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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo Gene description Rank measured final expected
Results: HTML CSV LaTeX Showing element 801 to 850 of 3206 in total
Hugo
description
Rank
measured
final
expected
CENTB2 CENTAURIN BETA 2 (CNT-B2). [SWISSPROT;Acc:Q15057] 1595 0.0726324 0.240255629 0.302313
CENTB5 CENTAURIN BETA 5 (CNT-B5). [SWISSPROT;Acc:Q96P50] 1593 0.0606318 0.240256297 0.252363
CENTG1 CENTAURIN GAMMA 1. [SWISSPROT;Acc:Q99490] 402 0.0439645 0.278252807 0.158002
CENTG2 CENTAURIN GAMMA 2. [SWISSPROT;Acc:Q9UPQ3] 403 0.0479426 0.27825234 0.172299
CENTG3 CENTAURIN GAMMA 3. [SWISSPROT;Acc:Q96P47] 405 0.0546138 0.278251433 0.196275
CEP164 2559 0.128297 0.214313038 0.598643
CEP70 P10-BINDING PROTEIN. [RefSeq;Acc:NM_024491] 2301 0.10445 0.222305464 0.469849
CFL1 "COFILIN, NON-MUSCLE ISOFORM (18 KDA PHOSPHOPROTEIN) (P18). [SWISSPROT;Acc:P23528]" 370 0.0460179 0.279207723 0.164816
CFL2 "COFILIN, MUSCLE ISOFORM (COFILIN 2). [SWISSPROT;Acc:Q9Y281]" 372
CHAC1 1587 0.0612982 0.240753309 0.25461
CHAT CHOLINE O-ACETYLTRANSFERASE (EC 2.3.1.6) (CHOACTASE) (CHOLINE ACETYLASE) (CHAT). [SWISSPROT;Acc:P28329] 938 0.0510434 0.256406727 0.199072
CHCHD3 485 0.0257019 0.274303992 0.0936986
CHCHD4 1325 0.0393961 0.245522816 0.160458
CHCHD6 490 0.0344618 0.274303135 0.125634
CHD3 CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 3 (CHD-3) (MI-2 AUTOANTIGEN 240 KDA PROTEIN) (MI2-ALPHA). [SWISSPROT;Acc:Q12873] 3104 0.0749538 0.092223589 0.81274
CHD5 CHROMODOMAIN HELICASE DNA BINDING PROTEIN 5. [RefSeq;Acc:NM_015557] 3107 0.0762705 0.092223507 0.827018
CHDH CHOLINE DEHYDROGENASE. [RefSeq;Acc:NM_018397] 662 0.100197 0.267112222 0.375112
CHL1 CELL ADHESION MOLECULE WITH HOMOLOGY TO L1CAM PRECURSOR; NEURAL CELL ADHESION MOLECULE; CELL ADHESION MOLECULE L1-LIKE; L1 CELL ADHESION MOLECULE 2. [RefSeq;Acc:NM_006614] 2674 0.0249248 0.209232319 0.119125
CHMP2A PUTATIVE BREAST ADENOCARCINOMA MARKER (32KD). [RefSeq;Acc:NM_014453] 3198 0.0100954 0.036862149 0.273869
CHMP2B 3199 0.00386024 0.036862138 0.104721
CHMP4A PROTEIN HSPC134 (PROTEIN CDA04). [SWISSPROT;Acc:Q9BY43] 3193 0.0228851 0.036862282 0.620827
CHMP4B 3196 0.031557 0.036862209 0.85608
CHMP4C 3194 0.0239451 0.036862264 0.649583
CHMP6 1726 0.10685 0.23703937 0.450769
CHRAC1 CHROMATIN ACCESSIBILITY COMPLEX PROTEIN 1 (CHRAC-1) (CHRAC-15) (HUCHRAC15) (DNA POLYMERASE EPSILON SUBUNIT P15). [SWISSPROT;Acc:Q9NRG0] 6 0.590586 0.609273641 0.969328
CHRNA2 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15822]" 2630 0.0142351 0.209999041 0.0677865
CHRNA3 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-3 CHAIN PRECURSOR. [SWISSPROT;Acc:P32297]" 2635 0.0132921 0.20999872 0.0632961
