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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Gene Hugo Rank measured description expected final
Results: HTML CSV LaTeX Showing element 451 to 500 of 3206 in total
Hugo
Rank
measured
description
expected
final
ANAPC10 2384 0.078258 ANAPHASE-PROMOTING COMPLEX SUBUNIT 10; ANAPHASE-PROMOTING COMPLEX 10. [RefSeq;Acc:NM_014885] 0.356213 0.219694396
ANAPC11 2145 0.170664 ANAPHASE PROMOTING COMPLEX SUBUNIT 11 (HEPATOCELLULAR CARCINOMA ASSOCIATED RING FINGER PROTEIN) (HSPC214). [SWISSPROT;Acc:Q9NYG5] 0.749796 0.227613911
ANAPC2 2437 0.171257 ANAPHASE-PROMOTING COMPLEX SUBUNIT 2; ANAPHASE-PROMOTING COMPLEX 2. [RefSeq;Acc:NM_013366] 0.788327 0.217241069
ANK2 1824 0.038359 "ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]" 0.163741 0.234266311
ANK3 1818 0.0299967 ANKYRIN 3 (ANK-3) (ANKYRIN G). [SWISSPROT;Acc:Q12955] 0.128045 0.234266859
ANKRA2 804 0.15014 ANKYRIN-REPEAT FAMILY A PROTEIN 2 (RFXANK-LIKE 2). [SWISSPROT;Acc:Q9H9E1] 0.573028 0.262011629
ANKS1B 19 0.310118 E2A-PBX1-ASSOCIATED PROTEIN; PUTATIVE 47 KDA PROTEIN. [RefSeq;Acc:NM_020140] 0.652691 0.475137546
ANKS6 2911 0.0420495 0.241467 0.174141808
ANLN 3202 0.0289077 "ANILLIN, ACTIN BINDING PROTEIN (SCRAPS HOMOLOG, DROSOPHILA); ANILLIN (DROSOPHILA SCRAPS HOMOLOG), ACTIN BINDING PROTEIN. [RefSeq;Acc:NM_018685]" 1.20992 0.023892241
ANXA11 1048 0.114013 ANNEXIN A11 (ANNEXIN XI) (CALCYCLIN-ASSOCIATED ANNEXIN 50) (CAP-50) (56 KDA AUTOANTIGEN). [SWISSPROT;Acc:P50995] 0.451047 0.252774101
ANXA7 1052 0.149169 ANNEXIN A7 (ANNEXIN VII) (SYNEXIN). [SWISSPROT;Acc:P20073] 0.590289 0.252705031
AOF2 706 0.220284 0.830799 0.265147166
AP1B1 1164 0.313086 ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT (BETA-ADAPTIN 1) (ADAPTOR PROTEIN COMPLEX AP-1 BETA-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN BETA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 BETA LARGE CHAIN). [SWISSPROT;Acc:Q10567] 1.25482 0.249506702
AP1G1 1162 0.230865 ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT (GAMMA-ADAPTIN) (ADAPTOR PROTEIN COMPLEX AP-1 GAMMA-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN GAMMA-1 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN). [SWISSPROT;Acc:O43747] 0.925078 0.24956274
AP1M1 1088 0.168157 "ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT (MU-ADAPTIN 1) (ADAPTOR PROTEIN COMPLEX AP-1 MU-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 1) (CLATHRIN COAT ASSEMBLY PROTEIN A" 0.668251 0.251637484
AP1M2 1095 0.138969 "ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 2 SUBUNIT (MU-ADAPTIN 2) (ADAPTOR PROTEIN COMPLEX AP-1 MU-2 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-2 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 2) (AP-MU CHAIN FAMILY MEMBER MU1B)." 0.552694 0.251439314
