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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 562 to 611 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
141 Ranked RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 59 49 1.20408
Squared CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 81520.8 56188.5 1.45084
Rooted REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 55.6161 66.7332 1.19989
142 Measured PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 7090.37 1.30832
Ranked RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 59 49 1.20408
Squared CDC2 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
Rooted PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 55.6161 66.7332 1.19989
143 Measured ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 9275.1 7089.65 1.30826
Ranked ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 59 49 1.20408
Squared PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 124319 86848.2 1.43145
Rooted PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 55.6161 66.7332 1.19989
144 Measured UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 3349.9 4362.61 1.30231
Ranked KCNIP1 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
Squared TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 123324 86277.9 1.42938
Rooted SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 55.6161 66.7332 1.19989
145 Measured no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 16771.5 12889.1 1.30122
Ranked KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 319.546 1.20293
Squared no value 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
146 Measured STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 1.30082
Ranked 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
Squared RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 103496 146848 1.41888
Rooted PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] 55.0737 66.0298 1.19894
147 Measured CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 11068 8508.5 1.30082
Ranked no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 50.7983 42.3003 1.2009
Squared RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 103496 146848 1.41888
Rooted FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 42.0574 50.4237 1.19893
148 Measured STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 11068 8508.5 1.30082
Ranked UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 296.677 247.559 1.19841
Squared RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 103496 146848 1.41888
Rooted FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 42.0577 50.424 1.19892
149 Measured VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 11068 8508.5 1.30082
Ranked no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718
Squared ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 103496 146848 1.41888
Rooted FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 42.0684 50.4323 1.19882
150 Measured CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] 11068 8508.5 1.30082
Ranked MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 55 46 1.19565
Squared CLP1 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 121200 85473.4 1.41799
Rooted PPP2CA 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 Measured SH2D3C 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
Ranked MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 55 46 1.19565
Squared DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 250303 354894 1.41786
Rooted 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
152 Measured MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 23693.7 18263 1.29736
Ranked no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 55 46 1.19565
Squared SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 90226 126939 1.4069
Rooted LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 55.2859 65.9288 1.19251
153 Measured MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 23693.7 18263 1.29736
Ranked RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 249.663 298.263 1.19466
Squared no value ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 70011 49783 1.40632

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/