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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Rank Gene measured description Hugo expected final
Results: HTML CSV LaTeX Showing element 3008 to 3057 of 3206 in total
Rank
measured
description
Hugo
expected
final
3008 0.116797 SEPTIN 6. [SWISSPROT;Acc:Q14141] SEPT6 0.952641 0.122603373
3009 0.09144 SEPTIN 7 (CDC10 PROTEIN HOMOLOG). [SWISSPROT;Acc:Q16181] SEPT7 0.749104 0.122065828
3010 0.0199967 BRAIN PROTEIN 44. [SWISSPROT;Acc:O95563] BRP44 0.163819 0.122065817
3011 0.0174686 LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR (LYMPHOCYTE IGE RECEPTOR) (FC-EPSILON-RII) (CD23) (BLAST-2) (IMMUNOGLOBULIN E-BINDING FACTOR). [SWISSPROT;Acc:P06734] FCER2 0.14338 0.121834287
3012 0.0231389 CD209 ANTIGEN; DENDRITIC CELL-SPECIFIC ICAM3-GRABBING NONINTEGRIN. [RefSeq;Acc:NM_021155] CD209 0.189922 0.1218337
3013 0.0325023 FRY 0.266776 0.121833673
3014 0.379831 SET DOMAIN AND MARINER TRANSPOSASE FUSION GENE. [RefSeq;Acc:NM_006515] SETMAR 3.11762 0.121833642
3015 0.0247893 CD209 ANTIGEN-LIKE; PUTATIVE TYPE II MEMBRANE PROTEIN. [RefSeq;Acc:NM_014257] CLEC4M 0.203469 0.121833301
3016 0.250617 COATOMER GAMMA SUBUNIT (GAMMA-COAT PROTEIN) (GAMMA-COP). [SWISSPROT;Acc:Q9Y678] COPG 2.06452 0.121392382
3017 0.293026 COATOMER DELTA SUBUNIT (DELTA-COAT PROTEIN) (DELTA-COP) (ARCHAIN). [SWISSPROT;Acc:P48444] ARCN1 2.41388 0.121392116
3018 0.0424091 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E (EC 5.2.1.8) (PPIASE E) (ROTAMASE E) (CYCLOPHILIN E) (CYCLOPHILIN 33). [SWISSPROT;Acc:Q9UNP9] PPIE 0.349357 0.121391871
3019 0.154284 COATOMER ZETA-2 SUBUNIT (ZETA-2 COAT PROTEIN) (ZETA-2 COP). [SWISSPROT;Acc:Q9P299] COPZ2 1.27096 0.121391704
3020 0.169636 COATOMER BETA' SUBUNIT (BETA'-COAT PROTEIN) (BETA'-COP) (P102). [SWISSPROT;Acc:P35606] COPB2 1.39743 0.121391411
3021 COATOMER ZETA-1 SUBUNIT (ZETA-1 COAT PROTEIN) (ZETA-1 COP) (CGI-120) (HSPC181). [SWISSPROT;Acc:Q9Y3C3] COPZ1
3022 0.106813 SEPTIN 10 ISOFORM 1. [RefSeq;Acc:NM_144710] SEPT10 0.88182 0.121127895
3023 0.118014 SEPTIN-LIKE PROTEIN KIAA0202 (FRAGMENT). [SWISSPROT;Acc:Q92599] SEPT8 0.986632 0.119612986
3024 0.0250043 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] no value 0.209553 0.119322081
3025 SEDLIN. [SWISSPROT;Acc:O14582] ZNF547
3026 0.125021 BET3 HOMOLOG. [SWISSPROT;Acc:O43617] TRAPPC3 1.04777 0.119321034
3027 0.0365656 T-COMPLEX ASSOCIATED-TESTIS-EXPRESSED 1-LIKE (PROTEIN 91/23). [SWISSPROT;Acc:P51808] DYNLT3 0.307503 0.11891136
3028 0.121552 DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11A (MRE11 HOMOLOG 1). [SWISSPROT;Acc:P49959] MRE11A 1.02221 0.118910987
3029 0.329144 COATOMER BETA SUBUNIT (BETA-COAT PROTEIN) (BETA-COP). [SWISSPROT;Acc:P53618] COPB1 2.79482 0.117769302
3030 0.167012 UBIQUITIN-CONJUGATING ENZYME E2E 3; UBIQUITIN CARRIER PROTEIN; UBIQUITIN-PROTEIN LIGASE. [RefSeq;Acc:NM_006357] UBE2E4P 1.41955 0.117651368
3031 0.128895 PTCD1 1.09557 0.117651086
3032 0.191363 UBE2E2 1.62653 0.117651073
3033 0.157204 UBIQUITIN-CONJUGATING ENZYME E2 E1 (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE E1) (UBIQUITIN CARRIER PROTEIN E1) (UBCH6). [SWISSPROT;Acc:P51965] UBE2E1 1.33619 0.117650933
3034 0.146213 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P44 SUBUNIT (BASIC TRANSCRIPTION FACTOR 2 44 KDA SUBUNIT) (BTF2-P44) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 2). [SWISSPROT;Acc:Q13888] no value 1.27404 0.114763273
