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 2832 to 2881 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
354 WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Rooted Divided 49.2848 54.5246 1.10632
355 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Measured Subtracted 4914.27 5907.12 992.85
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Divided 12839 10911.1 1.17669
EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Rooted Subtracted 50.2801 43.4779 6.8022
PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Squared 34129.6 40434.5 6304.9
PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Rooted Divided 58.0752 64.23 1.10598
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Ranked Subtracted 94 114 20
STX6 syntaxin 6. [swissprot;acc:o43752] Divided 234.673 257.414 1.09691
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Squared 15588.1 19381.8 1.24337
356 no value 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Ranked 243.24 266.796 1.09684
LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted Subtracted 56.031 62.8281 6.7971
PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Squared 34129.6 40434.5 6304.9
SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Rooted Divided 58.0752 64.23 1.10598
SH3GL3 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Squared 35247.5 43820.5 1.24322
SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Measured Subtracted 4914.27 5907.12 992.85
TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Divided 11004.2 12944.2 1.1763
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked Subtracted 94 114 20
357 no value 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Divided 243.12 266.661 1.09683
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Rooted Subtracted 46.3291 53.1063 6.7772
CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked 94 114 20
DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured 4977.09 5966.44 989.35
GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Rooted Divided 61.2684 67.755 1.10587
IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Measured 5061.11 5950.22 1.17567
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Squared 9811.86 7908.29 1.24071
PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Subtracted 34129.6 40434.5 6304.9
358 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Measured Divided 5061.11 5950.22 1.17567
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Squared 9811.73 7908.13 1.24071
DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Measured Subtracted 4977.8 5966.14 988.34
NEK2 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Rooted Divided 61.2684 67.755 1.10587
NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Subtracted 51.6736 58.4422 6.7686
PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Squared 34129.6 40434.5 6304.9
RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Ranked 240.287 260.193 19.906
RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] Divided 243.12 266.662 1.09683
359 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured 12798.9 10887.2 1.17559
NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted 1920.75 2907.43 986.68
PES1 pescadillo homolog 1. [swissprot;acc:o00541] Rooted Divided 49.2488 54.4603 1.10582
PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Squared 9812.34 7908.87 1.24068
PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 34129.4 40434.2 6304.8
RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5] Ranked 240.287 260.193 19.906
RPL4 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Divided 239.277 262.434 1.09678
SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Rooted Subtracted 57.6823 64.4212 6.7389
360 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Measured Divided 12796.8 10886 1.17553
DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Rooted Subtracted 46.901 53.624 6.723
GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Divided 49.3771 54.5905 1.10558
LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured Subtracted 4590.18 5575.52 985.34
POLR2C dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Ranked 240.287 260.193 19.906
PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Squared Divided 9814.47 7911.48 1.24054
SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 243.072 266.559 1.09663
VAV2 vav-2 protein. [swissprot;acc:p52735] Squared Subtracted 31377.3 37670.1 6292.8
361 CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Rooted 46.8525 53.5324 6.6799

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/