AP1S1 1163 0.113931 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT (SIGMA-ADAPTIN 1A) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1A SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1A SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1A SMALL CHAIN) (CLATHRIN COAT ASSEMBLY PROT 0.456524 0.249561907
AP1S3 1159 0.0558748 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1C SUBUNIT (SIGMA-ADAPTIN 1C) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1C SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1C SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1C SMALL CHAIN) (SIGMA 1C SUBUNIT OF AP-1 CL 0.22389 0.249563625
AP2B1 1158 0.29348 ADAPTER-RELATED PROTEIN COMPLEX 2 BETA 1 SUBUNIT (BETA-ADAPTIN) (PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN) (AP105B). [SWISSPROT;Acc:P21851] 1.17572 0.249617256
AP2M1 2912 0.268272 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] 1.54054 0.174141535
AP3B1 2882 0.0416917 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 1 SUBUNIT (BETA-ADAPTIN 3A) (AP-3 COMPLEX BETA-3A SUBUNIT) (BETA-3A-ADAPTIN). [SWISSPROT;Acc:O00203] 0.225994 0.184481446
AP3M1 2309 0.162756 ADAPTER-RELATED PROTEIN COMPLEX 3 MU 1 SUBUNIT (MU-ADAPTIN 3A) (AP-3 ADAPTER COMPLEX MU3A SUBUNIT). [SWISSPROT;Acc:Q9Y2T2] 0.732966 0.222051227
AP3M2 2312 0.183942 ADAPTER-RELATED PROTEIN COMPLEX 3 MU 2 SUBUNIT (CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG 2) (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG 2) (GOLGI ADAPTOR AP-1 47 KDA PROTEIN HOMOLOG 2) (HA1 47 KDA SUBUNIT HOMOLOG 2) (CLATHRIN ASSEMBLY PROTEIN ASSEMB 0.828397 0.22204571
APBA1 2560 0.16418 AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY A MEMBER 1 (NEURON- SPECIFIC X11 PROTEIN) (NEURONAL MUNC18-1-INTERACTING PROTEIN 1) (MINT-1) (ADAPTER PROTEIN X11ALPHA). [SWISSPROT;Acc:Q02410] 0.766097 0.214307066
APEX1 2193 0.0811054 DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE (EC 4.2.99.18) (AP ENDONUCLEASE 1) (APEX NUCLEASE) (APEN) (REF-1 PROTEIN). [SWISSPROT;Acc:P27695] 0.358823 0.226031776
APEX2 1655 0.0730689 APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [RefSeq;Acc:NM_014481] 0.305877 0.238883277
API5 1755 0.0646874 APOPTOSIS INHIBITOR 5; FIBROBLAST GROWTH FACTOR 2-INTERACTING FACTOR 2; API5-LIKE 1. [RefSeq;Acc:NM_006595] 0.27327 0.236716068
APIP 2408 0.184877 0.845209 0.218735248
APOA1BP 2284 0.180926 APOLIPOPROTEIN A-I BINDING PROTEIN; APOA-I BINDING PROTEIN. [RefSeq;Acc:NM_144772] 0.813521 0.222398684
APOB 1387 0.0307397 APOLIPOPROTEIN B-100 PRECURSOR (APO B-100) [CONTAINS: APOLIPOPROTEIN B-48 (APO B-48)]. [SWISSPROT;Acc:P04114] 0.125741 0.244468391
