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 Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 2814 to 2863 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
Value Type
description
red
network_comparison
green
352 Subtracted RBM39 Ranked rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 20.123 217.739
SF3A2 Measured splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 4911.81 997.37 5909.18
SRP9 Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 53.607 6.8382 60.4452
353 Divided GATAD2A Measured p66 alpha. [refseq;acc:nm_017660] 12839 1.17669 10911.1
GIPC1 Ranked rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 231.73 1.09694 211.252
NAV3 Rooted neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 61.3354 1.10641 67.8623
NONO Squared 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 71383 1.24362 57399.3
Subtracted KLF5 Measured 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] 4911.81 997.37 5909.18
PRKAA2 Squared 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 34129.7 6305.1 40434.8
PRPF31 Rooted pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 57.4274 6.8335 64.2609
STAMBPL1 Ranked associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 94 20 114
354 Divided GATAD2B Measured transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 12839 1.17669 10911.1
PSPC1 Squared paraspeckle protein 1. [refseq;acc:nm_018282] 71360.3 1.24352 57385.8
STX10 Ranked syntaxin 10 (syn10). [swissprot;acc:o60499] 234.691 1.09694 257.442
WDR12 Rooted wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 49.2848 1.10632 54.5246
Subtracted CHMP2A Ranked putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 94 20 114
EGFL8 Rooted palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 50.272 6.8086 43.4634
PRKAG1 Squared 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 34129.6 6304.9 40434.5
RRM1 Measured ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 6913.6 993.45 7907.05
355 Divided no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 12839 1.17669 10911.1
PRSS7 Rooted enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 58.0752 1.10598 64.23
STX6 Ranked syntaxin 6. [swissprot;acc:o43752] 234.673 1.09691 257.414
UNC84A Squared sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 15588.1 1.24337 19381.8
Subtracted no value Measured ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 4914.27 992.85 5907.12
EGFL7 Rooted egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 50.2801 6.8022 43.4779
PRKAB2 Squared 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 34129.6 6304.9 40434.5
STAMBP Ranked associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 94 20 114
356 Divided no value 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 1.09684 266.796
SF3B2 Rooted splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 58.0752 1.10598 64.23
SH3GL3 Squared sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 35247.5 1.24322 43820.5
TCP1 Measured t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 11004.2 1.1763 12944.2
Subtracted LSM8 Rooted u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 56.031 6.7971 62.8281
PRKAG3 Squared 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 34129.6 6304.9 40434.5
SNRPA1 Measured u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 4914.27 992.85 5907.12
VPS24 Ranked neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 94 20 114
357 Divided no value 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 243.12 1.09683 266.661
GRB2 Rooted growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 61.2684 1.10587 67.755
IMMP2L Measured imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 5061.11 1.17567 5950.22
PPP2R2D Squared uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 9811.86 1.24071 7908.29
Subtracted no value Rooted transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 46.3291 6.7772 53.1063
CHMP4A Ranked protein hspc134 (protein cda04). [swissprot;acc:q9by43] 94 20 114
DVL1 Measured segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 4977.09 989.35 5966.44
PRKAB1 Squared 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 34129.6 6304.9 40434.5
358 Divided no value Measured microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 5061.11 1.17567 5950.22
Squared 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] 9811.73 1.24071 7908.13
NEK2 Rooted 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] 61.2684 1.10587 67.755
RPL10L Ranked ribosomal protein l10-like protein. [refseq;acc:nm_080746] 243.12 1.09683 266.662
Subtracted DVL2 Measured segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 4977.8 988.34 5966.14
NFYB Rooted 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] 51.6736 6.7686 58.4422
PRKAG2 Squared 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 34129.6 6304.9 40434.5

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/