CHRNA4 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR. [SWISSPROT;Acc:P43681]" 2632 0.0186658 0.209998965 0.0888852
CHRNA6 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-6 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15825]" 2631 0.0131531 0.209999026 0.0626341
CHRNA7 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-7 CHAIN PRECURSOR. [SWISSPROT;Acc:P36544]" 842 0.077721 0.260704618 0.298119
CIRH1A "CIRHIN; TESTIS EXPRESSED GENE 292; CIRRHOSIS, AUTOSOMAL RECESSIVE 1A. [RefSeq;Acc:NM_032830]" 1502 0.588096 0.242717998 2.42296
CKB "CREATINE KINASE, B CHAIN (EC 2.7.3.2) (B-CK). [SWISSPROT;Acc:P12277]" 1870 0.235164 0.232840254 1.00998
CKM "CREATINE KINASE, M CHAIN (EC 2.7.3.2) (M-CK). [SWISSPROT;Acc:P06732]" 1894 0.219925 0.232621726 0.945419
CKMT2 "CREATINE KINASE, SARCOMERIC MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (S- MTCK) (MIB-CK) (BASIC-TYPE MITOCHONDRIAL CREATINE KINASE). [SWISSPROT;Acc:P17540]" 1883 0.197547 0.232752435 0.848743
CKS2 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 2 (CKS-2). [SWISSPROT;Acc:P33552] 2877 0.428065 0.188433772 2.2717
CLEC11A STEM CELL GROWTH FACTOR; LYMPHOCYTE SECRETED C-TYPE LECTIN; LYMPHOCYTE SECRETED C-TYPE LECTIN. [RefSeq;Acc:NM_002975] 2845 0.164601 0.191980937 0.857382
CLEC3A C-TYPE LECTIN SUPERFAMILY MEMBER 1 PRECURSOR (CARTILAGE-DERIVED C-TYPE LECTIN). [SWISSPROT;Acc:O75596] 2844 0.188839 0.192433465 0.981321
CLEC3B TETRANECTIN PRECURSOR (TN) (PLASMINOGEN-KRINGLE 4 BINDING PROTEIN). [SWISSPROT;Acc:P05452] 2830 0.259669 0.193275128 1.34352
CLEC4M CD209 ANTIGEN-LIKE; PUTATIVE TYPE II MEMBRANE PROTEIN. [RefSeq;Acc:NM_014257] 3015 0.0247893 0.121833301 0.203469
CLGN CALMEGIN PRECURSOR. [SWISSPROT;Acc:O14967] 1049 0.0356563 0.252773997 0.14106
CLK2 PROTEIN KINASE CLK2 (EC 2.7.1.-) (CDC-LIKE KINASE 2). [SWISSPROT;Acc:P49760] 511 0.131932 0.273350351 0.482648
CLK3 PROTEIN KINASE CLK3 (EC 2.7.1.-) (CDC-LIKE KINASE 3). [SWISSPROT;Acc:P49761] 512 0.1005 0.273287196 0.367745
CLP1 PRE-MRNA CLEAVAGE COMPLEX II PROTEIN CLP1. [SWISSPROT;Acc:Q92989] 1946 0.212972 0.231420118 0.920283
CLPTM1 CLEFT LIP AND PALATE ASSOCIATED TRANSMEMBRANE PROTEIN 1. [RefSeq;Acc:NM_001294] 2162 0.0206788 0.227243806 0.0909983
CLPX "ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:O76031]" 1977 0.139859 0.231079851 0.605241
CLSTN1 CALSYNTENIN-1 PRECURSOR. [SWISSPROT;Acc:O94985] 2836 0.0775327 0.193069127 0.40158
CLSTN2 CALSYNTENIN-2 PRECURSOR. [SWISSPROT;Acc:Q9H4D0] 2832 0.0653044 0.193098024 0.338193
CLSTN3 CALSYNTENIN-3 PRECURSOR. [SWISSPROT;Acc:Q9BQT9] 2831 0.0641829 0.193100969 0.33238
CLTC CLATHRIN HEAVY CHAIN 1 (CLH-17). [SWISSPROT;Acc:Q00610] 1053 0.264806 0.252672659 1.04802
CLTCL1 CLATHRIN HEAVY CHAIN 2 (CLH-22). [SWISSPROT;Acc:P53675] 1059 0.225517 0.252668222 0.892542

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/