APPBP1 2597 0.0719023 AMYLOID BETA PRECURSOR PROTEIN-BINDING PROTEIN 1; AMYLOID PROTEIN-BINDING PROTEIN 1. [RefSeq;Acc:NM_003905] 0.337743 0.212890571
AQP1 2839 0.0800859 AQUAPORIN-CHIP (WATER CHANNEL PROTEIN FOR RED BLOOD CELLS AND KIDNEY PROXIMAL TUBULE) (AQUAPORIN 1) (AQP-1) (URINE WATER CHANNEL). [SWISSPROT;Acc:P29972] 0.415411 0.192787143
AQP2 2841 0.0608484 AQUAPORIN-CD (AQP-CD) (WATER CHANNEL PROTEIN FOR RENAL COLLECTING DUCT) (ADH WATER CHANNEL) (AQUAPORIN 2) (COLLECTING DUCT WATER CHANNEL PROTEIN) (WCH-CD). [SWISSPROT;Acc:P41181] 0.315691 0.192746705
AQP4 2843 0.0599642 AQUAPORIN 4 (WCH4) (MERCURIAL-INSENSITIVE WATER CHANNEL) (MIWC). [SWISSPROT;Acc:P55087] 0.311107 0.192744618
AQP5 2842 0.0604602 AQUAPORIN 5. [SWISSPROT;Acc:P55064] 0.313678 0.192746064
AQR 1259 0.0339667 0.137332 0.247332741
ARAF 2956 0.218717 A-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (A-RAF-1) (PROTO-ONCOGENE PKS). [SWISSPROT;Acc:P10398] 1.48145 0.147637112
ARCN1 3017 0.293026 COATOMER DELTA SUBUNIT (DELTA-COAT PROTEIN) (DELTA-COP) (ARCHAIN). [SWISSPROT;Acc:P48444] 2.41388 0.121392116
ARD1A 1291 0.304267 N-TERMINAL ACETYLTRANSFERASE COMPLEX ARD1 SUBUNIT HOMOLOG (EC 2.3.1.-). [SWISSPROT;Acc:P41227] 1.23733 0.245906104
ARD1B 1319 0.269894 1.09872 0.245644022
ARF1 486 0.384939 ADP-RIBOSYLATION FACTOR 1. [SWISSPROT;Acc:P32889] 1.40333 0.274303977
ARF3 481 0.224714 ADP-RIBOSYLATION FACTOR 3. [SWISSPROT;Acc:P16587] 0.819215 0.274304059
ARF4 488 0.106754 ADP-RIBOSYLATION FACTOR 4. [SWISSPROT;Acc:P18085] 0.389182 0.274303539
ARFGAP1 2733 0.145697 ADP-RIBOSYLATION FACTOR GTPASE ACTIVATING PROTEIN 1 (ADP-RIBOSYLATION FACTOR 1 GTPASE ACTIVATING PROTEIN) (ARF1 GAP) (ARF1-DIRECTED GTPASE- ACTIVATING PROTEIN) (GAP PROTEIN). [SWISSPROT;Acc:Q8N6T3] 0.709572 0.205330819
ARFGAP3 491 0.0344618 ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3 (ARF GAP 3). [SWISSPROT;Acc:Q9NP61] 0.125634 0.274303135
ARFGEF1 1494 0.0337842 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 1 (BREFELDIN A-INHIBITED GEP 1) (P200 ARF-GEP1) (P200 ARF GUANINE NUCLEOTIDE EXCHANGE FACTOR). [SWISSPROT;Acc:Q9Y6D6] 0.139157 0.242777582
ARFGEF2 1496 0.036822 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 2 (BREFELDIN A-INHIBITED GEP 2). [SWISSPROT;Acc:Q9Y6D5] 0.15167 0.242777082
ARG1 1790 0.222245 ARGINASE 1 (EC 3.5.3.1) (LIVER-TYPE ARGINASE). [SWISSPROT;Acc:P05089] 0.945747 0.234994137
ARG2 1786 0.18522 "ARGINASE II, MITOCHONDRIAL PRECURSOR (EC 3.5.3.1) (NON-HEPATIC ARGINASE) (KIDNEY-TYPE ARGINASE). [SWISSPROT;Acc:P78540]" 0.787708 0.235137894
ARHGAP1 893 0.119625 RHO-GTPASE-ACTIVATING PROTEIN 1 (GTPASE-ACTIVATING PROTEIN RHOOGAP) (RHO-RELATED SMALL GTPASE PROTEIN ACTIVATOR) (CDC42 GTPASE-ACTIVATING PROTEIN) (P50-RHOGAP). [SWISSPROT;Acc:Q07960] 0.460314 0.259876954

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/