
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Divided 226.789 210.818 1.07576
475 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 226.727 210.816 1.07547
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Subtracted 236.964 252.86 15.896
476 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Divided 226.681 210.814 1.07527
Subtracted 15.867
477 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 220.183 236.015 15.832
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Divided 251.926 234.547 1.0741
478 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Subtracted 220.171 235.979 15.808
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Divided 228.051 212.321 1.07409
479 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Subtracted 220.172 235.98 15.808
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Divided 228.051 212.321 1.07409
480 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Subtracted 220.172 235.98 15.808
481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Divided 237.109 254.667 1.07405
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Subtracted 220.171 235.979 15.808
482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Divided 237.109 254.667 1.07405
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Subtracted 220.161 235.95 15.789
483 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Divided 237.109 254.667 1.07405
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Subtracted 228.051 212.321 15.73
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Divided 237.109 254.667 1.07405
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 228.051 212.321 15.73
485 60s ribosomal protein l18. [swissprot;acc:q07020] Divided 237.109 254.667 1.07405
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Subtracted 231.276 215.627 15.649
486 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 248.866 233.287 15.579
mct-1 protein. [refseq;acc:nm_014060] Divided 226.313 243.03 1.07387
487 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Subtracted 238.529 254.099 15.57
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Divided 226.313 243.03 1.07387

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/