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 1900 to 1949 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
475 protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Subtracted 1 236.964 252.86 15.896
476 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Divided 0 8403 8329 1.00888
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Subtracted 5558.06 5473.99 84.07
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Divided 1 226.681 210.814 1.07527
Subtracted 15.867
477 pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 0 12461.5 12542.3 80.8
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 1 220.183 236.015 15.832
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Divided 251.926 234.547 1.0741
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 0 15920 15780.2 1.00886
478 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 10156.4 10243.1 1.00854
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 1 220.171 235.979 15.808
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 775 696 79
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 1 228.051 212.321 1.07409
479 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 0 15155.8 15031.7 1.00826
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Subtracted 1 220.172 235.98 15.808
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Divided 228.051 212.321 1.07409
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Subtracted 0 13236.8 13159.3 77.5
480 heat shock factor binding protein 1. [swissprot;acc:o75506] 15204.2 15127.8 76.4
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Divided 1 237.109 254.667 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
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Divided 0 15155.8 15031.7 1.00826
481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 1 237.109 254.667 1.07405
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Subtracted 0 11489.7 11414.3 75.4
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 1 220.171 235.979 15.808
uridine kinase-like 1. [swissprot;acc:q9nwz5] Divided 0 11554.3 11462.4 1.00802
482 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Subtracted 8403 8329 74
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Divided 1 237.109 254.667 1.07405
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 0 6156.33 6205.67 1.00801
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Subtracted 1 220.161 235.95 15.789
483 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 0 1091 1021 70
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 1 237.109 254.667 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
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Divided 0 12223.8 12127.5 1.00794
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 1 237.109 254.667 1.07405
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 228.051 212.321 15.73
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Divided 0 11489.7 11414.3 1.00661
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] Subtracted 2939 2876 63
485 60s ribosomal protein l18. [swissprot;acc:q07020] Divided 1 237.109 254.667 1.07405
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Subtracted 0 10388.7 10338.7 50
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Divided 12461.5 12542.3 1.00648
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Subtracted 1 231.276 215.627 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
huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 0 13372.4 13288.3 1.00633
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Subtracted 6156.33 6205.67 49.34
mct-1 protein. [refseq;acc:nm_014060] Divided 1 226.313 243.03 1.07387
487 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Subtracted 0 8854.04 8811.09 42.95
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 1 238.529 254.099 15.57
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Divided 226.313 243.03 1.07387
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 0 13236.8 13159.3 1.00589
488 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Subtracted 11999.1 12041.7 42.6

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/