3035 0.0306863 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT (BASIC TRANSCRIPTION FACTOR 62 KDA SUBUNIT) (BTF2-P62) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1). [SWISSPROT;Acc:P32780] GTF2H1 0.267389 0.114762761
3036 0.125771 GABA(A) RECEPTOR-ASSOCIATED PROTEIN; GABA(A)-RECEPTOR-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007278] GABARAP 1.12068 0.112227398
3037 0.0193888 "PANTOTHENATE KINASE 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 2) (HPANK2). [SWISSPROT;Acc:Q9BZ23]" PANK2 0.176603 0.109787489
3038 0.0241982 PANTOTHENATE KINASE 1 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 1) (HPANK1) (HPANK). [SWISSPROT;Acc:Q8TE04] PANK1 0.22041 0.109787215
3039 "28S RIBOSOMAL PROTEIN S17, MITOCHONDRIAL PRECURSOR (MRP-S17) (HSPC011). [SWISSPROT;Acc:Q9Y2R5]" MRPS17
3040 0.0191226 PANTOTHENATE KINASE 3 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 3) (HPANK3). [SWISSPROT;Acc:Q9H999] PANK3 0.174179 0.109787058
3041 0.0228794 MITOCHONDRIAL SOLUTE CARRIER PROTEIN. [RefSeq;Acc:NM_145305] SLC25A43 0.208398 0.109787042
3042 0.0391008 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] no value 0.366305 0.106743834
3043 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-12 SUBUNIT. [SWISSPROT;Acc:Q9UBI6] GNG12
3044 0.0328245 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-4 SUBUNIT. [SWISSPROT;Acc:P50150] GNG4 0.307647 0.106695336
3045 0.0326969 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-3 SUBUNIT. [SWISSPROT;Acc:P29798] GNG3 0.306454 0.106694316
3046 0.032048 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-8 SUBUNIT (GAMMA-9). [SWISSPROT;Acc:Q9UK08] GNG8 0.300389 0.106688327
3047 0.0317927 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 SUBUNIT. [SWISSPROT;Acc:P30670] GNG5 0.298003 0.106685839
3048 0.031665 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-10 SUBUNIT. [SWISSPROT;Acc:P50151] GNG10 0.29681 0.106684411
3049 0.0312821 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] no value 0.293231 0.10668074
3050 0.0293247 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-11 SUBUNIT. [SWISSPROT;Acc:P50152] GNG11 0.274937 0.106659707
3051 0.204254 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 1 (TRANSDUCIN BETA CHAIN 1). [SWISSPROT;Acc:P04901] GNB1 1.92471 0.106121961
3052 0.090943 "BASIC HELIX-LOOP-HELIX DOMAIN CONTAINING, CLASS B, 5; TRINUCLEOTIDE REPEAT CONTAINING 20. [RefSeq;Acc:NM_152414]" BHLHB5 0.857352 0.106074285
3053 0.0691801 BA305P22.3 (BREAST CARCINOMA AMPLIFIED SEQUENCE 4). [SPTREMBL;Acc:Q8NDY6] BHLHB4 0.65236 0.106045895
3054 0.0392019 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Y), ALPHA SUBUNIT (ALPHA-11). [SWISSPROT;Acc:P29992]" GNA11 0.371714 0.105462533
3055 0.0395834 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Q), ALPHA SUBUNIT. [SWISSPROT;Acc:P50148]" GNAQ 0.375337 0.105460959
3056 0.0438075 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Z), ALPHA SUBUNIT (G(X) ALPHA CHAIN) (GZ-ALPHA). [SWISSPROT;Acc:P19086]" GNAZ 0.415448 0.10544641
3057 0.044407 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1 SUBUNIT (TRANSDUCIN ALPHA-1 CHAIN). [SWISSPROT;Acc:P11488]" GNAT1 0.421142 0.105444244

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/