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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 677 to 726 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
339 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] High confidence 20446.1 24136.4 1.18049
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Low confidence 9114.82 9621.71 1.05561
340 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 20446.1 24136.4 1.18049
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Low confidence 8940.43 9437.54 1.0556
341 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] High confidence 20446.1 24136.4 1.18049
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Low confidence 7151 7548.35 1.05557
342 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] High confidence 20446.1 24136.4 1.18049
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Low confidence 7309.92 7715.51 1.05548
343 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] High confidence 20446.1 24136.4 1.18049
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 7155.19 7551.48 1.05538
344 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 8926.58 9420 1.05528
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 20446.1 24136.4 1.18049
345 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Low confidence 8919.45 9410.98 1.05511
346 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 7453.11 7863.62 1.05508
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] High confidence 14229.2 16780.7 1.17931
347 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 4991.02 5885.09 1.17914
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Low confidence 7505.53 7918.67 1.05504
348 adapter-related protein complex 2 alpha 2 subunit (alpha-adaptin c) (clathrin assembly protein complex 2 alpha-c large chain) (100 kda coated vesicle protein c) (plasma membrane adaptor ha2/ap2 adaptin alpha c subunit) (huntingtin-interacting protein hypj). [swissprot;acc:o94973] 7619.78 8038.01 1.05489
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] High confidence 4991.02 5885.09 1.17914
349 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Low confidence 7619.78 8038.01 1.05489
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] High confidence 4714.85 5554.38 1.17806
350 clathrin coat assembly protein ap17 (clathrin coat associated protein ap17) (plasma membrane adaptor ap-2 17 kda protein) (ha2 17 kda subunit) (clathrin assembly protein 2 small chain). [swissprot;acc:p53680] Low confidence 7619.78 8038.01 1.05489
sedlin. [swissprot;acc:o14582] High confidence 17396.9 20483.9 1.17745
351 adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782] Low confidence 7619.78 8038.01 1.05489
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 17396.9 20483.9 1.17745
352 bet3 homolog. [swissprot;acc:o43617]
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Low confidence 8140.28 8586.61 1.05483
353 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] 7892.42 8325.09 1.05482
p66 alpha. [refseq;acc:nm_017660] High confidence 12839 10911.1 1.17669
354 integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3] Low confidence 7892.42 8325.09 1.05482
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] High confidence 12839 10911.1 1.17669
355 rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] Low confidence 7892.42 8325.09 1.05482
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] High confidence 12839 10911.1 1.17669
356 oxysterol binding protein-related protein 8 (osbp-related protein 8) (orp-8). [swissprot;acc:q9bzf1] Low confidence 8583.53 9053.93 1.0548
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] High confidence 11004.2 12944.2 1.1763
357 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] Low confidence 6822.68 7196.02 1.05472
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] High confidence 5061.11 5950.22 1.17567
358 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Low confidence 6822.26 7195.59 1.05472
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] High confidence 5061.11 5950.22 1.17567
359 aspartyl aminopeptidase (ec 3.4.11.21). [swissprot;acc:q9ula0] Low confidence 8966.11 9455.62 1.0546
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] High confidence 12798.9 10887.2 1.17559
360 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 12796.8 10886 1.17553
oxysterol binding protein-related protein 5 (osbp-related protein 5) (orp-5). [swissprot;acc:q9h0x9] Low confidence 8576.28 9043.11 1.05443
361 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] High confidence 12787.6 10880.5 1.17528
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Low confidence 7773.85 8196.54 1.05437
362 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] High confidence 12786.6 10879.9 1.17525
neuralized-like. [refseq;acc:nm_004210] Low confidence 6456.59 6807.5 1.05435
363 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] High confidence 12780.7 10876.4 1.17509
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Low confidence 9099.15 9593.54 1.05433

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/