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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 558 to 607 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
140 FLNB Rooted filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 55.6161 66.7332 1.19989
KCNIP2 Measured kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 2760.28 2100.27 1.31425
RRAGA Ranked ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 59 49 1.20408
141 CCNB1 Squared g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 81520.8 56188.5 1.45084
REV1 Rooted rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 55.6161 66.7332 1.19989
RRAGC Ranked ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 59 49 1.20408
SNRPD2 Measured small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 4405.4 5782.08 1.3125
142 CDC2 Squared cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 81478.9 56175.2 1.45044
PITRM1 Measured metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 7090.37 1.30832
PRMT1 Rooted protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 55.6161 66.7332 1.19989
RRAGB Ranked ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 59 49 1.20408
143 ALG1 Measured beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 9275.1 7089.65 1.30826
ANLN Ranked anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 59 49 1.20408
PPP1R13B Squared protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 124319 86848.2 1.43145
PRMT8 Rooted protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 55.6161 66.7332 1.19989
144 KCNIP1 Ranked kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 265.686 319.651 1.20312
SNRP70 Rooted u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 55.6161 66.7332 1.19989
TP53BP2 Squared tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 123324 86277.9 1.42938
UNC84A Measured sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 3349.9 4362.61 1.30231
145 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 16771.5 12889.1 1.30122
Squared nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 310840 442993 1.42515
Rooted filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 55.6161 66.7332 1.19989
KCNIP4 Ranked potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 1.20293
146 KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 265.632 319.531 1.20291
PRPF40B Rooted huntingtin interacting protein c. [refseq;acc:nm_012272] 55.0737 66.0298 1.19894
RRAGA Squared ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 103496 146848 1.41888
STAMBPL1 Measured associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 1.30082
147 no value Ranked nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 50.7983 42.3003 1.2009
CHMP2A Measured putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 11068 8508.5 1.30082
FOXP4 Rooted forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 42.0574 50.4237 1.19893
RRAGC Squared ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 103496 146848 1.41888
148 FOXP1 Rooted forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 42.0577 50.424 1.19892
RRAGB Squared ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 103496 146848 1.41888
STAMBP Measured associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 11068 8508.5 1.30082
UNC84A Ranked sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 296.677 247.559 1.19841
149 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718
ANLN Squared anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 103496 146848 1.41888
FOXP3 Rooted forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 42.0684 50.4323 1.19882
VPS24 Measured neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 11068 8508.5 1.30082
150 CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43]
CLP1 Squared pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 121200 85473.4 1.41799
MYO5B Ranked myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 55 46 1.19565
PPP2CA Rooted serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 63.5827 53.0856 1.19774
151 CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 38.8223 46.4975 1.1977
DNASE2B Squared deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 250303 354894 1.41786
MYO5C Ranked myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 55 46 1.19565
SH2D3C Measured sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 4578.09 5939.91 1.29746
152 no value Ranked myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 55 46 1.19565
LUC7L2 Rooted luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 55.2859 65.9288 1.19251
MAGED4 Measured melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 23693.7 18263 1.29736

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/