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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 560 to 609 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
280 TFCP2L1 lbp-9. [refseq;acc:nm_014553] Low confidence 219.758 210.509 1.04394
281 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] High confidence 241.808 267.335 1.10557
TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Low confidence 219.749 210.503 1.04392
282 AMY1C alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 219.742 210.498 1.04391
RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] High confidence 252.39 228.297 1.10553
283 RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 267.346 1.10552
UBP1 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Low confidence 219.722 210.484 1.04389
284 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] High confidence 224.657 203.235 1.10541
TNKS2 tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2] Low confidence 214.675 205.692 1.04367
285 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 224.647 203.242 1.10532
TAF4 transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Low confidence 202.354 211.175 1.04359
286 NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] High confidence 224.633 203.251 1.1052
TAF4B transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] Low confidence 202.356 211.174 1.04358
287 GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 210.132 201.397 1.04337
RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] High confidence 240.758 266.079 1.10517
288 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 266.078
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Low confidence 200.288 192.004 1.04314
289 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] High confidence 272.781 246.892 1.10486
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Low confidence 209.31 200.66 1.04311
290 LAPTM4B lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] 210 201.325 1.04309
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] High confidence 231.969 210.064 1.10428
291 NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 251.679 228.037 1.10368
TMEM115 pl6 protein (placental protein 6). [swissprot;acc:q12893] Low confidence 209.995 201.322 1.04308
292 LAPTM4A lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012]
RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] High confidence 241.411 266.414 1.10357
293 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 240.782 265.717 1.10356
ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Low confidence 218.785 209.763 1.04301
294 BCCIP brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] High confidence 240.782 265.717 1.10356
JAG2 jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Low confidence 218.715 209.71 1.04294
295 MEF2D myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] 218.713 209.709
SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] High confidence 223.273 202.423 1.103
296 JAG1 jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] Low confidence 218.714 209.709 1.04294
MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] High confidence 241.282 266.12 1.10294
297 no value 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 259.984 1.1029
MEF2C myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Low confidence 218.714 209.709 1.04294
298 CAPN2 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] High confidence 268.632 243.588 1.10281
MEF2A myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Low confidence 218.715 209.71 1.04294
299 CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] High confidence 268.635 243.592 1.10281
DICER1 endoribonuclease dicer (ec 3.1.26.-) (helicase with rnase motif) (helicase-moi). [swissprot;acc:q9upy3] Low confidence 208.915 200.322 1.0429
300 ATP2C1 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 218.661 209.669 1.04289
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] High confidence 150.959 166.351 1.10196
301 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 150.982 166.372 1.10193
SLC7A8 large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Low confidence 205.154 196.72 1.04287
302 RPL26 60s ribosomal protein l26. [swissprot;acc:q02877] High confidence 242.326 267.008 1.10185
XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Low confidence 209.12 200.548 1.04274
303 HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 210.057 201.45 1.04273
RPL35 60s ribosomal protein l35. [swissprot;acc:p42766] High confidence 242.333 266.999 1.10179
304 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 266.986 1.1017
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Low confidence 209.232 200.662 1.04271
305 HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 210.05 201.454 1.04267

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/