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 1130 to 1179 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
565 sedlin. [swissprot;acc:o14582] High confidence 129.219 121.261 1.06563
566 serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Low confidence 168.935 163.869 1.03091
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 129.219 121.261 1.06563
567 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] Low confidence 206.46 200.275 1.03088
bet3 homolog. [swissprot;acc:o43617] High confidence 129.219 121.261 1.06563
568 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Low confidence 202.86 196.783 1.03088
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] High confidence 226.3 212.38 1.06554
569 acidic leucine-rich nuclear phosphoprotein 32 family member a (potent heat-stable protein phosphatase 2a inhibitor i1pp2a) (hla-dr associated protein i) (phapi) (acidic nuclear phosphoprotein pp32) (cerebellar leucine rich acidic nuclear protein). [swissprot;acc:p39687] Low confidence 206.46 200.275 1.03088
t54 protein. [swissprot;acc:q92917] High confidence 226.3 212.38 1.06554
570 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] Low confidence 206.46 200.275 1.03088
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] High confidence 229.709 215.631 1.06529
571 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Low confidence 206.46 200.275 1.03088
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] High confidence 238.529 254.099 1.06528
572 acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] Low confidence 206.46 200.275 1.03088
cbf1 interacting corepressor. [refseq;acc:nm_004882] High confidence 227.86 213.945 1.06504
573 bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] Low confidence 206.46 200.275 1.03088
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] High confidence 227.86 213.945 1.06504
574 nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Low confidence 202.855 196.78 1.03087
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] High confidence 221.807 208.264 1.06503
575 arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] Low confidence 202.85 196.777 1.03086
dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] High confidence 221.807 208.264 1.06503
576 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 1.0648
intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Low confidence 169.097 164.039 1.03083
577 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] High confidence 224.606 210.944 1.06477
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Low confidence 207.131 200.94 1.03081
578 calponin h1, smooth muscle (basic calponin) (calponin 1). [swissprot;acc:p51911] 202.382 196.335 1.0308
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 224.606 210.944 1.06477
579 calponin, acidic isoform (calponin 3). [swissprot;acc:q15417] Low confidence 202.382 196.335 1.0308
zinc finger protein t86. [swissprot;acc:o00488] High confidence 246.805 231.796 1.06475
580 calponin h2, smooth muscle (neutral calponin). [swissprot;acc:q99439] Low confidence 202.382 196.334 1.0308
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] High confidence 236.751 252.038 1.06457
581 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Low confidence 205.428 199.293 1.03078
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] High confidence 237.28 252.492 1.06411
582 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Low confidence 203.164 197.1 1.03077
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] High confidence 237.28 252.492 1.06411
583 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Low confidence 203.166 197.101 1.03077
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] High confidence 237.28 252.492 1.06411
584 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Low confidence 203.163 197.102 1.03075
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] High confidence 237.28 252.492 1.06411
585 surfeit locus protein 6. [swissprot;acc:o75683] Low confidence 205.21 199.088 1.03075
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] High confidence 237.28 252.492 1.06411
586 enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Low confidence 205.506 199.406 1.03059
hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] High confidence 237.28 252.492 1.06411
587 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Low confidence 205.461 199.383 1.03048
homeobox protein barh-like 2. [swissprot;acc:q9umq3] High confidence 237.28 252.492 1.06411
588 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Low confidence 191.507 185.859 1.03039
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] High confidence 216.557 230.362 1.06375
589 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] Low confidence 204.056 198.046 1.03035
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] High confidence 228.215 214.546 1.06371
590 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Low confidence 211.788 218.216 1.03035

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/