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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2930 to 2979 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
367 DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Rooted Divided 49.0882 54.2027 1.10419
DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Ranked Subtracted 218.827 238.407 19.58
FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Measured 6102.59 7081.46 978.87
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked Divided 234.146 256.627 1.09601
PDCD6 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Squared Subtracted 29101.9 35347 6245.1
POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Measured Divided 4024.4 4719.35 1.17268
SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Rooted Subtracted 60.6732 67.2827 6.6095
368 ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Squared 29098.8 35342.6 6243.8
CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Measured Divided 5082.66 5959.99 1.17261
DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Ranked Subtracted 218.827 238.407 19.58
DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Squared Divided 51805.2 41916.4 1.23592
NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Measured Subtracted 7756.51 8731.76 975.25
PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Ranked Divided 242.66 265.715 1.09501
RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Rooted 49.5225 54.6817 1.10418
TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Subtracted 63.0663 56.4667 6.5996
369 CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Measured Divided 3583.56 4194.95 1.17061
LGALS9 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Squared 45960.8 56749.6 1.23474
METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Rooted 49.7435 45.0586 1.10397
MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Ranked 242.159 265.104 1.09475
NME2 nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Measured Subtracted 7755.69 8730.74 975.05
POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Ranked 239.977 259.525 19.548
SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared 29096 35338.7 6242.7
TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Rooted 63.0663 56.4667 6.5996
370 no value nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Measured 7753.59 8728.13 974.54
EPB41 protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Squared Divided 45986 56776.1 1.23464
GCA grancalcin. [swissprot;acc:p28676] Subtracted 29095.7 35338.3 6242.6
GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Rooted 61.4282 68.0107 6.5825
ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked 218.818 238.358 19.54
METAP2 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Rooted Divided 49.7435 45.0586 1.10397
NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Ranked 242.159 265.104 1.09475
SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Measured 4108.15 4808.93 1.17058
371 CAPNS1 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Squared Subtracted 29095.3 35337.6 6242.3
EPB41L1 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] Divided 45985.9 56776 1.23464
HTRA2 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Measured 5067.02 5926.46 1.16961
NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Rooted Subtracted 61.3383 67.8668 6.5285
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Measured 4855.46 5824.52 969.06
RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Ranked Divided 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
ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] Rooted Divided 49.3451 54.4606 1.10367
372 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Ranked 186.52 170.42 1.09447
EPB41L3 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Squared 45986.7 56776.8 1.23464
HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Measured 5067 5926.17 1.16956
NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Rooted Subtracted 61.3354 67.8623 6.5269
POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Ranked 239.709 259.038 19.329
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] Measured 4909.79 5878.79 969
SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Rooted Divided 49.3451 54.4606 1.10367
SORBS1 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Squared Subtracted 29335.6 35515.5 6179.9
373 no value guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Rooted Divided 49.3451 54.4606 1.10367
DCTN5 dynactin 4. [refseq;acc:nm_032486] Ranked Subtracted 233.142 252.253 19.111
EPB41L2 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Squared Divided 45986 56776.1 1.23464

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/